diff -pruN 3.15.4+dfsg-3/assembler/changelog.html 3.15.5+dfsg-1/assembler/changelog.html --- 3.15.4+dfsg-3/assembler/changelog.html 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/changelog.html 2022-07-16 09:53:26.000000000 +0000 @@ -3,6 +3,15 @@

SPAdes Genome Assembler changelog

+ +

SPAdes 3.15.5, 14 July 2022

+ +

NEW: Support DNA HMMs.

+ +

FIX: use-after-free in PB aligner.

+ +

FIX: duplicated sequences in metaplasmid / metaviral mode.

+

SPAdes 3.15.4, 1 February 2022

FIX: MacOS Monterey memory limit failure.

diff -pruN 3.15.4+dfsg-3/assembler/manual.html 3.15.5+dfsg-1/assembler/manual.html --- 3.15.4+dfsg-3/assembler/manual.html 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/manual.html 2022-07-16 09:53:26.000000000 +0000 @@ -1,10 +1,10 @@ - SPAdes 3.15.4 Manual

TeamCity Simple Build Status
+ SPAdes 3.15.5 Manual

TeamCity Simple Build Status
License
GitHub release (latest by date)
GitHub Downloads
BioConda Downloads
Contributor Covenant

-

SPAdes 3.15.4 Manual

+

SPAdes 3.15.5 Manual

  1. About SPAdes
    1.1. Supported data types
    @@ -39,14 +39,14 @@

About SPAdes

-

SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.4 was released under GPLv2 on February 1, 2021 and can be downloaded from http://cab.spbu.ru/software/spades/.

+

SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.5 was released under GPLv2 on July 14th, 2022 and can be downloaded from http://cab.spbu.ru/software/spades/.

The latest SPAdes paper describing various pipelines in a protocol format is available here.

Supported data types

The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.

-

Version 3.15.4 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.

-

If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use --isolate option.

-

SPAdes 3.15.4 includes the following additional pipelines:

+

Version 3.15.5 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.

+

If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use --isolate option.

+

SPAdes 3.15.5 includes the following additional pipelines:

-

In addition, we provide several stand-alone binaries with relatively simple command-line interface: k-mer counting (spades-kmercounter), assembly graph construction (spades-gbuilder) and long read to graph aligner (spades-gmapper). To learn options of these tools you can either run them without any parameters or read this section.

+

In addition, we provide several stand-alone binaries with relatively simple command-line interface: k-mer counting (spades-kmercounter), assembly graph construction (spades-gbuilder) and long read to graph aligner (spades-gmapper). To learn options of these tools you can either run them without any parameters or read this section.

SPAdes pipeline

@@ -139,42 +139,42 @@

Installation

SPAdes requires a 64-bit Linux system or Mac OS and Python (supported versions are Python 2.7, and Python3: 3.2 and higher) to be pre-installed on it. To obtain SPAdes you can either download binaries or download source code and compile it yourself.

-

In case of successful installation the following files will be placed in the bin directory:

+

In case of successful installation the following files will be placed in the bin directory:

Downloading SPAdes Linux binaries

-

To download SPAdes Linux binaries and extract them, go to the directory in which you wish SPAdes to be installed and run:

-
    wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz
-    tar -xzf SPAdes-3.15.4-Linux.tar.gz
-    cd SPAdes-3.15.4-Linux/bin/
-

In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the PATH variable.

+

To download SPAdes Linux binaries and extract them, go to the directory in which you wish SPAdes to be installed and run:

+
    wget http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Linux.tar.gz
+    tar -xzf SPAdes-3.15.5-Linux.tar.gz
+    cd SPAdes-3.15.5-Linux/bin/
+

In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the PATH variable.

Note, that pre-build binaries do not work on new Linux kernels.

Downloading SPAdes binaries for Mac

-

To obtain SPAdes binaries for Mac, go to the directory in which you wish SPAdes to be installed and run:

-
    curl http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Darwin.tar.gz -o SPAdes-3.15.4-Darwin.tar.gz
-    tar -zxf SPAdes-3.15.4-Darwin.tar.gz
-    cd SPAdes-3.15.4-Darwin/bin/
-

Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the PATH variable.

+

To obtain SPAdes binaries for Mac, go to the directory in which you wish SPAdes to be installed and run:

+
    curl http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Darwin.tar.gz -o SPAdes-3.15.5-Darwin.tar.gz
+    tar -zxf SPAdes-3.15.5-Darwin.tar.gz
+    cd SPAdes-3.15.5-Darwin/bin/
+

Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the PATH variable.

Downloading and compiling SPAdes source code

If you wish to compile SPAdes by yourself you will need the following libraries to be pre-installed:

@@ -184,27 +184,27 @@
  • zlib
  • libbz2
  • -

    If you meet these requirements, you can download the SPAdes source code:

    -
        wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4.tar.gz
    -    tar -xzf SPAdes-3.15.4.tar.gz
    -    cd SPAdes-3.15.4
    +

    If you meet these requirements, you can download the SPAdes source code:

    +
        wget http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5.tar.gz
    +    tar -xzf SPAdes-3.15.5.tar.gz
    +    cd SPAdes-3.15.5

    and build it with the following script:

        ./spades_compile.sh
    -

    SPAdes will be built in the directory ./bin. If you wish to install SPAdes into another directory, you can specify full path of destination folder by running the following command in bash or sh:

    +

    SPAdes will be built in the directory ./bin. If you wish to install SPAdes into another directory, you can specify full path of destination folder by running the following command in bash or sh:

        PREFIX=<destination_dir> ./spades_compile.sh

    for example:

        PREFIX=/usr/local ./spades_compile.sh
    -

    which will install SPAdes into /usr/local/bin.

    -

    After installation you will get the same files (listed above) in ./bin directory (or <destination_dir>/bin if you specified PREFIX). We also suggest adding bin directory to the PATH variable.

    +

    which will install SPAdes into /usr/local/bin.

    +

    After installation you will get the same files (listed above) in ./bin directory (or <destination_dir>/bin if you specified PREFIX). We also suggest adding bin directory to the PATH variable.

    Verifying your installation

    For testing purposes, SPAdes comes with a toy data set (reads that align to first 1000 bp of E. coli). To try SPAdes on this data set, run:

        <spades installation dir>/bin/spades.py --test
    -

    If you added bin folder from SPAdes installation directory to the PATH variable, you can run:

    +

    If you added bin folder from SPAdes installation directory to the PATH variable, you can run:

        spades.py --test
    -

    For the simplicity we further assume that bin folder from SPAdes installation directory is added to the PATH variable.

    +

    For the simplicity we further assume that bin folder from SPAdes installation directory is added to the PATH variable.

    If the installation is successful, you will find the following information at the end of the log:

    -
    
    +
    
     ===== Assembling finished. Used k-mer sizes: 21, 33, 55
     
      * Corrected reads are in spades_test/corrected/
    @@ -229,7 +229,7 @@ Thank you for using SPAdes!
     

    SPAdes input

    SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.

    -

    To run SPAdes 3.15.4 you need at least one library of the following types:

    +

    To run SPAdes 3.15.5 you need at least one library of the following types:

    • Illumina paired-end/high-quality mate-pairs/unpaired reads
    • IonTorrent paired-end/high-quality mate-pairs/unpaired reads
    • @@ -254,7 +254,7 @@ Thank you for using SPAdes!
    • In file pairs. In this case left and right reads are placed in different files and go in the same order in respective files.
    • In interleaved files. In this case, the reads are interlaced, so that each right read goes after the corresponding paired left read.
    -

    For example, Illumina produces paired-end reads in two files: R1.fastq and R2.fastq. If you choose to store reads in file pairs make sure that for every read from R1.fastq the corresponding paired read from R2.fastq is placed in the respective paired file on the same line number. If you choose to use interleaved files, every read from R1.fastq should be followed by the corresponding paired read from R2.fastq.

    +

    For example, Illumina produces paired-end reads in two files: R1.fastq and R2.fastq. If you choose to store reads in file pairs make sure that for every read from R1.fastq the corresponding paired read from R2.fastq is placed in the respective paired file on the same line number. If you choose to use interleaved files, every read from R1.fastq should be followed by the corresponding paired read from R2.fastq.

    If adapter and/or quality trimming software has been used prior to assembly, files with the orphan reads can be provided as "single read files" for the corresponding read-pair library.


    If you have merged some of the reads from your paired-end (not mate-pair or high-quality mate-pair) library (using tools s.a. BBMerge or STORM), you should provide the file with resulting reads as a "merged read file" for the corresponding library.
    @@ -269,44 +269,44 @@ Note that non-empty files with the remai

    PacBio and Oxford Nanopore reads

    SPAdes can take as an input an unlimited number of PacBio and Oxford Nanopore libraries.

    PacBio CLR and Oxford Nanopore reads are used for hybrid assemblies (e.g. with Illumina or IonTorrent). There is no need to pre-correct this kind of data. SPAdes will use PacBio CLR and Oxford Nanopore reads for gap closure and repeat resolution.

    -

    For PacBio you just need to have filtered subreads in FASTQ/FASTA format. Provide these filtered subreads using --pacbio option. Oxford Nanopore reads are provided with --nanopore option.

    +

    For PacBio you just need to have filtered subreads in FASTQ/FASTA format. Provide these filtered subreads using --pacbio option. Oxford Nanopore reads are provided with --nanopore option.

    PacBio CCS/Reads of Insert reads or pre-corrected (using third-party software) PacBio CLR / Oxford Nanopore reads can be simply provided as single reads to SPAdes.

    Additional contigs

    -

    In case you have contigs of the same genome generated by other assembler(s) and you wish to merge them into SPAdes assembly, you can specify additional contigs using --trusted-contigs or --untrusted-contigs. First option is used when high quality contigs are available. These contigs will be used for graph construction, gap closure and repeat resolution. Second option is used for less reliable contigs that may have more errors or contigs of unknown quality. These contigs will be used only for gap closure and repeat resolution. The number of additional contigs is unlimited.

    +

    In case you have contigs of the same genome generated by other assembler(s) and you wish to merge them into SPAdes assembly, you can specify additional contigs using --trusted-contigs or --untrusted-contigs. First option is used when high quality contigs are available. These contigs will be used for graph construction, gap closure and repeat resolution. Second option is used for less reliable contigs that may have more errors or contigs of unknown quality. These contigs will be used only for gap closure and repeat resolution. The number of additional contigs is unlimited.

    Note, that SPAdes does not perform assembly using genomes of closely-related species. Only contigs of the same genome should be specified.


    SPAdes command line options

    To run SPAdes from the command line, type

        spades.py [options] -o <output_dir>
    -

    Note that we assume that bin forder from SPAdes installation directory is added to the PATH variable (provide full path to SPAdes executable otherwise: <spades installation dir>/bin/spades.py).

    +

    Note that we assume that bin forder from SPAdes installation directory is added to the PATH variable (provide full path to SPAdes executable otherwise: <spades installation dir>/bin/spades.py).

    Basic options

    -

    -o <output_dir>
    +

    -o <output_dir>
    Specify the output directory. Required option.


    ---isolate
    +--isolate
    This flag is highly recommended for high-coverage isolate and multi-cell Illumina data; improves the assembly quality and running time.
    We also recommend to trim your reads prior to the assembly. More details can be found here.
    -This option is not compatible with --only-error-correction or --careful options.

    +This option is not compatible with --only-error-correction or --careful options.


    ---sc
    +--sc
    This flag is required for MDA (single-cell) data.


    ---meta (same as metaspades.py)
    -This flag is recommended when assembling metagenomic data sets (runs metaSPAdes, see paper for more details). Currently metaSPAdes supports only a single short-read library which has to be paired-end (we hope to remove this restriction soon). In addition, you can provide long reads (e.g. using --pacbio or --nanopore options), but hybrid assembly for metagenomes remains an experimental pipeline and optimal performance is not guaranteed. It does not support careful mode (mismatch correction is not available). In addition, you cannot specify coverage cutoff for metaSPAdes. Note that metaSPAdes might be very sensitive to presence of the technical sequences remaining in the data (most notably adapter readthroughs), please run quality control and pre-process your data accordingly.

    +--meta (same as metaspades.py)
    +This flag is recommended when assembling metagenomic data sets (runs metaSPAdes, see paper for more details). Currently metaSPAdes supports only a single short-read library which has to be paired-end (we hope to remove this restriction soon). In addition, you can provide long reads (e.g. using --pacbio or --nanopore options), but hybrid assembly for metagenomes remains an experimental pipeline and optimal performance is not guaranteed. It does not support careful mode (mismatch correction is not available). In addition, you cannot specify coverage cutoff for metaSPAdes. Note that metaSPAdes might be very sensitive to presence of the technical sequences remaining in the data (most notably adapter readthroughs), please run quality control and pre-process your data accordingly.


    ---plasmid (same as plasmidspades.py)
    +--plasmid (same as plasmidspades.py)
    This flag is required when assembling only plasmids from WGS data sets (runs plasmidSPAdes, see paper for the algorithm details). Note, that plasmidSPAdes is not compatible with single-cell mode. Additionally, we do not recommend to run plasmidSPAdes on more than one library.

    For plasmidSPAdes output details see section 3.6.


    ---metaplasmid (same as metaplasmidspades.py and --meta --plasmid) and

    -

    --metaviral (same as metaviralspades.py)

    +--metaplasmid (same as metaplasmidspades.py and --meta --plasmid) and

    +

    --metaviral (same as metaviralspades.py)

    These options works specially for extracting extrachromosomal elements from metagenomic assemblies. They run similar pipelines that slightly differ in the simplification step; another difference is that for metaviral mode we output linear putative extrachromosomal contigs and for metaplasmid mode we do not.
    See metaplasmid paper and metaviral paper for the algorithms details.

    For metaplasmidSPAdes/metaviralSPAdes output details see section 3.7.

    @@ -314,138 +314,138 @@ See Additionally for plasmidSPAdes, metaplasmidSPAdes and metaviralSPAdes we recommend to additionally verify resulting contigs with viralVerify tool.


    ---bio
    +--bio
    This flag is required when assembling only non-ribosomal and polyketide gene clusters from WGS data sets (runs biosyntheticSPAdes, see paper for the algorithm details). biosyntheticSPAdes is supposed to work on isolate or metagenomic WGS dataset. Note, that biosyntheticSPAdes is not compatible with any other modes. See section 3.8 for biosyntheticSPAdes output details.


    ---rna (same as rnaspades.py)
    +--rna (same as rnaspades.py)
    This flag should be used when assembling RNA-Seq data sets (runs rnaSPAdes). To learn more, see rnaSPAdes manual.
    -Not compatible with --only-error-correction or --careful options.

    +Not compatible with --only-error-correction or --careful options.


    ---rnaviral (same as rnaviralspades.py)
    +--rnaviral (same as rnaviralspades.py)
    This flag should be used when assembling viral RNA-Seq data sets (runs rnaviralSPAdes).
    -Not compatible with --only-error-correction or --careful options.

    -

    --iontorrent
    +Not compatible with --only-error-correction or --careful options.

    +

    --iontorrent
    This flag is required when assembling IonTorrent data. Allows BAM files as input. Carefully read section 3.3 before using this option.

    -

    --test
    +

    --test
    Runs SPAdes on the toy data set; see section 2.4.

    -

    -h (or --help)
    +

    -h (or --help)
    Prints help.

    -

    -v (or --version)
    +

    -v (or --version)
    Prints SPAdes version.


    Pipeline options

    -

    --only-error-correction
    +

    --only-error-correction
    Performs read error correction only.

    -

    --only-assembler
    +

    --only-assembler
    Runs assembly module only.



    ---careful
    +--careful
    Tries to reduce the number of mismatches and short indels. Also runs MismatchCorrector - a post processing tool, which uses BWA tool (comes with SPAdes). This option is recommended only for assembly of small genomes. We strongly recommend not to use it for large and medium-size eukaryotic genomes. Note, that this options is is not supported by metaSPAdes and rnaSPAdes.

    -

    --continue
    +

    --continue
    Continues SPAdes run from the specified output folder starting from the last available check-point. Check-points are made after:

    • error correction module is finished
    • iteration for each specified K value of assembly module is finished
    • mismatch correction is finished for contigs or scaffolds
    -

    For example, if specified K values are 21, 33 and 55 and SPAdes was stopped or crashed during assembly stage with K = 55, you can run SPAdes with the --continue option specifying the same output directory. SPAdes will continue the run starting from the assembly stage with K = 55. Error correction module and iterations for K equal to 21 and 33 will not be run again. If --continue is set, the only allowed option is -o <output_dir> .

    -

    --restart-from <check_point>
    +

    For example, if specified K values are 21, 33 and 55 and SPAdes was stopped or crashed during assembly stage with K = 55, you can run SPAdes with the --continue option specifying the same output directory. SPAdes will continue the run starting from the assembly stage with K = 55. Error correction module and iterations for K equal to 21 and 33 will not be run again. If --continue is set, the only allowed option is -o <output_dir> .

    +

    --restart-from <check_point>
    Restart SPAdes run from the specified output folder starting from the specified check-point. Check-points are:

      -
    • ec - start from error correction
    • -
    • as - restart assembly module from the first iteration
    • -
    • k<int> - restart from the iteration with specified k values, e.g. k55 (not available in RNA-Seq mode)
    • -
    • mc - restart mismatch correction
    • -
    • last - restart from the last available check-point (similar to --continue)
    • +
    • ec - start from error correction
    • +
    • as - restart assembly module from the first iteration
    • +
    • k<int> - restart from the iteration with specified k values, e.g. k55 (not available in RNA-Seq mode)
    • +
    • mc - restart mismatch correction
    • +
    • last - restart from the last available check-point (similar to --continue)
    -

    In contrast to the --continue option, you can change some of the options when using --restart-from. You can change any option except: all basic options, all options for specifying input data (including --dataset), --only-error-correction option and --only-assembler option. For example, if you ran assembler with k values 21,33,55 without mismatch correction, you can add one more iteration with k=77 and run mismatch correction step by running SPAdes with following options:
    ---restart-from k55 -k 21,33,55,77 --mismatch-correction -o <previous_output_dir>.
    +

    In contrast to the --continue option, you can change some of the options when using --restart-from. You can change any option except: all basic options, all options for specifying input data (including --dataset), --only-error-correction option and --only-assembler option. For example, if you ran assembler with k values 21,33,55 without mismatch correction, you can add one more iteration with k=77 and run mismatch correction step by running SPAdes with following options:
    +--restart-from k55 -k 21,33,55,77 --mismatch-correction -o <previous_output_dir>.
    Since all files will be overwritten, do not forget to copy your assembly from the previous run if you need it.

    -

    --disable-gzip-output
    -Forces read error correction module not to compress the corrected reads. If this options is not set, corrected reads will be in *.fastq.gz format.

    +

    --disable-gzip-output
    +Forces read error correction module not to compress the corrected reads. If this options is not set, corrected reads will be in *.fastq.gz format.

    Input data

    Specifying single library (paired-end or single-read)

    -

    --12 <file_name>
    +

    --12 <file_name>
    File with interlaced forward and reverse paired-end reads.

    -

    -1 <file_name>
    +

    -1 <file_name>
    File with forward reads.

    -

    -2 <file_name>
    +

    -2 <file_name>
    File with reverse reads.

    -

    --merged <file_name>
    +

    --merged <file_name>
    File with merged paired reads.
    If the properties of the library permit, overlapping paired-end reads can be merged using special software.
    Non-empty files with (remaining) unmerged left/right reads (separate or interlaced) must be provided for the same library for SPAdes to correctly detect the original read length.

    -

    -s <file_name>
    +

    -s <file_name>
    File with unpaired reads.

    Specifying multiple libraries

    Single-read libraries

    -

    --s<#> <file_name>
    -File for single-read library number <#> (<#> = 1,2,..,9). For example, for the first paired-end library the option is: --s1 <file_name>
    -Do not use -s options for single-read libraries, since it specifies unpaired reads for the first paired-end library.

    +

    --s<#> <file_name>
    +File for single-read library number <#> (<#> = 1,2,..,9). For example, for the first paired-end library the option is: --s1 <file_name>
    +Do not use -s options for single-read libraries, since it specifies unpaired reads for the first paired-end library.

    Paired-end libraries

    -

    --pe<#>-12 <file_name>
    -File with interlaced reads for paired-end library number <#> (<#> = 1,2,..,9). For example, for the first single-read library the option is: --pe1-12 <file_name>

    -

    --pe<#>-1 <file_name>
    -File with left reads for paired-end library number <#> (<#> = 1,2,..,9).

    -

    --pe<#>-2 <file_name>
    -File with right reads for paired-end library number <#> (<#> = 1,2,..,9).

    -

    --pe<#>-m <file_name>
    -File with merged reads from paired-end library number <#> (<#> = 1,2,..,9)
    +

    --pe<#>-12 <file_name>
    +File with interlaced reads for paired-end library number <#> (<#> = 1,2,..,9). For example, for the first single-read library the option is: --pe1-12 <file_name>

    +

    --pe<#>-1 <file_name>
    +File with left reads for paired-end library number <#> (<#> = 1,2,..,9).

    +

    --pe<#>-2 <file_name>
    +File with right reads for paired-end library number <#> (<#> = 1,2,..,9).

    +

    --pe<#>-m <file_name>
    +File with merged reads from paired-end library number <#> (<#> = 1,2,..,9)
    If the properties of the library permit, paired reads can be merged using special software. Non-empty files with (remaining) unmerged left/right reads (separate or interlaced) must be provided for the same library for SPAdes to correctly detect the original read length.

    -

    --pe<#>-s <file_name>
    -File with unpaired reads from paired-end library number <#> (<#> = 1,2,..,9)
    +

    --pe<#>-s <file_name>
    +File with unpaired reads from paired-end library number <#> (<#> = 1,2,..,9)
    For example, paired reads can become unpaired during the error correction procedure.

    -

    --pe<#>-<or>
    -Orientation of reads for paired-end library number <#> (<#> = 1,2,..,9; <or> = "fr","rf","ff").
    -The default orientation for paired-end libraries is forward-reverse (--> <--). For example, to specify reverse-forward orientation for the second paired-end library, you should use the flag: --pe2-rf
    +

    --pe<#>-<or>
    +Orientation of reads for paired-end library number <#> (<#> = 1,2,..,9; <or> = "fr","rf","ff").
    +The default orientation for paired-end libraries is forward-reverse (--> <--). For example, to specify reverse-forward orientation for the second paired-end library, you should use the flag: --pe2-rf
    Should not be confused with FR and RF strand-specificity for RNA-Seq data (see rnaSPAdes manual).


    Mate-pair libraries

    -

    --mp<#>-12 <file_name>
    -File with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9).

    -

    --mp<#>-1 <file_name>
    -File with left reads for mate-pair library number <#> (<#> = 1,2,..,9).

    -

    --mp<#>-2 <file_name>
    -File with right reads for mate-pair library number <#> (<#> = 1,2,..,9).

    -

    --mp<#>-<or>
    -Orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = "fr","rf","ff").
    -The default orientation for mate-pair libraries is reverse-forward (<-- -->). For example, to specify forward-forward orientation for the first mate-pair library, you should use the flag: --mp1-ff

    +

    --mp<#>-12 <file_name>
    +File with interlaced reads for mate-pair library number <#> (<#> = 1,2,..,9).

    +

    --mp<#>-1 <file_name>
    +File with left reads for mate-pair library number <#> (<#> = 1,2,..,9).

    +

    --mp<#>-2 <file_name>
    +File with right reads for mate-pair library number <#> (<#> = 1,2,..,9).

    +

    --mp<#>-<or>
    +Orientation of reads for mate-pair library number <#> (<#> = 1,2,..,9; <or> = "fr","rf","ff").
    +The default orientation for mate-pair libraries is reverse-forward (<-- -->). For example, to specify forward-forward orientation for the first mate-pair library, you should use the flag: --mp1-ff


    High-quality mate-pair libraries (can be used for mate-pair only assembly)

    -

    --hqmp<#>-12 <file_name>
    -File with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9).

    -

    --hqmp<#>-1 <file_name>
    -File with left reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9).

    -

    --hqmp<#>-2 <file_name>
    -File with right reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9).

    -

    --hqmp<#>-s <file_name>
    -File with unpaired reads from high-quality mate-pair library number <#> (<#> = 1,2,..,9)

    -

    --hqmp<#>-<or>
    -Orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = "fr","rf","ff").
    -The default orientation for high-quality mate-pair libraries is forward-reverse (--> <--). For example, to specify reverse-forward orientation for the first high-quality mate-pair library, you should use the flag: --hqmp1-rf

    +

    --hqmp<#>-12 <file_name>
    +File with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9).

    +

    --hqmp<#>-1 <file_name>
    +File with left reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9).

    +

    --hqmp<#>-2 <file_name>
    +File with right reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9).

    +

    --hqmp<#>-s <file_name>
    +File with unpaired reads from high-quality mate-pair library number <#> (<#> = 1,2,..,9)

    +

    --hqmp<#>-<or>
    +Orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,..,9; <or> = "fr","rf","ff").
    +The default orientation for high-quality mate-pair libraries is forward-reverse (--> <--). For example, to specify reverse-forward orientation for the first high-quality mate-pair library, you should use the flag: --hqmp1-rf


    Specifying data for hybrid assembly

    -

    --pacbio <file_name>
    -File with PacBio CLR reads. For PacBio CCS reads use -s option. More information on PacBio reads is provided in section 3.1.

    -

    --nanopore <file_name>
    +

    --pacbio <file_name>
    +File with PacBio CLR reads. For PacBio CCS reads use -s option. More information on PacBio reads is provided in section 3.1.

    +

    --nanopore <file_name>
    File with Oxford Nanopore reads.

    -

    --sanger <file_name>
    +

    --sanger <file_name>
    File with Sanger reads

    -

    --trusted-contigs <file_name>
    +

    --trusted-contigs <file_name>
    Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species.

    -

    --untrusted-contigs <file_name>
    +

    --untrusted-contigs <file_name>
    Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species.

    Other input

    -

    --assembly-graph <file_name>
    -File with assembly graph. Could only be used in plasmid, metaplasmid, metaviral and biosynthetic mode. The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline. Original reads the graph was constructed from need to be specified as well. Exact k-mer length (via -k option) should be provided. Note that the output would be different as compared to standalone runs of these pipelines as they setup graph simplification options as well.

    +

    --assembly-graph <file_name>
    +File with assembly graph. Could only be used in plasmid, metaplasmid, metaviral and biosynthetic mode. The primary purpose of this option to run these pipelines on already constructed and simplified assembly graph this way skipping a large part of SPAdes pipeline. Original reads the graph was constructed from need to be specified as well. Exact k-mer length (via -k option) should be provided. Note that the output would be different as compared to standalone runs of these pipelines as they setup graph simplification options as well.


    Specifying input data with YAML data set file (advanced)

    An alternative way to specify an input data set for SPAdes is to create a YAML data set file. By using a YAML file you can provide an unlimited number of paired-end, mate-pair and unpaired libraries. Basically, YAML data set file is a text file, in which input libraries are provided as a comma-separated list in square brackets. Each library is provided in braces as a comma-separated list of attributes. The following attributes are available:

    @@ -508,33 +508,33 @@ File with assembly graph. Could only be ] } ]
    -

    Once you have created a YAML file save it with .yaml extension (e.g. as my_data_set.yaml) and run SPAdes using the --dataset option:
    ---dataset <your YAML file>
    +

    Once you have created a YAML file save it with .yaml extension (e.g. as my_data_set.yaml) and run SPAdes using the --dataset option:
    +--dataset <your YAML file>
    Notes:

      -
    • The --dataset option cannot be used with any other options for specifying input data.
    • +
    • The --dataset option cannot be used with any other options for specifying input data.
    • We recommend to nest all files with long reads of the same data type in a single library block.

    Advanced options

    -

    -t <int> (or --threads <int>)
    +

    -t <int> (or --threads <int>)
    Number of threads. The default value is 16.

    -

    -m <int> (or --memory <int>)
    +

    -m <int> (or --memory <int>)
    Set memory limit in Gb. SPAdes terminates if it reaches this limit. The default value is 250 Gb. Actual amount of consumed RAM will be below this limit. Make sure this value is correct for the given machine. SPAdes uses the limit value to automatically determine the sizes of various buffers, etc.

    -

    --tmp-dir <dir_name>
    -Set directory for temporary files from read error correction. The default value is <output_dir>/corrected/tmp

    -

    -k <int,int,...>
    -Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). If --sc is set the default values are 21,33,55. For multicell data sets K values are automatically selected using maximum read length (see note for assembling long Illumina paired reads for details). To properly select K values for IonTorrent data read section 3.3.

    -

    --cov-cutoff <float>
    +

    --tmp-dir <dir_name>
    +Set directory for temporary files from read error correction. The default value is <output_dir>/corrected/tmp

    +

    -k <int,int,...>
    +Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128 and listed in ascending order). If --sc is set the default values are 21,33,55. For multicell data sets K values are automatically selected using maximum read length (see note for assembling long Illumina paired reads for details). To properly select K values for IonTorrent data read section 3.3.

    +

    --cov-cutoff <float>
    Read coverage cutoff value. Must be a positive float value, or "auto", or "off". Default value is "off". When set to "auto" SPAdes automatically computes coverage threshold using conservative strategy. Note, that this option is not supported by metaSPAdes.

    -

    --phred-offset <33 or 64>
    +

    --phred-offset <33 or 64>
    PHRED quality offset for the input reads, can be either 33 or 64. It will be auto-detected if it is not specified.

    -

    --custom-hmms <file or directory>
    +

    --custom-hmms <file or directory>
    File or directory with amino acid HMMs for HMM-guided mode.

    Examples

    -

    To test the toy data set, you can also run the following command from the SPAdes bin directory:

    +

    To test the toy data set, you can also run the following command from the SPAdes bin directory:

        spades.py --pe1-1 ../share/spades/test_dataset/ecoli_1K_1.fq.gz \
         --pe1-2 ../share/spades/test_dataset/ecoli_1K_2.fq.gz -o spades_test

    If you have your library separated into several pairs of files, for example:

    @@ -585,9 +585,9 @@ File or directory with amino acid HMMs f

    Assembling IonTorrent reads

    Only FASTQ or BAM files are supported as input.

    -

    The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our recommendation for long reads (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We are planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.

    +

    The selection of k-mer length is non-trivial for IonTorrent. If the dataset is more or less conventional (good coverage, not high GC, etc), then use our recommendation for long reads (e.g. assemble using k-mer lengths 21,33,55,77,99,127). However, due to increased error rate some changes of k-mer lengths (e.g. selection of shorter ones) may be required. For example, if you ran SPAdes with k-mer lengths 21,33,55,77 and then decided to assemble the same data set using more iterations and larger values of K, you can run SPAdes once again specifying the same output folder and the following options: --restart-from k77 -k 21,33,55,77,99,127 --mismatch-correction -o <previous_output_dir>. Do not forget to copy contigs and scaffolds from the previous run. We are planning to tackle issue of selecting k-mer lengths for IonTorrent reads in next versions.

    You may need no error correction for Hi-Q enzyme at all. However, we suggest trying to assemble your data with and without error correction and select the best variant.

    -

    For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.

    +

    For non-trivial datasets (e.g. with high GC, low or uneven coverage) we suggest to enable single-cell mode (setting --sc option) and use k-mer lengths of 21,33,55.


    Assembling long Illumina paired reads (2x150 and 2x250)

    @@ -598,7 +598,7 @@ File or directory with amino acid HMMs f

    Multi-cell data set with read length 2x150 bp

    Do not turn off SPAdes error correction (BayesHammer module), which is included in SPAdes default pipeline.

    If you have enough coverage (50x+), then you may want to try to set k-mer lengths of 21, 33, 55, 77 (selected by default for reads with length 150bp).

    -

    Make sure you run assembler with the --careful option to minimize number of mismatches in the final contigs.

    +

    Make sure you run assembler with the --careful option to minimize number of mismatches in the final contigs.

    We recommend that you check the SPAdes log file at the end of the each iteration to control the average coverage of the contigs.

    For reads corrected prior to running the assembler:

        spades.py -k 21,33,55,77 --careful --only-assembler <your reads> -o spades_output
    @@ -608,7 +608,7 @@ File or directory with amino acid HMMs f

    Multi-cell data set with read lengths 2x250 bp

    Do not turn off SPAdes error correction (BayesHammer module), which is included in SPAdes default pipeline.

    By default we suggest to increase k-mer lengths in increments of 22 until the k-mer length reaches 127. The exact length of the k-mer depends on the coverage: k-mer length of 127 corresponds to 50x k-mer coverage and higher. For read length 250bp SPAdes automatically chooses K values equal to 21, 33, 55, 77, 99, 127.

    -

    Make sure you run assembler with --careful option to minimize number of mismatches in the final contigs.

    +

    Make sure you run assembler with --careful option to minimize number of mismatches in the final contigs.

    We recommend you to check the SPAdes log file at the end of the each iteration to control the average coverage of the contigs.

    For reads corrected prior to running the assembler:

        spades.py -k 21,33,55,77,99,127 --careful --only-assembler <your reads> -o spades_output
    @@ -622,50 +622,50 @@ File or directory with amino acid HMMs f

    HMM-guided mode

    The majority of SPAdes assembly modes (normal multicell, single-cell, rnaviral, meta and of course biosynthetic) also supports HMM-guided mode as implemented in biosyntheticSPAdes. The detailed description could be found in biosyntheticSPAdes paper, but in short: amino acid profile HMMs are aligned to the edges of assembly graph. After this the subgraphs containing the set of matches ("domains") are extracted and all possible paths through the domains that are supported both by paired-end data (via scaffolds) and graph topology are obtained (putative biosynthetic gene clusters).

    -

    HMM-guided mode could be enabled via providing a set of HMMs via --custom-hmms option. In HMM guided mode the set of contigs and scaffolds (see section SPAdes output for more information about SPAdes output) is kept intact, however additional biosyntheticSPAdes output represents the output of HMM-guided assembly.

    -

    Note that normal biosyntheticSPAdes mode (via --bio option) is a bit different from HMM-guided mode: besides using the special set of profile HMMS representing a family of NRSP/PKS domains also includes a set of assembly graph simplification and processing settings aimed for fuller recovery of biosynthetic gene clusters.

    -

    Given an increased interest in coronavirus research we developed a coronavirus assembly mode for SPAdes assembler (also known as coronaSPAdes). It allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. Algorithmically, coronaSPAdes is an rnaviralSPAdes that uses the set of HMMs from Pfam SARS-CoV-2 2.0 set as well as additional HMMs as outlined by (Phan et al, 2019). coronaSPAdes could be run via a dedicated coronaspades.py script. See coronaSPAdes preprint for more information about rnaviralSPAdes, coronaSPAdes and HMM-guided mode. Output for any HMM-related mode (--bio, --corona, or --custom-hmms flags) is the same with biosyntheticSPAdes' output.

    +

    HMM-guided mode could be enabled via providing a set of HMMs via --custom-hmms option. In HMM guided mode the set of contigs and scaffolds (see section SPAdes output for more information about SPAdes output) is kept intact, however additional biosyntheticSPAdes output represents the output of HMM-guided assembly.

    +

    Note that normal biosyntheticSPAdes mode (via --bio option) is a bit different from HMM-guided mode: besides using the special set of profile HMMS representing a family of NRSP/PKS domains also includes a set of assembly graph simplification and processing settings aimed for fuller recovery of biosynthetic gene clusters.

    +

    Given an increased interest in coronavirus research we developed a coronavirus assembly mode for SPAdes assembler (also known as coronaSPAdes). It allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. Algorithmically, coronaSPAdes is an rnaviralSPAdes that uses the set of HMMs from Pfam SARS-CoV-2 2.0 set as well as additional HMMs as outlined by (Phan et al, 2019). coronaSPAdes could be run via a dedicated coronaspades.py script. See coronaSPAdes preprint for more information about rnaviralSPAdes, coronaSPAdes and HMM-guided mode. Output for any HMM-related mode (--bio, --corona, or --custom-hmms flags) is the same with biosyntheticSPAdes' output.

    SPAdes output

    -

    SPAdes stores all output files in <output_dir> , which is set by the user.

    +

    SPAdes stores all output files in <output_dir> , which is set by the user.

      -
    • <output_dir>/corrected/ directory contains reads corrected by BayesHammer in *.fastq.gz files; if compression is disabled, reads are stored in uncompressed *.fastq files
    • -
    • <output_dir>/scaffolds.fasta contains resulting scaffolds (recommended for use as resulting sequences)
    • -
    • <output_dir>/contigs.fasta contains resulting contigs
    • -
    • <output_dir>/assembly_graph_with_scaffolds.gfa contains SPAdes assembly graph and scaffolds paths in GFA 1.0 format
    • -
    • <output_dir>/assembly_graph.fastg contains SPAdes assembly graph in FASTG format
    • -
    • <output_dir>/contigs.paths contains paths in the assembly graph corresponding to contigs.fasta (see details below)
    • -
    • <output_dir>/scaffolds.paths contains paths in the assembly graph corresponding to scaffolds.fasta (see details below)
    • +
    • <output_dir>/corrected/ directory contains reads corrected by BayesHammer in *.fastq.gz files; if compression is disabled, reads are stored in uncompressed *.fastq files
    • +
    • <output_dir>/scaffolds.fasta contains resulting scaffolds (recommended for use as resulting sequences)
    • +
    • <output_dir>/contigs.fasta contains resulting contigs
    • +
    • <output_dir>/assembly_graph_with_scaffolds.gfa contains SPAdes assembly graph and scaffolds paths in GFA 1.0 format
    • +
    • <output_dir>/assembly_graph.fastg contains SPAdes assembly graph in FASTG format
    • +
    • <output_dir>/contigs.paths contains paths in the assembly graph corresponding to contigs.fasta (see details below)
    • +
    • <output_dir>/scaffolds.paths contains paths in the assembly graph corresponding to scaffolds.fasta (see details below)

    Contigs and scaffolds format

    Contigs/scaffolds names in SPAdes output FASTA files have the following format:
    ->NODE_3_length_237403_cov_243.207
    -Here 3 is the number of the contig/scaffold, 237403 is the sequence length in nucleotides and 243.207 is the k-mer coverage for the last (largest) k value used. Note that the k-mer coverage is always lower than the read (per-base) coverage.

    +>NODE_3_length_237403_cov_243.207
    +Here 3 is the number of the contig/scaffold, 237403 is the sequence length in nucleotides and 243.207 is the k-mer coverage for the last (largest) k value used. Note that the k-mer coverage is always lower than the read (per-base) coverage.

    In general, SPAdes uses two techniques for joining contigs into scaffolds. First one relies on read pairs and tries to estimate the size of the gap separating contigs. The second one relies on the assembly graph: e.g. if two contigs are separated by a complex tandem repeat, that cannot be resolved exactly, contigs are joined into scaffold with a fixed gap size of 100 bp. Contigs produced by SPAdes do not contain N symbols.

    Assembly graph formats

    -

    To view FASTG and GFA files we recommend to use Bandage visualization tool. Note that sequences stored in assembly_graph.fastg correspond to contigs before repeat resolution (edges of the assembly graph). Paths corresponding to contigs after repeat resolution (scaffolding) are stored in contigs.paths (scaffolds.paths) in the format accepted by Bandage (see Bandage wiki for details). The example is given below.

    -

    Let the contig with the name NODE_5_length_100000_cov_215.651 consist of the following edges of the assembly graph:

    -
        >EDGE_2_length_33280_cov_199.702
    +

    To view FASTG and GFA files we recommend to use Bandage visualization tool. Note that sequences stored in assembly_graph.fastg correspond to contigs before repeat resolution (edges of the assembly graph). Paths corresponding to contigs after repeat resolution (scaffolding) are stored in contigs.paths (scaffolds.paths) in the format accepted by Bandage (see Bandage wiki for details). The example is given below.

    +

    Let the contig with the name NODE_5_length_100000_cov_215.651 consist of the following edges of the assembly graph:

    +
        >EDGE_2_length_33280_cov_199.702
         >EDGE_5_length_84_cov_321.414"
         >EDGE_3_length_111_cov_175.304
         >EDGE_5_length_84_cov_321.414"
         >EDGE_4_length_66661_cov_223.548
     
    -

    Then, contigs.paths will contain the following record:

    -
        NODE_5_length_100000_cov_215.651
    +

    Then, contigs.paths will contain the following record:

    +
        NODE_5_length_100000_cov_215.651
         2+,5-,3+,5-,4+
     

    Since the current version of Bandage does not accept paths with gaps, paths corresponding contigs/scaffolds jumping over a gap in the assembly graph are split by semicolon at the gap positions. For example, the following record

    -
        NODE_3_length_237403_cov_243.207
    +
        NODE_3_length_237403_cov_243.207
         21-,17-,15+,17-,16+;
         31+,23-,22+,23-,4-
     
    -

    states that NODE_3_length_237403_cov_243.207 corresponds to the path with 10 edges, but jumps over a gap between edges EDGE_16_length_21503_cov_482.709 and EDGE_31_length_140767_cov_220.239.

    +

    states that NODE_3_length_237403_cov_243.207 corresponds to the path with 10 edges, but jumps over a gap between edges EDGE_16_length_21503_cov_482.709 and EDGE_31_length_140767_cov_220.239.

    Complete list of output files

    -

    The full list of <output_dir> content is presented below:

    +

    The full list of <output_dir> content is presented below:

    • scaffolds.fasta - resulting scaffolds (recommended for use as resulting sequences)

      @@ -709,18 +709,18 @@ Here 3 is the number of the

      K<##>/ - directory containing intermediate files from the run with K=<##>. These files should not be used as assembly results; use resulting contigs/scaffolds in files mentioned above.

    -

    SPAdes will overwrite these files and directories if they exist in the specified <output_dir>.

    +

    SPAdes will overwrite these files and directories if they exist in the specified <output_dir>.

    plasmidSPAdes output

    plasmidSPAdes and metaplasmidSPAdes output only DNA sequences from putative plasmids. Output file names and formats remain the same as in SPAdes (see previous section), with the following differences.

    -

    For all plasmidSPAdes' contig names in contigs.fasta, scaffolds.fasta and assembly_graph.fastg we append suffix _component_X, where X is the id of the putative plasmid, which the contig belongs to. Note that plasmidSPAdes may not be able to separate similar plasmids and thus their contigs may appear with the same id.

    +

    For all plasmidSPAdes' contig names in contigs.fasta, scaffolds.fasta and assembly_graph.fastg we append suffix _component_X, where X is the id of the putative plasmid, which the contig belongs to. Note that plasmidSPAdes may not be able to separate similar plasmids and thus their contigs may appear with the same id.

    metaplasmidSPAdes/metaviralSPAdes output

    -

    The repeat resolution and extrachromosomal element detection in metaplasmidSPAdes/metaviralSPAdes is run independently for different coverage cutoffs values (see paper for details). In order to distinguish contigs with putative plasmids detected at different cutoff levels we extend the contig name in FASTA file with cutoff value used for this particular contig (in format _cutoff_N). This is why, in the contrast to regular SPAdes pipeline, there might be a contig with NODE_1_ prefix for each cutoff with potential plasmids detected. In following example, there were detected two potential viruses using cutoff 0, one virus was detected with cutoff 5 and one with cutoff 10.
    +

    The repeat resolution and extrachromosomal element detection in metaplasmidSPAdes/metaviralSPAdes is run independently for different coverage cutoffs values (see paper for details). In order to distinguish contigs with putative plasmids detected at different cutoff levels we extend the contig name in FASTA file with cutoff value used for this particular contig (in format _cutoff_N). This is why, in the contrast to regular SPAdes pipeline, there might be a contig with NODE_1_ prefix for each cutoff with potential plasmids detected. In following example, there were detected two potential viruses using cutoff 0, one virus was detected with cutoff 5 and one with cutoff 10.
    Also, we add a suffix that shows the structure of the suspective extrachromosomal element.
    For metaplasmid mode we output only circular putative plasmids.
    For metaviral mode we also output linear putative viruses and linear viruses with simple repeats ('9'-shaped components in the assembly graph) sequences.

    -
    >NODE_1_length_40003_cov_13.48_cutoff_0_type_circular
    +
    >NODE_1_length_40003_cov_13.48_cutoff_0_type_circular
     >NODE_2_length_30000_cov_4.20_cutoff_0_type_linear
     >NODE_1_length_20000_cov_20.42_cutoff_5_type_circular
     >NODE_1_length_10000_cov_198.4_cutoff_10_type_linearrepeat
    @@ -729,7 +729,7 @@ For metaviral mode we also output linear
     

    biosyntheticSPAdes output

    biosyntheticSPAdes outputs four files of interest:

      -
    • scaffolds.fasta – contains DNA sequences from putative biosynthetic gene clusters (BGC). Since each sample may contain multiple BGCs and biosyntheticSPAdes can output several putative DNA sequences for eash cluster, for each contig name we append suffix _cluster_X_candidate_Y, where X is the id of the BGC and Y is the id of the candidate from the BGC.
    • +
    • scaffolds.fasta – contains DNA sequences from putative biosynthetic gene clusters (BGC). Since each sample may contain multiple BGCs and biosyntheticSPAdes can output several putative DNA sequences for eash cluster, for each contig name we append suffix _cluster_X_candidate_Y, where X is the id of the BGC and Y is the id of the candidate from the BGC.
    • raw_scaffolds.fasta – SPAdes scaffolds generated without domain-graph related algorithms. Very close to regular scaffolds.fasta file.
    • hmm_statistics.txt – contains statistics about BGC composition in the sample. First, it outputs number of domain hits in the sample. Then, for each BGC candidate we output domain order with positions on the corresponding DNA sequence from scaffolds.fasta.
    • domain_graph.dot – contains domain graph structure, that can be used to assess complexity of the sample and structure of BGCs. For more information about domain graph construction, please refer to the paper.
    • @@ -742,7 +742,7 @@ For metaviral mode we also output linear

      Stand-alone binaries released within SPAdes package

      k-mer counting

      -

      To provide input data to SPAdes k-mer counting tool spades-kmercounter you may just specify files in SPAdes-supported formats without any flags (after all options) or provide dataset description file in YAML format.

      +

      To provide input data to SPAdes k-mer counting tool spades-kmercounter you may just specify files in SPAdes-supported formats without any flags (after all options) or provide dataset description file in YAML format.

      Output: <output_dir>/final_kmers - unordered set of kmers in binary format. Kmers from both forward a
      nd reverse-complementary reads are taken into account.

      Output format: All kmers are written sequentially without any separators. Each kmer takes the same nu
      @@ -750,7 +750,7 @@ mber of bits. One kmer of length K takes r with length=21 takes 8 bytes, with length=33 takes 16 bytes, and with length=55 takes 16 bytes. Eac
      h nucleotide is coded with 2 bits: 00 - A, 01 - C, 10 - G, 11 - T.

      Example:

      -
          For kmer: AGCTCT
      +
          For kmer: AGCTCT
           Memory: 6 bits * 2 = 12, 64 bits (8 bytes)
           Let’s describe bytes:
           data[0] = AGCT -> 11 01 10 00 -> 0xd8                                
      @@ -762,103 +762,103 @@ h nucleotide is coded with 2 bits: 00 -
           data[6] = 0000 -> 00 00 00 00 -> 0x00
           data[7] = 0000 -> 00 00 00 00 -> 0x00
       
      -

      Synopsis: spades-kmercount [OPTION...] <input files>

      +

      Synopsis: spades-kmercount [OPTION...] <input files>

      The options are:

      -

      -d, --dataset file <file name>
      +

      -d, --dataset file <file name>
      dataset description (in YAML format), input files ignored

      -

      -k, --kmer <int>
      +

      -k, --kmer <int>
      k-mer length (default: 21)

      -

      -t, --threads <int>
      +

      -t, --threads <int>
      number of threads to use (default: number of CPUs)

      -

      -w, --workdir <dir name>
      +

      -w, --workdir <dir name>
      working directory to use (default: current directory)

      -

      -b, --bufsize <int>
      +

      -b, --bufsize <int>
      sorting buffer size in bytes, per thread (default 536870912)

      -

      -h, --help
      +

      -h, --help
      print help message

      k-mer coverage read filter

      -

      spades-read-filter is a tool for filtering reads with median kmer coverage less than threshold.

      -

      To provide input data to SPAdes k-mer read filter tool spades-read-filter you should provide dataset description file in YAML format.

      -

      Synopsis: spades-read-filter [OPTION...] -d <yaml>

      +

      spades-read-filter is a tool for filtering reads with median kmer coverage less than threshold.

      +

      To provide input data to SPAdes k-mer read filter tool spades-read-filter you should provide dataset description file in YAML format.

      +

      Synopsis: spades-read-filter [OPTION...] -d <yaml>

      The options are:

      -

      -d, --dataset file <file name>
      +

      -d, --dataset file <file name>
      dataset description (in YAML format)

      -

      -k, --kmer <int>
      +

      -k, --kmer <int>
      k-mer length (default: 21)

      -

      -t, --threads <int>
      +

      -t, --threads <int>
      number of threads to use (default: number of CPUs)

      -

      -o, --outdir <dir>
      +

      -o, --outdir <dir>
      output directory to use (default: current directory)

      -

      -c, --cov <value>
      +

      -c, --cov <value>
      median kmer count threshold (read pairs, s.t. kmer count median for BOTH reads LESS OR EQUAL to this value will be ignored)

      -

      -h, --help
      +

      -h, --help
      print help message

      k-mer cardinality estimating

      -

      spades-kmer-estimating is a tool for estimating approximate number of unique k-mers in the provided reads. Kmers from reverse-complementary reads aren"t taken into account for k-mer cardinality estimating.

      -

      To provide input data to SPAdes k-mer cardinality estimating tool spades-kmer-estimating you should provide dataset description file in YAML format.

      -

      Synopsis: spades-kmer-estimating [OPTION...] -d <yaml>

      +

      spades-kmer-estimating is a tool for estimating approximate number of unique k-mers in the provided reads. Kmers from reverse-complementary reads aren"t taken into account for k-mer cardinality estimating.

      +

      To provide input data to SPAdes k-mer cardinality estimating tool spades-kmer-estimating you should provide dataset description file in YAML format.

      +

      Synopsis: spades-kmer-estimating [OPTION...] -d <yaml>

      The options are:

      -

      -d, --dataset file <file name>
      +

      -d, --dataset file <file name>
      dataset description (in YAML format)

      -

      -k, --kmer <int>
      +

      -k, --kmer <int>
      k-mer length (default: 21)

      -

      -t, --threads <int>
      +

      -t, --threads <int>
      number of threads to use (default: number of CPUs)

      -

      -h, --help
      +

      -h, --help
      print help message

      Graph construction

      -

      Graph construction tool spades-gbuilder has two mandatory options: dataset description file in YAML format and an output file name.

      -

      Synopsis: spades-gbuilder <dataset description (in YAML)> <output filename> [-k <value>] [-t <value>] [-tmpdir <dir>] [-b <value>] [-unitigs|-fastg|-gfa|-spades]

      +

      Graph construction tool spades-gbuilder has two mandatory options: dataset description file in YAML format and an output file name.

      +

      Synopsis: spades-gbuilder <dataset description (in YAML)> <output filename> [-k <value>] [-t <value>] [-tmpdir <dir>] [-b <value>] [-unitigs|-fastg|-gfa|-spades]

      Additional options are:

      -

      -k <int>
      +

      -k <int>
      k-mer length used for construction (must be odd)

      -

      -t <int>
      +

      -t <int>
      number of threads

      -

      -tmp-dir <dir_name>
      +

      -tmp-dir <dir_name>
      scratch directory to use

      -

      -b <int>
      +

      -b <int>
      sorting buffer size (per thread, in bytes)

      -

      -unitigs
      +

      -unitigs
      k-mer length used for construction (must be odd)

      -

      -fastg
      +

      -fastg
      output graph in FASTG format

      -

      -gfa
      +

      -gfa
      output graph in GFA1 format

      -

      -spades
      +

      -spades
      output graph in SPAdes internal format

      Long read to graph alignment

      hybridSPAdes aligner

      -

      A tool spades-gmapper gives opportunity to extract long read alignments generated with hybridSPAdes pipeline options. It has three mandatory options: dataset description file in YAML format, graph file in GFA format and an output file name.

      -

      Synopsis: spades-gmapper <dataset description (in YAML)> <graph (in GFA)> <output filename> [-k <value>] [-t <value>] [-tmpdir <dir>]

      +

      A tool spades-gmapper gives opportunity to extract long read alignments generated with hybridSPAdes pipeline options. It has three mandatory options: dataset description file in YAML format, graph file in GFA format and an output file name.

      +

      Synopsis: spades-gmapper <dataset description (in YAML)> <graph (in GFA)> <output filename> [-k <value>] [-t <value>] [-tmpdir <dir>]

      Additional options are:

      -

      -k <int>
      +

      -k <int>
      k-mer length that was used for graph construction

      -

      -t <int>
      +

      -t <int>
      number of threads

      -

      -tmpdir <dir_name>
      +

      -tmpdir <dir_name>
      scratch directory to use

      -

      While spades-mapper is a solution for those who work on hybridSPAdes assembly and want to get exactly its intermediate results, SPAligner is an end-product application for sequence-to-graph alignment with tunable parameters and output types.

      +

      While spades-mapper is a solution for those who work on hybridSPAdes assembly and want to get exactly its intermediate results, SPAligner is an end-product application for sequence-to-graph alignment with tunable parameters and output types.

      SPAligner

      A tool for fast and accurate alignment of nucleotide sequences to assembly graphs. It takes file with sequences (in fasta/fastq format) and assembly in GFA format and outputs long read to graph alignment in various formats (such as tsv, fasta and GPA).

      -

      Synopsis: spaligner assembly/src/projects/spaligner_config.yaml -d <value> -s <value> -g <value> -k <value> [-t <value>] [-o <value>]

      +

      Synopsis: spaligner assembly/src/projects/spaligner_config.yaml -d <value> -s <value> -g <value> -k <value> [-t <value>] [-o <value>]

      Parameters are:

      -

      -d <type>
      +

      -d <type>
      long reads type: nanopore, pacbio

      -

      -s <filename>
      +

      -s <filename>
      file with sequences (in fasta/fastq)

      -

      -g <filename>
      +

      -g <filename>
      file with graph (in GFA)

      -

      -k <int>
      +

      -k <int>
      k-mer length that was used for graph construction

      -

      -t <int>
      +

      -t <int>
      number of threads (default: 8)

      -

      -o, --outdir <dir>
      +

      -o, --outdir <dir>
      output directory to use (default: spaligner_result/)

      For more information on parameters and options please refer to main SPAligner manual (assembler/src/projects/spaligner/README.md).

      Also if you want to align protein sequences please refer to our pre-release version.

      @@ -880,5 +880,5 @@ output directory to use (default: spalig

      In addition, we would like to list your publications that use our software on our website. Please email the reference, the name of your lab, department and institution to spades.support@cab.spbu.ru

      Feedback and bug reports

      -

      Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve SPAdes. If you have any troubles running SPAdes, please send us params.txt and spades.log from the directory <output_dir>.

      +

      Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve SPAdes. If you have any troubles running SPAdes, please send us params.txt and spades.log from the directory <output_dir>.

      You can leave your comments and bug reports at our GitHub repository tracker or sent it via e-mail: spades.support@cab.spbu.ru






      diff -pruN 3.15.4+dfsg-3/assembler/src/cmake/pack.cmake 3.15.5+dfsg-1/assembler/src/cmake/pack.cmake --- 3.15.4+dfsg-3/assembler/src/cmake/pack.cmake 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/cmake/pack.cmake 2022-07-16 09:53:26.000000000 +0000 @@ -12,10 +12,10 @@ set(CPACK_PACKAGE_NAME "SPAdes") set(CPACK_PACKAGE_VENDOR "Saint Petersburg State University") #set(CPACK_PACKAGE_DESCRIPTION_FILE "${SPADES_MAIN_SRC_DIR}/../README") set(CPACK_RESOURCE_FILE_LICENSE "${SPADES_MAIN_SRC_DIR}/../LICENSE") -set(CPACK_PACKAGE_VERSION "3.15.4") +set(CPACK_PACKAGE_VERSION "3.15.5") set(CPACK_PACKAGE_VERSION_MAJOR "3") set(CPACK_PACKAGE_VERSION_MINOR "15") -set(CPACK_PACKAGE_VERSION_PATCH "4") +set(CPACK_PACKAGE_VERSION_PATCH "5") set(CPACK_STRIP_FILES bin/spades-bwa bin/spades-core bin/spades-corrector-core bin/spades-gbuilder bin/spades-gmapper bin/spades-hammer bin/spades-ionhammer bin/spades-kmercount bin/spades-truseq-scfcorrection) diff -pruN 3.15.4+dfsg-3/assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp 3.15.5+dfsg-1/assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp --- 3.15.4+dfsg-3/assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp 1970-01-01 00:00:00.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/common/assembly_graph/handlers/used_edge_handler.hpp 2022-07-16 09:53:26.000000000 +0000 @@ -0,0 +1,79 @@ +//*************************************************************************** +//* Copyright (c) 2022 Saint-Petersburg State University +//* All Rights Reserved +//* See file LICENSE for details. +//**************************************************************************** +#pragma once +#include "assembly_graph/core/action_handlers.hpp" +#include + +using namespace omnigraph; + +namespace omnigraph { + + template + class UsedEdgeHandler : omnigraph::GraphActionHandler { + typedef typename Graph::EdgeId EdgeId; + + std::unordered_map storage_; + size_t banned_bases_ = 0; + + public: + UsedEdgeHandler(const Graph &g) : + omnigraph::GraphActionHandler(g, "UsedEdgeHandler"), storage_() { } + + void HandleAdd(EdgeId e) override { + storage_.emplace(e, 0); + } + + void HandleDelete(EdgeId e) override { + storage_.erase(e); + } + + void HandleMerge(const std::vector &old_edges, EdgeId new_edge) override { + DEBUG("merging "); + size_t sum = 0; + for (EdgeId e : old_edges) { + DEBUG(e.int_id()); + auto it = storage_.find(e); + if (it != storage_.end()) + sum += it->second; + } + DEBUG("into " << new_edge.int_id()); + storage_[new_edge] = sum; + } + + void HandleGlue(EdgeId /*new_edge*/, EdgeId /*edge1*/, EdgeId /*edge2*/) override { + VERIFY(false); + } + + void HandleSplit(EdgeId /*old_edge*/, EdgeId /*new_edge_1*/, + EdgeId /*new_edge_2*/) override { + VERIFY(false); + } + + void AddUsed(EdgeId e) { + size_t was_used = 0; + auto it = storage_.find(e); + if (it != storage_.end()) + was_used = it->second; + + size_t new_used = this->g().length(e); + VERIFY(new_used >= was_used); + storage_[e] = new_used; + banned_bases_ += (new_used - was_used); + } + + size_t GetUsedLength(EdgeId e) const { + auto it = storage_.find(e); + return it != storage_.end() ? it->second : 0; + } + + size_t size() const { + return banned_bases_; + } + }; + +} + + diff -pruN 3.15.4+dfsg-3/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp 3.15.5+dfsg-1/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp --- 3.15.4+dfsg-3/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/common/modules/alignment/pacbio/gap_filler.hpp 2022-07-16 09:53:26.000000000 +0000 @@ -120,7 +120,7 @@ class GapFiller { MappingPoint p, PathRange &range, bool forward, GraphPosition &old_start_pos) const; const debruijn_graph::Graph &g_; - const GAlignerConfig &cfg_; + const GAlignerConfig cfg_; }; diff -pruN 3.15.4+dfsg-3/assembler/src/projects/spades/contig_output_stage.cpp 3.15.5+dfsg-1/assembler/src/projects/spades/contig_output_stage.cpp --- 3.15.4+dfsg-3/assembler/src/projects/spades/contig_output_stage.cpp 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/projects/spades/contig_output_stage.cpp 2022-07-16 09:53:26.000000000 +0000 @@ -10,6 +10,7 @@ #include "assembly_graph/core/graph.hpp" #include "assembly_graph/paths/bidirectional_path.hpp" #include "assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp" +#include "assembly_graph/handlers/used_edge_handler.hpp" #include "modules/path_extend/pe_resolver.hpp" #include "modules/path_extend/pe_utils.hpp" #include "io/dataset_support/read_converter.hpp" @@ -19,10 +20,11 @@ namespace { using namespace debruijn_graph; +using UsedEdges = omnigraph::UsedEdgeHandler; static constexpr double LARGE_FRACTION = 0.8; -bool CheckUsedPath(const path_extend::BidirectionalPath &path, std::unordered_set &used_edges) { +bool CheckUsedPath(const path_extend::BidirectionalPath &path, UsedEdges &used_edges) { const Graph& g = path.g(); size_t used_len = 0; size_t total_len = 0; @@ -30,22 +32,20 @@ bool CheckUsedPath(const path_extend::Bi for (size_t i = 0; i < path_len; i++) { size_t cur_len = g.length(path.At(i)); total_len += cur_len; - if (used_edges.count(path.At(i))) { - used_len += cur_len; - } + used_len += used_edges.GetUsedLength(path.At(i)); } for (size_t i = 0; i < path_len; i++) { - used_edges.insert(path.At(i)); - used_edges.insert(g.conjugate(path.At(i))); + used_edges.AddUsed(path.At(i)); + used_edges.AddUsed(g.conjugate(path.At(i))); } //FIXME: constant return (math::ge((double)used_len, (double)total_len * LARGE_FRACTION)); } -path_extend::PathContainer GetCircularScaffolds(const path_extend::PathContainer &sc_storage, std::unordered_set &used_edges, size_t min_circular_length) { +path_extend::PathContainer GetCircularScaffolds(const path_extend::PathContainer &sc_storage, UsedEdges &used_edges, size_t min_circular_length) { path_extend::PathContainer res; - INFO("Banned " << used_edges.size() <<" used edges"); + INFO("Banned " << used_edges.size() <<" used bases"); for (const auto &entry : sc_storage) { const path_extend::BidirectionalPath &path = *entry.first; @@ -61,7 +61,7 @@ path_extend::PathContainer GetCircularSc return res; } -path_extend::PathContainer GetTipScaffolds(const path_extend::PathContainer &sc_storage, const std::unordered_set &forbidden_vertices, std::unordered_set &used_edges, size_t min_linear_length) { +path_extend::PathContainer GetTipScaffolds(const path_extend::PathContainer &sc_storage, const std::unordered_set &forbidden_vertices, UsedEdges &used_edges, size_t min_linear_length) { path_extend::PathContainer res; for (const auto &entry : sc_storage) { const path_extend::BidirectionalPath &path = *entry.first; @@ -211,7 +211,6 @@ void ContigOutput::run(GraphPack &gp, co fastg_writer)); if (outputs_.count(Kind::PlasmidContigs)) { - using UsedEdges = omnigraph::SmartContainer, Graph>; if (!gp.count("used_edges")) gp.add("used_edges", UsedEdges(graph)); PathContainer circulars = GetCircularScaffolds(broken_scaffolds, gp.get_mutable("used_edges"), cfg::get().pd->min_circular_length); diff -pruN 3.15.4+dfsg-3/assembler/src/projects/spades/domain_matcher.cpp 3.15.5+dfsg-1/assembler/src/projects/spades/domain_matcher.cpp --- 3.15.4+dfsg-3/assembler/src/projects/spades/domain_matcher.cpp 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/projects/spades/domain_matcher.cpp 2022-07-16 09:53:26.000000000 +0000 @@ -32,14 +32,20 @@ extern "C" { namespace nrps { -static void match_contigs_internal(hmmer::HMMMatcher &matcher, const path_extend::BidirectionalPath &path, - const std::string &path_string, - const std::string &type, const std::string &desc, - ContigAlnInfo &res, io::OFastaReadStream &oss_contig, size_t model_length) { - for (size_t shift = 0; shift < 3; ++shift) { - std::string ref_shift = std::to_string(path.GetId()) + "_" + std::to_string(shift); - std::string seq_aas = aa::translate(path_string.c_str() + shift); - matcher.match(ref_shift.c_str(), seq_aas.c_str()); +static void MatchContigsInternal(hmmer::HMMMatcher &matcher, const path_extend::BidirectionalPath &path, + const std::string &path_string, + const std::string &type, const std::string &desc, + ContigAlnInfo &res, io::OFastaReadStream &oss_contig, size_t model_length, + bool isAA = true) { + if (isAA) { + for (size_t shift = 0; shift < 3; ++shift) { + std::string ref_shift = std::to_string(path.GetId()) + "_" + std::to_string(shift); + std::string seq_aas = aa::translate(path_string.c_str() + shift); + matcher.match(ref_shift.c_str(), seq_aas.c_str()); + } + } else { + std::string ref_shift = std::to_string(path.GetId()) + "_0"; + matcher.match(ref_shift.c_str(), path_string.c_str()); } matcher.summarize(); @@ -57,8 +63,8 @@ static void match_contigs_internal(hmmer continue; } int shift = hit.name()[strlen(hit.name()) - 1] - '0'; - seqpos.first = seqpos.first * 3 + shift; - seqpos.second = seqpos.second * 3 + shift; + seqpos.first = seqpos.first * (isAA ? 3 : 1) + shift; + seqpos.second = seqpos.second * (isAA ? 3 : 1) + shift; std::string name(hit.name()); #pragma omp critical @@ -75,30 +81,31 @@ static void match_contigs_internal(hmmer matcher.reset_top_hits(); } -static void match_contigs(const path_extend::PathContainer &contig_paths, const path_extend::ScaffoldSequenceMaker &scaffold_maker, - const hmmer::HMM &hmm, const hmmer::hmmer_cfg &cfg, - ContigAlnInfo &res, io::OFastaReadStream &oss_contig) { +static void MatchContigs(const path_extend::PathContainer &contig_paths, const path_extend::ScaffoldSequenceMaker &scaffold_maker, + const hmmer::HMM &hmm, const hmmer::hmmer_cfg &cfg, + ContigAlnInfo &res, io::OFastaReadStream &oss_contig) { DEBUG("Total contigs: " << contig_paths.size()); DEBUG("Model length - " << hmm.length()); hmmer::HMMMatcher matcher(hmm, cfg); + bool isAA = hmm.abc()->type == eslAMINO; for (auto iter = contig_paths.begin(); iter != contig_paths.end(); ++iter) { const path_extend::BidirectionalPath &path = iter.get(); if (path.Length() <= 0) continue; std::string path_string = scaffold_maker.MakeSequence(path); - match_contigs_internal(matcher, path, path_string, - hmm.name(), hmm.desc() ? hmm.desc() : "", - res, oss_contig, hmm.length()); + MatchContigsInternal(matcher, path, path_string, + hmm.name(), hmm.desc() ? hmm.desc() : "", + res, oss_contig, hmm.length(), isAA); const path_extend::BidirectionalPath& conj_path = iter.getConjugate(); if (conj_path.Length() <= 0) continue; std::string path_string_conj = scaffold_maker.MakeSequence(conj_path); - match_contigs_internal(matcher, conj_path, path_string_conj, - hmm.name(), hmm.desc() ? hmm.desc() : "", - res, oss_contig, hmm.length()); + MatchContigsInternal(matcher, conj_path, path_string_conj, + hmm.name(), hmm.desc() ? hmm.desc() : "", + res, oss_contig, hmm.length(), isAA); } } @@ -116,10 +123,12 @@ static void ParseHMMFile(std::vector &hmms, const std::string &filename) { - hmmer::HMMSequenceBuilder builder(hmmer::Alphabet::AMINO, hmmer::ScoreSystem::Default); +static void ParseFASTAFile(std::vector &hmms, + const std::string &filename, bool useAA = true) { + hmmer::HMMSequenceBuilder builder(useAA ? hmmer::Alphabet::AMINO : hmmer::Alphabet::DNA, + hmmer::ScoreSystem::Default); - ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO); + ESL_ALPHABET *abc = esl_alphabet_Create(useAA ? eslAMINO : eslDNA); ESL_SQ *qsq = esl_sq_CreateDigital(abc); ESL_SQFILE *qfp = NULL; const char *qfile = filename.c_str(); @@ -138,7 +147,7 @@ static void ParseFASTAFile(std::vectorname << ", len: " << qsq->n); + INFO("Converting " << (useAA ? "AA" : "DNA") << " sequence " << qsq->name << ", len: " << qsq->n); hmms.push_back(builder.from_string(qsq)); esl_sq_Reuse(qsq); } @@ -174,14 +183,19 @@ ContigAlnInfo DomainMatcher::MatchDomain std::vector hmms; for (const auto &f : hmm_files) { if (utils::ends_with(f, ".aa") || utils::ends_with(f, ".aa.gz")) { - ParseFASTAFile(hmms, f); + ParseFASTAFile(hmms, f, true); + hcfg.E = hcfg.domE = 0.01; + } else if (utils::ends_with(f, ".fa") || utils::ends_with(f, ".fa.gz") | + utils::ends_with(f, ".fna") || utils::ends_with(f, ".fna.gz")) { + ParseFASTAFile(hmms, f, false); hcfg.E = hcfg.domE = 0.01; } else { ParseHMMFile(hmms, f); } } - // Setup E-value search space size + // Setup E-value search space size. We always use larger size (AA-based), + // so it will be a bit conservative for nucleotide HMMs / sequences hcfg.Z = 3 * broken_scaffolds.size(); # pragma omp parallel for @@ -193,9 +207,9 @@ ContigAlnInfo DomainMatcher::MatchDomain INFO("Matching contigs with " << name); } - match_contigs(broken_scaffolds, scaffold_maker, - hmms[i], hcfg, - local_res, oss_contig); + MatchContigs(broken_scaffolds, scaffold_maker, + hmms[i], hcfg, + local_res, oss_contig); # pragma omp critical { diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/options_parser.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/options_parser.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/options_parser.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/options_parser.py 2022-07-16 09:53:26.000000000 +0000 @@ -940,7 +940,9 @@ def add_to_cfg(cfg, log, bin_home, spade hmms = "" is_hmmfile= lambda hmmfile: os.path.isfile(hmmfile) \ and (hmmfile.endswith("hmm") or hmmfile.endswith("hmm.gz") or \ - hmmfile.endswith("aa") or hmmfile.endswith("aa.gz")) + hmmfile.endswith("aa") or hmmfile.endswith("aa.gz") or \ + hmmfile.endswith("fa") or hmmfile.endswith("fa.gz") or \ + hmmfile.endswith("fna") or hmmfile.endswith("fna.gz")) if os.path.isdir(hmms_path): hmms = ",".join([os.path.join(hmms_path, hmmfile) for hmmfile in os.listdir(hmms_path) @@ -1044,10 +1046,19 @@ def postprocessing(args, cfg, dataset_da if args.careful: support.error("you cannot specify --careful in RNA-Seq mode!", log) - modes_count = [args.meta, args.large_genome, args.truseq_mode, args.rna, args.plasmid, args.single_cell, args.isolate, args.rnaviral].count(True) - if modes_count > 1 and ([args.meta, args.plasmid].count(True) < 2 and [args.meta, args.bio].count(True) < 2 and [args.meta, args.rnaviral].count(True) < 2): - support.error("you cannot simultaneously use more than one mode out of " - "Isolate, Metagenomic, Large genome, Illumina TruSeq, RNA-Seq, Plasmid, and Single-cell (except combining Metagenomic and Plasmid)!", log) + modes_count = [args.large_genome, args.rna, args.plasmid, args.meta, args.single_cell, args.isolate, args.rnaviral, + args.corona, args.metaviral, args.metaplasmid, args.bio].count(True) + is_metaplasmid = modes_count == 3 and [args.meta, args.plasmid, args.metaplasmid].count(True) == 3 + is_bgc = modes_count == 2 and [args.meta, args.bio].count(True) == 2 + is_metaviral = modes_count == 3 and [args.meta, args.plasmid, args.metaviral].count(True) == 3 + is_rnaviral = modes_count == 2 and [args.meta, args.rnaviral].count(True) == 2 + is_corona = modes_count == 3 and [args.meta, args.rnaviral, args.corona].count(True) == 3 + if not (modes_count <= 1 or is_metaplasmid or is_bgc or is_metaviral or is_rnaviral or is_corona): + # correct cases: + # - either there is 1 or 0 modes specified + # - or there is 1 of 5 allowed combinations + # everything else is forbidden + support.error("Specified mode combination is not supported! Check out user manual for available modes.", log) elif modes_count == 0: support.warning("No assembly mode was specified! If you intend to assemble high-coverage multi-cell/isolate data, use '--isolate' option.") diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/correction_stage.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/correction_stage.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/correction_stage.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/correction_stage.py 2022-07-16 09:53:26.000000000 +0000 @@ -10,7 +10,6 @@ import os import shutil import sys -from distutils import dir_util from site import addsitedir from stages import stage @@ -71,7 +70,7 @@ class CorrectionIterationStage(stage.Sta dst_configs = os.path.join(self.cfg.output_dir, "configs") if os.path.isdir(dst_configs): shutil.rmtree(dst_configs) - dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "corrector"), dst_configs, preserve_times=False) + support.copy_tree(os.path.join(self.tmp_configs_dir, "corrector"), dst_configs, preserve_times=False) cfg_file_name = os.path.join(dst_configs, "corrector.info") self.cfg.tmp_dir = support.get_tmp_dir(prefix="corrector_") diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/error_correction_stage.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/error_correction_stage.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/error_correction_stage.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/error_correction_stage.py 2022-07-16 09:53:26.000000000 +0000 @@ -10,7 +10,6 @@ import os import shutil import sys -from distutils import dir_util from site import addsitedir import commands_parser @@ -63,10 +62,10 @@ class ECRunningToolStage(stage.Stage): if os.path.isdir(dst_configs): shutil.rmtree(dst_configs) if cfg.iontorrent: - dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "ionhammer"), dst_configs, preserve_times=False) + support.copy_tree(os.path.join(self.tmp_configs_dir, "ionhammer"), dst_configs, preserve_times=False) cfg_file_name = os.path.join(dst_configs, "ionhammer.cfg") else: - dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "hammer"), dst_configs, preserve_times=False) + support.copy_tree(os.path.join(self.tmp_configs_dir, "hammer"), dst_configs, preserve_times=False) cfg_file_name = os.path.join(dst_configs, "config.info") cfg.tmp_dir = support.get_tmp_dir(prefix="hammer_") diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/pipeline.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/pipeline.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/pipeline.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/pipeline.py 2022-07-16 09:53:26.000000000 +0000 @@ -9,8 +9,8 @@ import os import shutil -from distutils import dir_util +import support import options_storage class Pipeline(object): @@ -22,10 +22,10 @@ class Pipeline(object): shutil.rmtree(tmp_configs_dir) if not os.path.isdir(tmp_configs_dir): if options_storage.args.configs_dir: - dir_util.copy_tree(options_storage.args.configs_dir, tmp_configs_dir, preserve_times=False, + support.copy_tree(options_storage.args.configs_dir, tmp_configs_dir, preserve_times=False, preserve_mode=False) else: - dir_util.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False, + support.copy_tree(os.path.join(spades_home, "configs"), tmp_configs_dir, preserve_times=False, preserve_mode=False) def add(self, stage): diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/scaffold_correction_stage.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/scaffold_correction_stage.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/scaffold_correction_stage.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/scaffold_correction_stage.py 1970-01-01 00:00:00.000000000 +0000 @@ -1,112 +0,0 @@ -#!/usr/bin/env python - -############################################################################ -# Copyright (c) 2015-2019 Saint Petersburg State University -# Copyright (c) 2011-2014 Saint Petersburg Academic University -# All Rights Reserved -# See file LICENSE for details. -############################################################################ - -import os -import shutil -from distutils import dir_util - -import commands_parser -import options_storage -from stages import stage -import process_cfg -from process_cfg import bool_to_str - -# TODO copypast from iteraton stage -READS_TYPES_USED_IN_CONSTRUCTION = ["paired-end", "single", "hq-mate-pairs"] -READS_TYPES_USED_IN_RNA_SEQ = ["paired-end", "single", "trusted-contigs", "untrusted-contigs"] - - -def prepare_config_scaffold_correction(filename, cfg, log, saves_dir, K): - subst_dict = dict() - - subst_dict["K"] = str(K) - subst_dict["dataset"] = process_cfg.process_spaces(cfg.dataset) - subst_dict["output_base"] = process_cfg.process_spaces(os.path.join(cfg.output_dir, "SCC")) - subst_dict["tmp_dir"] = process_cfg.process_spaces(cfg.tmp_dir) - subst_dict["use_additional_contigs"] = bool_to_str(False) - subst_dict["main_iteration"] = bool_to_str(False) - subst_dict["entry_point"] = options_storage.BASE_STAGE - subst_dict["load_from"] = saves_dir - subst_dict["developer_mode"] = bool_to_str(cfg.developer_mode) - subst_dict["max_threads"] = cfg.max_threads - subst_dict["max_memory"] = cfg.max_memory - - # todo - process_cfg.substitute_params(filename, subst_dict, log) - - -def add_configs(command, configs_dir): - # Order matters here! - mode_config_mapping = [("single_cell", "mda_mode"), - ("meta", "meta_mode"), - ("truseq_mode", "moleculo_mode"), - ("rna", "rna_mode"), - ("large_genome", "large_genome_mode"), - ("plasmid", "plasmid_mode")] - # ("careful", "careful_mode"), - for (mode, config) in mode_config_mapping: - if options_storage.args.__dict__[mode]: - if mode == "rna" or mode == "meta": - command.append(os.path.join(configs_dir, "mda_mode.info")) - command.append(os.path.join(configs_dir, config + ".info")) - if options_storage.args.__dict__["careful"]: - if options_storage.args.__dict__["single_cell"]: - command.append(os.path.join(configs_dir, "careful_mda_mode.info")) - else: - command.append(os.path.join(configs_dir, "careful_mode.info")) - - # special case: extra config - if options_storage.args.rna and options_storage.args.fast: - command.append(os.path.join(configs_dir, "rna_fast_mode.info")) - - -class ScaffoldCorrectionStage(stage.Stage): - def __init__(self, latest, *args): - super(ScaffoldCorrectionStage, self).__init__(*args) - self.latest = latest - - def generate_config(self, cfg): - K = cfg.iterative_K[-1] - latest = os.path.join(cfg.output_dir, "K%d" % K) - K = options_storage.SCC_K - data_dir = os.path.join(cfg.output_dir, "SCC", "K%d" % K) - saves_dir = os.path.join(data_dir, "saves") - dst_configs = os.path.join(data_dir, "configs") - cfg_file_name = os.path.join(dst_configs, "config.info") - - if os.path.isdir(data_dir): - shutil.rmtree(data_dir) - os.makedirs(data_dir) - - dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False) - - scaffolds_file = os.path.join(latest, "scaffolds.fasta") - if "read_buffer_size" in cfg.__dict__: - construction_cfg_file_name = os.path.join(dst_configs, "construction.info") - process_cfg.substitute_params(construction_cfg_file_name, {"read_buffer_size": cfg.read_buffer_size}, - self.log) - process_cfg.substitute_params(os.path.join(dst_configs, "moleculo_mode.info"), - {"scaffolds_file": scaffolds_file}, self.log) - prepare_config_scaffold_correction(cfg_file_name, cfg, self.log, saves_dir, K) - - def get_command(self, cfg): - K = options_storage.SCC_K - data_dir = os.path.join(cfg.output_dir, "SCC", "K%d" % K) - dst_configs = os.path.join(data_dir, "configs") - cfg_file_name = os.path.join(dst_configs, "config.info") - - args = [cfg_file_name] - add_configs(args, dst_configs) - command = [commands_parser.Command( - STAGE="SCC", - path=os.path.join(self.bin_home, "spades-truseq-scfcorrection"), - args=args, - config_dir=os.path.relpath(data_dir, options_storage.args.output_dir), - short_name=self.short_name)] - return command diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/spades_iteration_stage.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/spades_iteration_stage.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/spades_iteration_stage.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/spades_iteration_stage.py 2022-07-16 09:53:26.000000000 +0000 @@ -9,11 +9,11 @@ import os import shutil -from distutils import dir_util import commands_parser import options_storage from stages import stage +import support import process_cfg from process_cfg import bool_to_str @@ -139,9 +139,7 @@ class IterationStage(stage.Stage): if self.get_stage(self.short_name) == options_storage.BASE_STAGE: if not os.path.isdir(data_dir): os.makedirs(data_dir) - - dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree - dir_util.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False) + support.copy_tree(os.path.join(self.tmp_configs_dir, "debruijn"), dst_configs, preserve_times=False) if self.prev_K: additional_contigs_dname = os.path.join(cfg.output_dir, "K%d" % self.prev_K, "simplified_contigs") diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/spades_stage.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/spades_stage.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/stages/spades_stage.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/stages/spades_stage.py 2022-07-16 09:53:26.000000000 +0000 @@ -15,7 +15,6 @@ from site import addsitedir import commands_parser import options_storage from stages import stage -from stages import scaffold_correction_stage from stages import spades_iteration_stage import support from process_cfg import merge_configs @@ -325,16 +324,6 @@ class SpadesStage(stage.Stage): if last_one: break - if self.cfg.correct_scaffolds: - self.stages.append(scaffold_correction_stage.ScaffoldCorrectionStage(self.latest, - "scc", - self.output_files, - self.tmp_configs_dir, - self.dataset_data, self.log, - self.bin_home, - self.ext_python_modules_home, - self.python_modules_home)) - self.latest = os.path.join(os.path.join(self.cfg.output_dir, "SCC"), "K21") if options_storage.args.plasmid and options_storage.args.meta: self.stages.append(PlasmidGlueFileStage(self.latest, "plasmid_copy_files", self.output_files, diff -pruN 3.15.4+dfsg-3/assembler/src/spades_pipeline/support.py 3.15.5+dfsg-1/assembler/src/spades_pipeline/support.py --- 3.15.4+dfsg-3/assembler/src/spades_pipeline/support.py 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/src/spades_pipeline/support.py 2022-07-16 09:53:26.000000000 +0000 @@ -940,3 +940,30 @@ def is_int(value): return True except ValueError: return False + + +# shutil.copyfile does not copy any metadata (time and permission), so one +# cannot expect preserve_mode = False and preserve_times = True to work. +def copy_tree(src, dst, preserve_times=True, preserve_mode=True): + if sys.version.split()[0][0] == '2': + from distutils import dir_util + dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree + dir_util.copy_tree(src, dst, preserve_times=preserve_times, preserve_mode=preserve_mode) + return + + if not preserve_mode: + copy_fn = shutil.copyfile + else: + copy_fn = shutil.copy2 + + if os.path.exists(dst): + shutil.rmtree(dst) + + # shutil.copytree preserves the timestamp, so we must update it afterwards. + shutil.copytree(src, dst, copy_function = copy_fn) + + if not preserve_times: + for dirpath, _, filenames in os.walk(dst): + os.utime(dirpath, None) + for file in filenames: + os.utime(os.path.join(dirpath, file), None) diff -pruN 3.15.4+dfsg-3/assembler/VERSION 3.15.5+dfsg-1/assembler/VERSION --- 3.15.4+dfsg-3/assembler/VERSION 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/assembler/VERSION 2022-07-16 09:53:26.000000000 +0000 @@ -1 +1 @@ -3.15.4 +3.15.5 diff -pruN 3.15.4+dfsg-3/debian/changelog 3.15.5+dfsg-1/debian/changelog --- 3.15.4+dfsg-3/debian/changelog 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/changelog 2022-08-01 19:11:59.000000000 +0000 @@ -1,3 +1,21 @@ +spades (3.15.5+dfsg-1) unstable; urgency=medium + + * New upstream version 3.15.5+dfsg + * d/patches/: + + fix-privacy-breaches.patch: update badges list. + + python3.patch: refresh. + + 0003_accept-system-bwa.patch: unfuzz. + + yaml_load.patch: unfuzz. + * d/m/coronaspades.1.adoc: add manual page for coronaspades. + * d/links: create a link for coronaspades.py manual. + * d/t/run-upstreams-tests: add self tests for plasmidspades and coronaspades. + Also, the truspades command is deprecated, so don't make it's self-test + failure critical. + * d/salsa-ci.yml: disable run for i386 architecture. + * d/NEWS: forward deprecation of truspades with notice it may not work well. + + -- Étienne Mollier Mon, 01 Aug 2022 21:11:59 +0200 + spades (3.15.4+dfsg-3) unstable; urgency=medium * d/t/run-upstreams-tests: make tests a bit more verbose. diff -pruN 3.15.4+dfsg-3/debian/links 3.15.5+dfsg-1/debian/links --- 3.15.4+dfsg-3/debian/links 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/links 2022-08-01 19:11:59.000000000 +0000 @@ -15,4 +15,5 @@ usr/share/man/man1/truspades.1.gz /usr/s usr/share/man/man1/metaspades.1.gz /usr/share/man/man1/metaspades.py.1.gz usr/share/man/man1/plasmidspades.1.gz /usr/share/man/man1/plasmidspades.py.1.gz usr/share/man/man1/rnaspades.1.gz /usr/share/man/man1/rnaspades.py.1.gz +usr/share/man/man1/coronaspades.1.gz /usr/share/man/man1/coronaspades.py.1.gz usr/share/spades/VERSION usr/libexec/spades/VERSION diff -pruN 3.15.4+dfsg-3/debian/man_src/coronaspades.1.adoc 3.15.5+dfsg-1/debian/man_src/coronaspades.1.adoc --- 3.15.4+dfsg-3/debian/man_src/coronaspades.1.adoc 1970-01-01 00:00:00.000000000 +0000 +++ 3.15.5+dfsg-1/debian/man_src/coronaspades.1.adoc 2022-08-01 19:11:59.000000000 +0000 @@ -0,0 +1,18 @@ += coronaspades(1) + +## NAME + +coronaspades - SPAdes genome assembler (coronaSPAdes mode) + +## SYNOPSIS + +*coronaspades* [options] -o + +## DESCRIPTION + +*coronaspades* runs **SPAdes** in coronaSPAdes mode. All parameters are +identical to the regular SPAdes. + +## SEE ALSO + +spades(1) diff -pruN 3.15.4+dfsg-3/debian/NEWS 3.15.5+dfsg-1/debian/NEWS --- 3.15.4+dfsg-3/debian/NEWS 1970-01-01 00:00:00.000000000 +0000 +++ 3.15.5+dfsg-1/debian/NEWS 2022-08-01 19:11:59.000000000 +0000 @@ -0,0 +1,12 @@ +spades (3.15.5+dfsg-1) unstable; urgency=medium + + Since version 3.15, the truspades command is deprecated upstream and + will be removed in an upcoming spades version[1]. Please be aware + that the truspades version still provided by Debian Med may not work + properly anymore: it has been noticed that it failed its self-test + since version 3.15.5. Other spades commands are not affected and are + working as usual. + + [1]: https://github.com/ablab/spades/issues/560#issuecomment-675915841 + + -- Étienne Mollier Mon, 01 Aug 2022 21:11:03 +0200 diff -pruN 3.15.4+dfsg-3/debian/patches/0003_accept-system-bwa.patch 3.15.5+dfsg-1/debian/patches/0003_accept-system-bwa.patch --- 3.15.4+dfsg-3/debian/patches/0003_accept-system-bwa.patch 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/patches/0003_accept-system-bwa.patch 2022-08-01 19:11:59.000000000 +0000 @@ -56,7 +56,7 @@ Description: Enable using Debian package def check_file_existence(input_filename, message="", log=None): --- spades.orig/assembler/src/spades_pipeline/options_parser.py +++ spades/assembler/src/spades_pipeline/options_parser.py -@@ -992,7 +992,10 @@ +@@ -994,7 +994,10 @@ if (not args.only_error_correction) and args.mismatch_corrector: cfg["mismatch_corrector"] = empty_config() cfg["mismatch_corrector"].__dict__["skip-masked"] = None diff -pruN 3.15.4+dfsg-3/debian/patches/fix-privacy-breaches.patch 3.15.5+dfsg-1/debian/patches/fix-privacy-breaches.patch --- 3.15.4+dfsg-3/debian/patches/fix-privacy-breaches.patch 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/patches/fix-privacy-breaches.patch 2022-08-01 19:11:59.000000000 +0000 @@ -8,13 +8,13 @@ This patch header follows DEP-3: http:// --- spades.orig/assembler/manual.html +++ spades/assembler/manual.html @@ -1,9 +1,4 @@ -- SPAdes 3.15.4 Manual

      TeamCity Simple Build Status
      +- SPAdes 3.15.5 Manual

      TeamCity Simple Build Status
      -License
      -GitHub release (latest by date)
      -GitHub Downloads
      -BioConda Downloads
      -Contributor Covenant

      -+ SPAdes 3.15.4 Manual -

      SPAdes 3.15.4 Manual

      ++ SPAdes 3.15.5 Manual

      +

      SPAdes 3.15.5 Manual

      1. About SPAdes
        diff -pruN 3.15.4+dfsg-3/debian/patches/python3.patch 3.15.5+dfsg-1/debian/patches/python3.patch --- 3.15.4+dfsg-3/debian/patches/python3.patch 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/patches/python3.patch 2022-08-01 19:11:59.000000000 +0000 @@ -2,81 +2,81 @@ Author: Andreas Tille Last-Update: Tue, 12 Nov 2019 17:11:17 +0100 Description: Make sure Python3 interpreter is used in scripts ---- a/assembler/changer_of_K.py -+++ b/assembler/changer_of_K.py +--- spades.orig/assembler/changer_of_K.py ++++ spades/assembler/changer_of_K.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import os import shutil ---- a/assembler/ext/src/samtools/misc/varfilter.py -+++ b/assembler/ext/src/samtools/misc/varfilter.py +--- spades.orig/assembler/ext/src/samtools/misc/varfilter.py ++++ spades/assembler/ext/src/samtools/misc/varfilter.py @@ -1,4 +1,4 @@ -#!/software/bin/python +#!/usr/bin/python3 # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally # ---- a/assembler/show_saves.py -+++ b/assembler/show_saves.py +--- spades.orig/assembler/show_saves.py ++++ spades/assembler/show_saves.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2018 Saint Petersburg State University ---- a/assembler/spades.py -+++ b/assembler/spades.py +--- spades.orig/assembler/spades.py ++++ spades/assembler/spades.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/spades_dev.sh -+++ b/assembler/spades_dev.sh -@@ -8,5 +8,5 @@ mkdir -p bin; +--- spades.orig/assembler/spades_dev.sh ++++ spades/assembler/spades_dev.sh +@@ -8,5 +8,5 @@ rm bin/*; cp build/release/debruijn/spades bin/spades; cp build/release/hammer/hammer bin/hammer; -python spades.py "$@"; +python3 spades.py "$@"; ---- a/assembler/spades_init.py -+++ b/assembler/spades_init.py +--- spades.orig/assembler/spades_init.py ++++ spades/assembler/spades_init.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/projects/ionhammer/comparator.py -+++ b/assembler/src/projects/ionhammer/comparator.py +--- spades.orig/assembler/src/projects/ionhammer/comparator.py ++++ spades/assembler/src/projects/ionhammer/comparator.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/python3 # -*- coding: UTF-8 -*- import subprocess import os ---- a/assembler/src/projects/kmercount/kmerbin_converter.py -+++ b/assembler/src/projects/kmercount/kmerbin_converter.py +--- spades.orig/assembler/src/projects/kmercount/kmerbin_converter.py ++++ spades/assembler/src/projects/kmercount/kmerbin_converter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University -@@ -50,4 +50,4 @@ def main(): +@@ -50,4 +50,4 @@ if __name__ == "__main__": - main() \ No newline at end of file + main() ---- a/assembler/src/projects/mts/binners/gattaca.snake -+++ b/assembler/src/projects/mts/binners/gattaca.snake -@@ -32,8 +32,8 @@ rule gattaca: +--- spades.orig/assembler/src/projects/mts/binners/gattaca.snake ++++ spades/assembler/src/projects/mts/binners/gattaca.snake +@@ -32,8 +32,8 @@ threads: THREADS log: "binning/gattaca.log" message: "Running GATTACA clustering" @@ -87,8 +87,8 @@ Description: Make sure Python3 interpret " --coverage {input.profiles} --algorithm dirichlet --clusters {output} >{log} 2>&1\n" "rm -f assembly/splits/all_filtered.fasta.fai" ---- a/assembler/src/projects/mts/mts.py -+++ b/assembler/src/projects/mts/mts.py +--- spades.orig/assembler/src/projects/mts/mts.py ++++ spades/assembler/src/projects/mts/mts.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -96,8 +96,8 @@ Description: Make sure Python3 interpret import argparse import subprocess ---- a/assembler/src/projects/mts/multirun.py -+++ b/assembler/src/projects/mts/multirun.py +--- spades.orig/assembler/src/projects/mts/multirun.py ++++ spades/assembler/src/projects/mts/multirun.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -105,15 +105,15 @@ Description: Make sure Python3 interpret import argparse import os ---- a/assembler/src/projects/mts/scripts/bhtsne.py -+++ b/assembler/src/projects/mts/scripts/bhtsne.py +--- spades.orig/assembler/src/projects/mts/scripts/bhtsne.py ++++ spades/assembler/src/projects/mts/scripts/bhtsne.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ''' A simple Python wrapper for the bh_tsne binary that makes it easier to use it -@@ -15,7 +15,7 @@ Example: +@@ -15,7 +15,7 @@ The output will not be normalised, maybe the below one-liner is of interest?: @@ -122,7 +122,7 @@ Description: Make sure Python3 interpret d = numpy.loadtxt(stdin); d -= d.min(axis=0); d /= d.max(axis=0); numpy.savetxt(stdout, d, fmt="%.8f", delimiter="\t")' -@@ -207,7 +207,7 @@ def run_bh_tsne(data, no_dims=2, perplex +@@ -207,7 +207,7 @@ try: os.waitpid(child_pid, 0) except KeyboardInterrupt: @@ -131,16 +131,16 @@ Description: Make sure Python3 interpret print("This is an issue due to asynchronous error handling.") res = [] ---- a/assembler/src/projects/mts/scripts/bin_profiles.py -+++ b/assembler/src/projects/mts/scripts/bin_profiles.py +--- spades.orig/assembler/src/projects/mts/scripts/bin_profiles.py ++++ spades/assembler/src/projects/mts/scripts/bin_profiles.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 from __future__ import (print_function) import pandas ---- a/assembler/src/projects/mts/scripts/choose_bins.py -+++ b/assembler/src/projects/mts/scripts/choose_bins.py +--- spades.orig/assembler/src/projects/mts/scripts/choose_bins.py ++++ spades/assembler/src/projects/mts/scripts/choose_bins.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -148,8 +148,8 @@ Description: Make sure Python3 interpret import re import sys ---- a/assembler/src/projects/mts/scripts/choose_samples.py -+++ b/assembler/src/projects/mts/scripts/choose_samples.py +--- spades.orig/assembler/src/projects/mts/scripts/choose_samples.py ++++ spades/assembler/src/projects/mts/scripts/choose_samples.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -157,8 +157,8 @@ Description: Make sure Python3 interpret import argparse from operator import itemgetter ---- a/assembler/src/projects/mts/scripts/clusters2csv.py -+++ b/assembler/src/projects/mts/scripts/clusters2csv.py +--- spades.orig/assembler/src/projects/mts/scripts/clusters2csv.py ++++ spades/assembler/src/projects/mts/scripts/clusters2csv.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function @@ -166,8 +166,8 @@ Description: Make sure Python3 interpret import sys from Bio import SeqIO ---- a/assembler/src/projects/mts/scripts/combine_contigs.py -+++ b/assembler/src/projects/mts/scripts/combine_contigs.py +--- spades.orig/assembler/src/projects/mts/scripts/combine_contigs.py ++++ spades/assembler/src/projects/mts/scripts/combine_contigs.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function @@ -175,8 +175,8 @@ Description: Make sure Python3 interpret import sys import os import os.path ---- a/assembler/src/projects/mts/scripts/contig_name_filter.py -+++ b/assembler/src/projects/mts/scripts/contig_name_filter.py +--- spades.orig/assembler/src/projects/mts/scripts/contig_name_filter.py ++++ spades/assembler/src/projects/mts/scripts/contig_name_filter.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function @@ -184,24 +184,24 @@ Description: Make sure Python3 interpret import sys from Bio import SeqIO ---- a/assembler/src/projects/mts/scripts/cut_fasta.py -+++ b/assembler/src/projects/mts/scripts/cut_fasta.py +--- spades.orig/assembler/src/projects/mts/scripts/cut_fasta.py ++++ spades/assembler/src/projects/mts/scripts/cut_fasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 """Cut up fasta file in non-overlapping or overlapping parts of equal length. """ from __future__ import print_function ---- a/assembler/src/projects/mts/scripts/filter_nucmer.py -+++ b/assembler/src/projects/mts/scripts/filter_nucmer.py +--- spades.orig/assembler/src/projects/mts/scripts/filter_nucmer.py ++++ spades/assembler/src/projects/mts/scripts/filter_nucmer.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 from __future__ import print_function import re ---- a/assembler/src/projects/mts/scripts/gather_stats.py -+++ b/assembler/src/projects/mts/scripts/gather_stats.py +--- spades.orig/assembler/src/projects/mts/scripts/gather_stats.py ++++ spades/assembler/src/projects/mts/scripts/gather_stats.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -209,16 +209,16 @@ Description: Make sure Python3 interpret import argparse from collections import OrderedDict ---- a/assembler/src/projects/mts/scripts/gen_samples.py -+++ b/assembler/src/projects/mts/scripts/gen_samples.py +--- spades.orig/assembler/src/projects/mts/scripts/gen_samples.py ++++ spades/assembler/src/projects/mts/scripts/gen_samples.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/python3 from __future__ import print_function import argparse ---- a/assembler/src/projects/mts/scripts/multi_stats.py -+++ b/assembler/src/projects/mts/scripts/multi_stats.py +--- spades.orig/assembler/src/projects/mts/scripts/multi_stats.py ++++ spades/assembler/src/projects/mts/scripts/multi_stats.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -226,8 +226,8 @@ Description: Make sure Python3 interpret import argparse import os ---- a/assembler/src/projects/mts/scripts/split_bins.py -+++ b/assembler/src/projects/mts/scripts/split_bins.py +--- spades.orig/assembler/src/projects/mts/scripts/split_bins.py ++++ spades/assembler/src/projects/mts/scripts/split_bins.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import print_function @@ -235,8 +235,8 @@ Description: Make sure Python3 interpret from operator import itemgetter import os ---- a/assembler/src/projects/mts/scripts/subsample.py -+++ b/assembler/src/projects/mts/scripts/subsample.py +--- spades.orig/assembler/src/projects/mts/scripts/subsample.py ++++ spades/assembler/src/projects/mts/scripts/subsample.py @@ -1,5 +1,4 @@ -#!/usr/bin/env python -from __future__ import (print_function) @@ -244,17 +244,17 @@ Description: Make sure Python3 interpret import argparse import gzip ---- a/assembler/src/projects/mts/test.py -+++ b/assembler/src/projects/mts/test.py +--- spades.orig/assembler/src/projects/mts/test.py ++++ spades/assembler/src/projects/mts/test.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 from __future__ import print_function import argparse ---- a/assembler/src/projects/spaligner/benchmarking/GraphAligner.snake -+++ b/assembler/src/projects/spaligner/benchmarking/GraphAligner.snake -@@ -43,7 +43,7 @@ rule fix_graph_nodeids: +--- spades.orig/assembler/src/projects/spaligner/benchmarking/GraphAligner.snake ++++ spades/assembler/src/projects/spaligner/benchmarking/GraphAligner.snake +@@ -43,7 +43,7 @@ "{org}/GraphAligner/tmp/graph_idfix.gfa", "{org}/GraphAligner/tmp/graph_nodemapping.txt" shell: @@ -263,7 +263,7 @@ Description: Make sure Python3 interpret rule make_graphreference: input: -@@ -52,7 +52,7 @@ rule make_graphreference: +@@ -52,7 +52,7 @@ "{org}/GraphAligner/tmp/{graph}_refnodes.txt", "{org}/GraphAligner/tmp/{graph}_gfareference.fa" shell: @@ -272,364 +272,356 @@ Description: Make sure Python3 interpret rule reverse_reads: input: -@@ -158,4 +158,4 @@ rule convert_to_json: +@@ -158,4 +158,4 @@ selected_alns = "{org}/GraphAligner/output/aln_{reads}_selected.json", full_len_alns = "{org}/GraphAligner/output/aln_{reads}_full_length.json", shell: - "{VGPATH}/vg view -aj {input.all_alns} > {output.all_alns} && {VGPATH}/vg view -aj {input.selected_alns} > {output.selected_alns} && {VGPATH}/vg view -aj {input.full_len_alns} > {output.full_len_alns}" \ No newline at end of file + "{VGPATH}/vg view -aj {input.all_alns} > {output.all_alns} && {VGPATH}/vg view -aj {input.selected_alns} > {output.selected_alns} && {VGPATH}/vg view -aj {input.full_len_alns} > {output.full_len_alns}" ---- a/assembler/src/projects/spaligner/benchmarking/benchmarking_stats.py -+++ b/assembler/src/projects/spaligner/benchmarking/benchmarking_stats.py +--- spades.orig/assembler/src/projects/spaligner/benchmarking/benchmarking_stats.py ++++ spades/assembler/src/projects/spaligner/benchmarking/benchmarking_stats.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import sys import json import unicodedata ---- a/assembler/src/projects/spaligner/benchmarking/test_spaligner.py -+++ b/assembler/src/projects/spaligner/benchmarking/test_spaligner.py +--- spades.orig/assembler/src/projects/spaligner/benchmarking/test_spaligner.py ++++ spades/assembler/src/projects/spaligner/benchmarking/test_spaligner.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import sys import json import unicodedata ---- a/assembler/src/spades_pipeline/commands_parser.py -+++ b/assembler/src/spades_pipeline/commands_parser.py +--- spades.orig/assembler/src/spades_pipeline/commands_parser.py ++++ spades/assembler/src/spades_pipeline/commands_parser.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/executors/executor_local.py -+++ b/assembler/src/spades_pipeline/executors/executor_local.py +--- spades.orig/assembler/src/spades_pipeline/executors/executor_local.py ++++ spades/assembler/src/spades_pipeline/executors/executor_local.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University -@@ -75,4 +75,4 @@ class Executor(executors.ExecutorBase): +@@ -75,4 +75,4 @@ path = options_storage.get_stage_filename(num, command.short_name) if not os.path.exists(os.path.dirname(path)): os.makedirs(os.path.dirname(path)) - open(path, 'a').close() \ No newline at end of file + open(path, 'a').close() ---- a/assembler/src/spades_pipeline/executors/executor_save_yaml.py -+++ b/assembler/src/spades_pipeline/executors/executor_save_yaml.py +--- spades.orig/assembler/src/spades_pipeline/executors/executor_save_yaml.py ++++ spades/assembler/src/spades_pipeline/executors/executor_save_yaml.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/executors/executors.py -+++ b/assembler/src/spades_pipeline/executors/executors.py +--- spades.orig/assembler/src/spades_pipeline/executors/executors.py ++++ spades/assembler/src/spades_pipeline/executors/executors.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/options_parser.py -+++ b/assembler/src/spades_pipeline/options_parser.py +--- spades.orig/assembler/src/spades_pipeline/options_parser.py ++++ spades/assembler/src/spades_pipeline/options_parser.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/options_storage.py -+++ b/assembler/src/spades_pipeline/options_storage.py +--- spades.orig/assembler/src/spades_pipeline/options_storage.py ++++ spades/assembler/src/spades_pipeline/options_storage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/process_cfg.py -+++ b/assembler/src/spades_pipeline/process_cfg.py +--- spades.orig/assembler/src/spades_pipeline/process_cfg.py ++++ spades/assembler/src/spades_pipeline/process_cfg.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/run_contig_breaker.py -+++ b/assembler/src/spades_pipeline/run_contig_breaker.py +--- spades.orig/assembler/src/spades_pipeline/run_contig_breaker.py ++++ spades/assembler/src/spades_pipeline/run_contig_breaker.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/breaking_scaffolds_script.py -+++ b/assembler/src/spades_pipeline/scripts/breaking_scaffolds_script.py +--- spades.orig/assembler/src/spades_pipeline/scripts/breaking_scaffolds_script.py ++++ spades/assembler/src/spades_pipeline/scripts/breaking_scaffolds_script.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/check_test_script.py -+++ b/assembler/src/spades_pipeline/scripts/check_test_script.py +--- spades.orig/assembler/src/spades_pipeline/scripts/check_test_script.py ++++ spades/assembler/src/spades_pipeline/scripts/check_test_script.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/compress_all.py -+++ b/assembler/src/spades_pipeline/scripts/compress_all.py +--- spades.orig/assembler/src/spades_pipeline/scripts/compress_all.py ++++ spades/assembler/src/spades_pipeline/scripts/compress_all.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/copy_files.py -+++ b/assembler/src/spades_pipeline/scripts/copy_files.py +--- spades.orig/assembler/src/spades_pipeline/scripts/copy_files.py ++++ spades/assembler/src/spades_pipeline/scripts/copy_files.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/correction_iteration_script.py -+++ b/assembler/src/spades_pipeline/scripts/correction_iteration_script.py +--- spades.orig/assembler/src/spades_pipeline/scripts/correction_iteration_script.py ++++ spades/assembler/src/spades_pipeline/scripts/correction_iteration_script.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/plasmid_glue.py -+++ b/assembler/src/spades_pipeline/scripts/plasmid_glue.py +--- spades.orig/assembler/src/spades_pipeline/scripts/plasmid_glue.py ++++ spades/assembler/src/spades_pipeline/scripts/plasmid_glue.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import os import sys ---- a/assembler/src/spades_pipeline/scripts/postprocessing_script.py -+++ b/assembler/src/spades_pipeline/scripts/postprocessing_script.py +--- spades.orig/assembler/src/spades_pipeline/scripts/postprocessing_script.py ++++ spades/assembler/src/spades_pipeline/scripts/postprocessing_script.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/preprocess_contigs.py -+++ b/assembler/src/spades_pipeline/scripts/preprocess_contigs.py +--- spades.orig/assembler/src/spades_pipeline/scripts/preprocess_contigs.py ++++ spades/assembler/src/spades_pipeline/scripts/preprocess_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/scripts/preprocess_interlaced_reads.py -+++ b/assembler/src/spades_pipeline/scripts/preprocess_interlaced_reads.py +--- spades.orig/assembler/src/spades_pipeline/scripts/preprocess_interlaced_reads.py ++++ spades/assembler/src/spades_pipeline/scripts/preprocess_interlaced_reads.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/before_start_stage.py -+++ b/assembler/src/spades_pipeline/stages/before_start_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/before_start_stage.py ++++ spades/assembler/src/spades_pipeline/stages/before_start_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University -@@ -44,4 +44,4 @@ class BeforeStartStage(stage.Stage): +@@ -44,4 +44,4 @@ def add_to_pipeline(pipeline, cfg, output_files, tmp_configs_dir, dataset_data, log, bin_home, ext_python_modules_home, python_modules_home): pipeline.add(BeforeStartStage(cfg, "before_start", output_files, tmp_configs_dir, - dataset_data, log, bin_home, ext_python_modules_home, python_modules_home)) \ No newline at end of file + dataset_data, log, bin_home, ext_python_modules_home, python_modules_home)) ---- a/assembler/src/spades_pipeline/stages/breaking_scaffolds_stage.py -+++ b/assembler/src/spades_pipeline/stages/breaking_scaffolds_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/breaking_scaffolds_stage.py ++++ spades/assembler/src/spades_pipeline/stages/breaking_scaffolds_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/check_test_stage.py -+++ b/assembler/src/spades_pipeline/stages/check_test_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/check_test_stage.py ++++ spades/assembler/src/spades_pipeline/stages/check_test_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/correction_stage.py -+++ b/assembler/src/spades_pipeline/stages/correction_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/correction_stage.py ++++ spades/assembler/src/spades_pipeline/stages/correction_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/error_correction_stage.py -+++ b/assembler/src/spades_pipeline/stages/error_correction_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/error_correction_stage.py ++++ spades/assembler/src/spades_pipeline/stages/error_correction_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/pipeline.py -+++ b/assembler/src/spades_pipeline/stages/pipeline.py +--- spades.orig/assembler/src/spades_pipeline/stages/pipeline.py ++++ spades/assembler/src/spades_pipeline/stages/pipeline.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/postprocessing_stage.py -+++ b/assembler/src/spades_pipeline/stages/postprocessing_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/postprocessing_stage.py ++++ spades/assembler/src/spades_pipeline/stages/postprocessing_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/preprocess_reads_stage.py -+++ b/assembler/src/spades_pipeline/stages/preprocess_reads_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/preprocess_reads_stage.py ++++ spades/assembler/src/spades_pipeline/stages/preprocess_reads_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/scaffold_correction_stage.py -+++ b/assembler/src/spades_pipeline/stages/scaffold_correction_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/spades_iteration_stage.py ++++ spades/assembler/src/spades_pipeline/stages/spades_iteration_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/spades_iteration_stage.py -+++ b/assembler/src/spades_pipeline/stages/spades_iteration_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/spades_stage.py ++++ spades/assembler/src/spades_pipeline/stages/spades_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/spades_stage.py -+++ b/assembler/src/spades_pipeline/stages/spades_stage.py -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!/usr/bin/python3 - - ############################################################################ - # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/stage.py -+++ b/assembler/src/spades_pipeline/stages/stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/stage.py ++++ spades/assembler/src/spades_pipeline/stages/stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/stages/terminating_stage.py -+++ b/assembler/src/spades_pipeline/stages/terminating_stage.py +--- spades.orig/assembler/src/spades_pipeline/stages/terminating_stage.py ++++ spades/assembler/src/spades_pipeline/stages/terminating_stage.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University -@@ -33,4 +33,4 @@ def add_to_pipeline(pipeline, cfg, outpu +@@ -33,4 +33,4 @@ ext_python_modules_home, python_modules_home): pipeline.add(TerminatingStage("terminate", output_files, tmp_configs_dir, dataset_data, log, bin_home, - ext_python_modules_home, python_modules_home)) \ No newline at end of file + ext_python_modules_home, python_modules_home)) ---- a/assembler/src/spades_pipeline/support.py -+++ b/assembler/src/spades_pipeline/support.py +--- spades.orig/assembler/src/spades_pipeline/support.py ++++ spades/assembler/src/spades_pipeline/support.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2019 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/truspades/break_by_coverage.py -+++ b/assembler/src/spades_pipeline/truspades/break_by_coverage.py +--- spades.orig/assembler/src/spades_pipeline/truspades/break_by_coverage.py ++++ spades/assembler/src/spades_pipeline/truspades/break_by_coverage.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py -+++ b/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py +--- spades.orig/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py ++++ spades/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/spades_pipeline/truspades/reference_construction.py -+++ b/assembler/src/spades_pipeline/truspades/reference_construction.py +--- spades.orig/assembler/src/spades_pipeline/truspades/reference_construction.py ++++ spades/assembler/src/spades_pipeline/truspades/reference_construction.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/test/teamcity/assess.py -+++ b/assembler/src/test/teamcity/assess.py +--- spades.orig/assembler/src/test/teamcity/assess.py ++++ spades/assembler/src/test/teamcity/assess.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/test/teamcity/assess_reads.py -+++ b/assembler/src/test/teamcity/assess_reads.py +--- spades.orig/assembler/src/test/teamcity/assess_reads.py ++++ spades/assembler/src/test/teamcity/assess_reads.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University -@@ -34,4 +34,4 @@ if mapped < mapped_limit: +@@ -34,4 +34,4 @@ print 'Not enough genome mapped, less than', mapped_limit lvl += 2 f.close() -sys.exit(lvl) \ No newline at end of file +sys.exit(lvl) ---- a/assembler/src/test/teamcity/clean_old_contigs.py -+++ b/assembler/src/test/teamcity/clean_old_contigs.py +--- spades.orig/assembler/src/test/teamcity/clean_old_contigs.py ++++ spades/assembler/src/test/teamcity/clean_old_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/test/teamcity/compare_w_master.py -+++ b/assembler/src/test/teamcity/compare_w_master.py +--- spades.orig/assembler/src/test/teamcity/compare_w_master.py ++++ spades/assembler/src/test/teamcity/compare_w_master.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh -+++ b/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh -@@ -11,6 +11,6 @@ set -e +--- spades.orig/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh ++++ spades/assembler/src/test/teamcity/deprecated/bh_ecoli_1k.sh +@@ -11,6 +11,6 @@ pushd ../../../ rm -rf spades_output/ECOLI_1K_TEAMCITY_BH ./spades.py --only-error-correction -1 ./data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 ./data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_1K_TEAMCITY_BH @@ -638,9 +630,9 @@ Description: Make sure Python3 interpret +python3 src/tools/reads_utils/reads_quality.py -r test_dataset/reference_1K.fa.gz -o spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results spades_output/ECOLI_1K_TEAMCITY_BH/corrected/dataset.info +python3 src/test/teamcity/assess_reads.py spades_output/ECOLI_1K_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 100 100 popd ---- a/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh -+++ b/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh -@@ -11,6 +11,6 @@ set -e +--- spades.orig/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh ++++ spades/assembler/src/test/teamcity/deprecated/bh_ecoli_mda_lane1.sh +@@ -11,6 +11,6 @@ pushd ../../../ rm -rf /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH ./spades.py --sc --only-error-correction --12 ./data/input/E.coli/sc_lane_1/ecoli_mda_lane1.fastq.gz -m 160 -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH @@ -649,8 +641,8 @@ Description: Make sure Python3 interpret +python3 src/tools/reads_utils/reads_quality.py -r data/input/E.coli/MG1655-K12.fasta.gz -o /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/corrected/dataset.info +python3 src/test/teamcity/assess_reads.py /tmp/data/output/spades_output/ECOLI_MDA_LANE1_TEAMCITY_BH/reads_quality_results/report.horizontal.tsv 90 97 # 97 97 popd ---- a/assembler/src/test/teamcity/deprecated/full_run.sh -+++ b/assembler/src/test/teamcity/deprecated/full_run.sh +--- spades.orig/assembler/src/test/teamcity/deprecated/full_run.sh ++++ spades/assembler/src/test/teamcity/deprecated/full_run.sh @@ -1,10 +1,3 @@ - - @@ -662,7 +654,7 @@ Description: Make sure Python3 interpret #!/bin/bash ############################################################################ -@@ -26,7 +19,7 @@ mkdir $project_dir -p +@@ -26,7 +19,7 @@ read line < $options_dir"spades.options" echo $line ./cpcfg @@ -671,7 +663,7 @@ Description: Make sure Python3 interpret read line < $options_dir"quast.options" echo $line -@@ -45,7 +38,7 @@ cp $work_contigs $dir$(date +%Y%m%d_%H%M +@@ -45,7 +38,7 @@ cp $project_dir"/scaffolds.fasta" $dir$(date +%Y%m%d_%H%M%S)_scaf".fasta" @@ -680,7 +672,7 @@ Description: Make sure Python3 interpret rm $dir"/quast_all" -rf #echo $dir"*.fasta" $line -o $dir"/quast_all" dirtmp=$dir"tmp/" -@@ -60,7 +53,7 @@ for i in $dir*.fasta ; do +@@ -60,7 +53,7 @@ # echo $j if [ -f $j ] ; then @@ -689,7 +681,7 @@ Description: Make sure Python3 interpret # echo $compare_res if [ $compare_res = "True" ]; then -@@ -79,8 +72,8 @@ quast_line="$output_pref/quast-1.3/quast +@@ -79,8 +72,8 @@ quast1_2_line="$output_pref/quast-1.2/quast.py -M 500 $dirtmp* $line -o $dir/quast1_2_all/" echo "$quast_line" @@ -700,7 +692,7 @@ Description: Make sure Python3 interpret ssh -n antipov@194.85.238.21 mkdir -p "/var/www/teamcity_runs/$1$2" & -@@ -98,7 +91,7 @@ do +@@ -98,7 +91,7 @@ splitted_opts=$splitted_opts" "${opts[$i * 2 + 1]} done echo $splitted_opts @@ -709,9 +701,9 @@ Description: Make sure Python3 interpret rm $project_dir"/corrected/" -rf ---- a/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh -@@ -12,6 +12,6 @@ pushd ../../../ +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_mc_bfaecium_ant.sh +@@ -12,6 +12,6 @@ rm -rf /tmp/data/output/spades_output/BFAECIUM_QUAKE ./spades.py -k 21,33,55 -m 16 --only-assembler -1 data/input/B.faecium/std_left.cor.fastq.gz -2 data/input/B.faecium/std_right.cor.fastq.gz -s data/input/B.faecium/std_right.cor_single.fastq.gz -s data/input/B.faecium/std_left.cor_single.fastq.gz -o /tmp/data/output/spades_output/BFAECIUM_QUAKE rm -rf ~/quast-1.3/BFAECIUM_QUAKE/ @@ -720,14 +712,14 @@ Description: Make sure Python3 interpret +python3 ~/quast-1.3/quast.py -R /tmp/data/input/B.faecium/ref.fasta.gz -o ~/quast-1.3/BFAECIUM_QUAKE/ /tmp/data/output/spades_output/BFAECIUM_QUAKE/contigs.fasta +python3 src/test/teamcity/assess.py ~/quast-1.3/BFAECIUM_QUAKE/transposed_report.tsv 330000 0 popd ---- a/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_mc_is220.sh @@ -1,4 +1,3 @@ - #!/bin/bash ############################################################################ -@@ -13,6 +12,6 @@ pushd ../../../ +@@ -13,6 +12,6 @@ rm -rf /tmp/data/output/spades_output/ECOLI_IS220_QUAKE ./spades.py --generate-sam-file --only-assembler -m 12 -k 21,33,55 -1 data/input/E.coli/is220/s_6_1.cor.fastq.gz -2 data/input/E.coli/is220/s_6_2.cor.fastq.gz -s data/input/E.coli/is220/s_6_1.cor_single.fastq.gz -s data/input/E.coli/is220/s_6_2.cor_single.fastq.gz -o /tmp/data/output/spades_output/ECOLI_IS220_QUAKE rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE/ @@ -736,9 +728,9 @@ Description: Make sure Python3 interpret +python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS220_QUAKE/contigs.fasta +python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE/transposed_report.tsv 80000 3 popd ---- a/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh -@@ -12,6 +12,6 @@ pushd ../../../ +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k.sh +@@ -12,6 +12,6 @@ rm -rf spades_output/ECOLI_IS220_QUAKE_1K ./spades.py --only-assembler --generate-sam-file -k 21,55 -1 ./data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 ./data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_IS220_QUAKE_1K rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ @@ -747,9 +739,9 @@ Description: Make sure Python3 interpret +python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta +python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0 popd ---- a/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh -@@ -12,6 +12,6 @@ pushd ../../../ +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_mc_is220_1k_ant.sh +@@ -12,6 +12,6 @@ rm -rf spades_output/ECOLI_IS220_QUAKE_1K ./spades.py -k 21,55 --only-assembler -1 /tmp/data/input/E.coli/is220/cropped/s_6.first1000_1.fastq.gz -2 /tmp/data/input/E.coli/is220/cropped/s_6.first1000_2.fastq.gz -o spades_output/ECOLI_IS220_QUAKE_1K rm -rf ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ @@ -758,14 +750,14 @@ Description: Make sure Python3 interpret +python3 ~/quast-1.3/quast.py -R /tmp/data/input/E.coli/MG1655-K12.fasta.gz -G /tmp/data/input/E.coli/genes/genes.gff -O /tmp/data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS220_QUAKE_1K/ spades_output/ECOLI_IS220_QUAKE_1K/contigs.fasta +python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS220_QUAKE_1K/transposed_report.tsv 1000 0 popd ---- a/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_mc_is480.sh @@ -1,4 +1,3 @@ - #!/bin/bash ############################################################################ -@@ -13,6 +12,6 @@ pushd ../../../ +@@ -13,6 +12,6 @@ rm -rf /tmp/data/output/spades_output/ECOLI_IS480_QUAKE ./spades.py --only-assembler -k 21,33,55 -m 12 -1 data/input/E.coli/is480/ERR022075_1.cor.fastq.gz -2 data/input/E.coli/is480/ERR022075_2.cor.fastq.gz -s data/input/E.coli/is480/ERR022075_1.cor_single.fastq.gz -s data/input/E.coli/is480/ERR022075_2.cor_single.fastq.gz -o /tmp/data/output/spades_output/ECOLI_IS480_QUAKE rm -rf ~/quast-1.3/ECOLI_IS480_QUAKE/ @@ -774,9 +766,9 @@ Description: Make sure Python3 interpret +python3 ~/quast-1.3/quast.py -R data/input/E.coli/MG1655-K12.fasta.gz -G data/input/E.coli/genes/genes.gff -O data/input/E.coli/genes/operons.gff -o ~/quast-1.3/ECOLI_IS480_QUAKE/ /tmp/data/output/spades_output/ECOLI_IS480_QUAKE/contigs.fasta +python3 src/test/teamcity/assess.py ~/quast-1.3/ECOLI_IS480_QUAKE/transposed_report.tsv 133000 4 popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/ECOLI_SC_JGI_LANE_7/ @@ -788,9 +780,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_jgi_lane7_pre.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/ECOLI_SC_JGI_LANE_7_PRENORM/ @@ -802,9 +794,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_lane1.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/ECOLI_SC_LANE_1_BH_woHUMAN/ @@ -816,9 +808,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/EC +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_lane1_full.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/ECOLI_SC_LANE_1/ @@ -830,9 +822,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/MR +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_mruber.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/MRUBER/ @@ -844,9 +836,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/MR +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_mruber_pre.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/MRUBER_PRENORM/ @@ -858,9 +850,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh -@@ -17,8 +17,8 @@ rm -rf /tmp/data/output/spades_output/PH +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_phepa.sh +@@ -17,8 +17,8 @@ rm -rf ~/quast-1.3/PHEPARINUS/ @@ -871,9 +863,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/PH +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_phepa_pre.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/PHEPARINUS_PRENORM/ @@ -885,9 +877,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/PM +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_pmarinus.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/PMARINUS/ @@ -899,9 +891,9 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh -+++ b/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh -@@ -17,9 +17,9 @@ rm -rf /tmp/data/output/spades_output/SA +--- spades.orig/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh ++++ spades/assembler/src/test/teamcity/deprecated/spades_sc_saureus_lane7.sh +@@ -17,9 +17,9 @@ rm -rf ~/quast-1.3/SAUREUS_LANE_7/ @@ -913,23 +905,23 @@ Description: Make sure Python3 interpret exitlvl=$? popd ---- a/assembler/src/test/teamcity/force_update_symlinks.py -+++ b/assembler/src/test/teamcity/force_update_symlinks.py +--- spades.orig/assembler/src/test/teamcity/force_update_symlinks.py ++++ spades/assembler/src/test/teamcity/force_update_symlinks.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/test/teamcity/teamcity.py -+++ b/assembler/src/test/teamcity/teamcity.py +--- spades.orig/assembler/src/test/teamcity/teamcity.py ++++ spades/assembler/src/test/teamcity/teamcity.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2017 Saint Petersburg State University -@@ -27,7 +27,7 @@ from teamcity_support import * +@@ -27,7 +27,7 @@ ### main ### try: if len(sys.argv) == 1: @@ -938,15 +930,15 @@ Description: Make sure Python3 interpret subprocess.call(command, shell=True) sys.exit(1) ---- a/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py -+++ b/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py +--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py ++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University -@@ -156,7 +156,7 @@ def etalon_saves(dataset_info, output_di +@@ -156,7 +156,7 @@ ### main ### try: if len(sys.argv) == 1: @@ -955,15 +947,15 @@ Description: Make sure Python3 interpret subprocess.call(command, shell=True) sys.exit(1) ---- a/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py -+++ b/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py +--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py ++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University -@@ -157,7 +157,7 @@ def etalon_saves(dataset_info, output_di +@@ -157,7 +157,7 @@ ### main ### try: if len(sys.argv) == 1: @@ -972,15 +964,15 @@ Description: Make sure Python3 interpret subprocess.call(command, shell=True) sys.exit(1) ---- a/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py -+++ b/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py +--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py ++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2019 Saint Petersburg State University -@@ -163,7 +163,7 @@ def etalon_saves(dataset_info, output_di +@@ -163,7 +163,7 @@ ### main ### try: if len(sys.argv) == 1: @@ -989,31 +981,31 @@ Description: Make sure Python3 interpret subprocess.call(command, shell=True) sys.exit(1) ---- a/assembler/src/test/teamcity/teamcity_support.py -+++ b/assembler/src/test/teamcity/teamcity_support.py +--- spades.orig/assembler/src/test/teamcity/teamcity_support.py ++++ spades/assembler/src/test/teamcity/teamcity_support.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2020 Saint Petersburg State University ---- a/assembler/src/test/teamcity/teamcity_truspades_test.py -+++ b/assembler/src/test/teamcity/teamcity_truspades_test.py +--- spades.orig/assembler/src/test/teamcity/teamcity_truspades_test.py ++++ spades/assembler/src/test/teamcity/teamcity_truspades_test.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/test/teamcity/update_threshold.py -+++ b/assembler/src/test/teamcity/update_threshold.py +--- spades.orig/assembler/src/test/teamcity/update_threshold.py ++++ spades/assembler/src/test/teamcity/update_threshold.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015-2020 Saint Petersburg State University -@@ -262,7 +262,7 @@ def check_args(args): +@@ -262,7 +262,7 @@ ### main ### try: if len(sys.argv) == 1: @@ -1022,9 +1014,9 @@ Description: Make sure Python3 interpret subprocess.call(command, shell=True) sys.exit(1) ---- a/assembler/src/tools/IlluminaTech/tru_quast.py -+++ b/assembler/src/tools/IlluminaTech/tru_quast.py -@@ -93,6 +93,6 @@ def RunTruQuast(input_dir, reference_dir +--- spades.orig/assembler/src/tools/IlluminaTech/tru_quast.py ++++ spades/assembler/src/tools/IlluminaTech/tru_quast.py +@@ -93,6 +93,6 @@ if __name__ == "__main__": if len(sys.argv) != 5: @@ -1032,33 +1024,33 @@ Description: Make sure Python3 interpret + sys.stderr.write("Usage: python3 src/tools/IlluminaTech/tru_quast.py \n") else: RunTruQuast(sys.argv[1], sys.argv[2], sys.argv[3], int(sys.argv[4])) ---- a/assembler/src/tools/blast-fasta/blast_fasta.py -+++ b/assembler/src/tools/blast-fasta/blast_fasta.py +--- spades.orig/assembler/src/tools/blast-fasta/blast_fasta.py ++++ spades/assembler/src/tools/blast-fasta/blast_fasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/clean_contaminations/16SrRNA/parse_tax_from_bowtie.py -+++ b/assembler/src/tools/clean_contaminations/16SrRNA/parse_tax_from_bowtie.py +--- spades.orig/assembler/src/tools/clean_contaminations/16SrRNA/parse_tax_from_bowtie.py ++++ spades/assembler/src/tools/clean_contaminations/16SrRNA/parse_tax_from_bowtie.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.py -+++ b/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.py +--- spades.orig/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.py ++++ spades/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh -+++ b/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh -@@ -23,8 +23,8 @@ echo Building taxonomy index for $1 ... +--- spades.orig/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh ++++ spades/assembler/src/tools/clean_contaminations/16SrRNA/preprocessing.sh +@@ -23,8 +23,8 @@ echo Temporary file: $tempfile echo Index prefix: $indxfile @@ -1070,25 +1062,25 @@ Description: Make sure Python3 interpret -rm $tempfile \ No newline at end of file +rm $tempfile ---- a/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh -+++ b/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh -@@ -24,4 +24,4 @@ fi +--- spades.orig/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh ++++ spades/assembler/src/tools/clean_contaminations/16SrRNA/taxonomy.sh +@@ -24,4 +24,4 @@ echo Analyzing taxonomy for $1 ... -bowtie --threads $threads -k 10 --best --chunkmbs 1024 SSURef_108_NR_tax_silva_v2.fasta $1 | python parse_tax_from_bowtie.py +bowtie --threads $threads -k 10 --best --chunkmbs 1024 SSURef_108_NR_tax_silva_v2.fasta $1 | python3 parse_tax_from_bowtie.py ---- a/assembler/src/tools/clean_contaminations/build_index_for_multifasta.py -+++ b/assembler/src/tools/clean_contaminations/build_index_for_multifasta.py +--- spades.orig/assembler/src/tools/clean_contaminations/build_index_for_multifasta.py ++++ spades/assembler/src/tools/clean_contaminations/build_index_for_multifasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh -+++ b/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh -@@ -111,7 +111,7 @@ function clean_paired () +--- spades.orig/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh ++++ spades/assembler/src/tools/clean_contaminations/clean_contam_by_index_id.sh +@@ -111,7 +111,7 @@ bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedleft > "${output_folder}/paired_log1_${timestamp}.tmp" 2> /dev/null bowtie -c -q -p 16 --suppress 6,7,8 $i $cleanedright > "${output_folder}/paired_log2_${timestamp}.tmp" 2> /dev/null echo "running filter_reads.py" @@ -1097,7 +1089,7 @@ Description: Make sure Python3 interpret mv $filteredleft $cleanedleft mv $filteredright $cleanedright done -@@ -199,7 +199,7 @@ do +@@ -199,7 +199,7 @@ then echo "building index for sequence $i" mkdir -p "${path_to_db}/index/${i:0:2}" @@ -1106,7 +1098,7 @@ Description: Make sure Python3 interpret bowtie-build "${i}.fasta.tmp" "${path_to_db}/index/${i:0:2}/${i}" rm "${i}.fasta.tmp" fi -@@ -220,7 +220,7 @@ then +@@ -220,7 +220,7 @@ else ln -s $all_reads "${output_folder}/${filename}" fi @@ -1115,72 +1107,72 @@ Description: Make sure Python3 interpret filename=${filename%.*} left="${output_folder}/${filename}_left.${extension}" right="${output_folder}/${filename}_right.${extension}" ---- a/assembler/src/tools/clean_contaminations/process_blast_output.py -+++ b/assembler/src/tools/clean_contaminations/process_blast_output.py +--- spades.orig/assembler/src/tools/clean_contaminations/process_blast_output.py ++++ spades/assembler/src/tools/clean_contaminations/process_blast_output.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/clean_contaminations/read_fasta_using_index.py -+++ b/assembler/src/tools/clean_contaminations/read_fasta_using_index.py +--- spades.orig/assembler/src/tools/clean_contaminations/read_fasta_using_index.py ++++ spades/assembler/src/tools/clean_contaminations/read_fasta_using_index.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/cleancontigs/cleancontigs.py -+++ b/assembler/src/tools/cleancontigs/cleancontigs.py +--- spades.orig/assembler/src/tools/cleancontigs/cleancontigs.py ++++ spades/assembler/src/tools/cleancontigs/cleancontigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/cleancontigs/sort_contigs.py -+++ b/assembler/src/tools/cleancontigs/sort_contigs.py +--- spades.orig/assembler/src/tools/cleancontigs/sort_contigs.py ++++ spades/assembler/src/tools/cleancontigs/sort_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/analyze_sinks.py -+++ b/assembler/src/tools/contig_analysis/analyze_sinks.py +--- spades.orig/assembler/src/tools/contig_analysis/analyze_sinks.py ++++ spades/assembler/src/tools/contig_analysis/analyze_sinks.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py -+++ b/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py +--- spades.orig/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py ++++ spades/assembler/src/tools/contig_analysis/break_scaffolds_into_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/compare_fasta.py -+++ b/assembler/src/tools/contig_analysis/compare_fasta.py +--- spades.orig/assembler/src/tools/contig_analysis/compare_fasta.py ++++ spades/assembler/src/tools/contig_analysis/compare_fasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/compare_gaps.py -+++ b/assembler/src/tools/contig_analysis/compare_gaps.py +--- spades.orig/assembler/src/tools/contig_analysis/compare_gaps.py ++++ spades/assembler/src/tools/contig_analysis/compare_gaps.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/compare_gaps_pos.py -+++ b/assembler/src/tools/contig_analysis/compare_gaps_pos.py +--- spades.orig/assembler/src/tools/contig_analysis/compare_gaps_pos.py ++++ spades/assembler/src/tools/contig_analysis/compare_gaps_pos.py @@ -1,5 +1,4 @@ - -#!/usr/bin/python @@ -1188,8 +1180,8 @@ Description: Make sure Python3 interpret ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/compare_runs.sh -+++ b/assembler/src/tools/contig_analysis/compare_runs.sh +--- spades.orig/assembler/src/tools/contig_analysis/compare_runs.sh ++++ spades/assembler/src/tools/contig_analysis/compare_runs.sh @@ -11,5 +11,5 @@ for file in $(ls $1/saves/*.sqn) do @@ -1197,112 +1189,112 @@ Description: Make sure Python3 interpret - python compare_fasta.py $1/saves/$(basename $file) $2/saves/$(basename $file) + python3 compare_fasta.py $1/saves/$(basename $file) $2/saves/$(basename $file) done ---- a/assembler/src/tools/contig_analysis/compare_used_snps.py -+++ b/assembler/src/tools/contig_analysis/compare_used_snps.py +--- spades.orig/assembler/src/tools/contig_analysis/compare_used_snps.py ++++ spades/assembler/src/tools/contig_analysis/compare_used_snps.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/contigs_concatenator.py -+++ b/assembler/src/tools/contig_analysis/contigs_concatenator.py +--- spades.orig/assembler/src/tools/contig_analysis/contigs_concatenator.py ++++ spades/assembler/src/tools/contig_analysis/contigs_concatenator.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/gap_finder.py -+++ b/assembler/src/tools/contig_analysis/gap_finder.py +--- spades.orig/assembler/src/tools/contig_analysis/gap_finder.py ++++ spades/assembler/src/tools/contig_analysis/gap_finder.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/get_misassembled_contigs.py -+++ b/assembler/src/tools/contig_analysis/get_misassembled_contigs.py +--- spades.orig/assembler/src/tools/contig_analysis/get_misassembled_contigs.py ++++ spades/assembler/src/tools/contig_analysis/get_misassembled_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/real_misassembly_counter.py -+++ b/assembler/src/tools/contig_analysis/real_misassembly_counter.py +--- spades.orig/assembler/src/tools/contig_analysis/real_misassembly_counter.py ++++ spades/assembler/src/tools/contig_analysis/real_misassembly_counter.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/texify_results.py -+++ b/assembler/src/tools/contig_analysis/texify_results.py +--- spades.orig/assembler/src/tools/contig_analysis/texify_results.py ++++ spades/assembler/src/tools/contig_analysis/texify_results.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/arcs.py -+++ b/assembler/src/tools/contig_analysis/visualizer/arcs.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/arcs.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/arcs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/main.py -+++ b/assembler/src/tools/contig_analysis/visualizer/main.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/main.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/main.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/mis_parser.py -+++ b/assembler/src/tools/contig_analysis/visualizer/mis_parser.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/mis_parser.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/mis_parser.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/misassemblies.py -+++ b/assembler/src/tools/contig_analysis/visualizer/misassemblies.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/misassemblies.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/misassemblies.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py -+++ b/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/misassemblies_old.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py -+++ b/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/miss_nocov.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/parser.py -+++ b/assembler/src/tools/contig_analysis/visualizer/parser.py +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/parser.py ++++ spades/assembler/src/tools/contig_analysis/visualizer/parser.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/contig_analysis/visualizer/run_parser.sh -+++ b/assembler/src/tools/contig_analysis/visualizer/run_parser.sh +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/run_parser.sh ++++ spades/assembler/src/tools/contig_analysis/visualizer/run_parser.sh @@ -10,5 +10,5 @@ for file in $(ls *.stdout) @@ -1310,9 +1302,9 @@ Description: Make sure Python3 interpret - python parser.py $file >> list.txt + python3 parser.py $file >> list.txt done ---- a/assembler/src/tools/contig_analysis/visualizer/run_viz.sh -+++ b/assembler/src/tools/contig_analysis/visualizer/run_viz.sh -@@ -13,9 +13,9 @@ touch list.txt +--- spades.orig/assembler/src/tools/contig_analysis/visualizer/run_viz.sh ++++ spades/assembler/src/tools/contig_analysis/visualizer/run_viz.sh +@@ -13,9 +13,9 @@ for file in $(ls *.stdout) do @@ -1324,62 +1316,62 @@ Description: Make sure Python3 interpret +python3 misassemblies.py -o plot -a list.txt --arcs rm list.txt ---- a/assembler/src/tools/correctionEvaluator/bowtieOutputTranslator.py -+++ b/assembler/src/tools/correctionEvaluator/bowtieOutputTranslator.py +--- spades.orig/assembler/src/tools/correctionEvaluator/bowtieOutputTranslator.py ++++ spades/assembler/src/tools/correctionEvaluator/bowtieOutputTranslator.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -OO +#!/usr/bin/python3 -OO ############################################################################ # Copyright (c) 2015 Saint Petersburg State University -@@ -100,4 +100,4 @@ print("Beginning translation...") +@@ -100,4 +100,4 @@ bowtieTranslator = BowtieOutputTranslator(args.bowtieOutputFile, args.alignedReadsFile) bowtieTranslator.translate(args.useRegExp, args.useRam) print("Translation finished. Took: %s." % (time.clock() - startTime)) -print("Done.") \ No newline at end of file +print("Done.") ---- a/assembler/src/tools/correctionEvaluator/comparator.py -+++ b/assembler/src/tools/correctionEvaluator/comparator.py +--- spades.orig/assembler/src/tools/correctionEvaluator/comparator.py ++++ spades/assembler/src/tools/correctionEvaluator/comparator.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University -@@ -352,4 +352,4 @@ t0 = time.clock() +@@ -352,4 +352,4 @@ print("Beginning comparison...") comparator = Comparator(args.originalReadsFile, args.alignedReadsFile, args.correctedReadsFile, args.failedToAlignReadsFile, args.reportDir, args.reportTotals, args.noSmartGraphics) comparator.compare() -print("Comparison finished. Took: %s." % (time.clock() - t0)) \ No newline at end of file +print("Comparison finished. Took: %s." % (time.clock() - t0)) ---- a/assembler/src/tools/coverage_based_rr/coverage.py -+++ b/assembler/src/tools/coverage_based_rr/coverage.py +--- spades.orig/assembler/src/tools/coverage_based_rr/coverage.py ++++ spades/assembler/src/tools/coverage_based_rr/coverage.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/dataset.py -+++ b/assembler/src/tools/dataset.py +--- spades.orig/assembler/src/tools/dataset.py ++++ spades/assembler/src/tools/dataset.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/dataset_check -+++ b/assembler/src/tools/dataset_check +--- spades.orig/assembler/src/tools/dataset_check ++++ spades/assembler/src/tools/dataset_check @@ -3,4 +3,4 @@ DIR="$( cd "$( dirname "$0" )" && pwd )" BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )" pushd $BASE/data/input > /dev/null -python $BASE/src/tools/dataset.py check $BASE/configs/debruijn/datasets.info +python3 $BASE/src/tools/dataset.py check $BASE/configs/debruijn/datasets.info ---- a/assembler/src/tools/dataset_hammer -+++ b/assembler/src/tools/dataset_hammer +--- spades.orig/assembler/src/tools/dataset_hammer ++++ spades/assembler/src/tools/dataset_hammer @@ -3,7 +3,7 @@ DIR="$( cd "$( dirname "$0" )" && pwd )" BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )" @@ -1389,24 +1381,24 @@ Description: Make sure Python3 interpret #src/tools/dataset_hammer /mnt/ace/acestorage/snikolenko/090408_ultrashort/09 #src/tools/dataset_hammer /mnt/ace/acestorage/data/input/x5/makarich.fbb.msu.ru/run1_fca/Quaked/ #src/tools/dataset_hammer ~/temp/02 ---- a/assembler/src/tools/dataset_md5 -+++ b/assembler/src/tools/dataset_md5 +--- spades.orig/assembler/src/tools/dataset_md5 ++++ spades/assembler/src/tools/dataset_md5 @@ -3,4 +3,4 @@ DIR="$( cd "$( dirname "$0" )" && pwd )" BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )" pushd $BASE/data/input > /dev/null -python $BASE/src/tools/dataset.py md5 $BASE/configs/debruijn/datasets.info $1 +python3 $BASE/src/tools/dataset.py md5 $BASE/configs/debruijn/datasets.info $1 ---- a/assembler/src/tools/dataset_tar -+++ b/assembler/src/tools/dataset_tar +--- spades.orig/assembler/src/tools/dataset_tar ++++ spades/assembler/src/tools/dataset_tar @@ -3,4 +3,4 @@ DIR="$( cd "$( dirname "$0" )" && pwd )" BASE="$( cd "$( dirname "$0" )" && cd ../.. && pwd )" pushd $BASE/data/input > /dev/null -python $BASE/src/tools/dataset.py tar $BASE/configs/debruijn/datasets.info $1 +python3 $BASE/src/tools/dataset.py tar $BASE/configs/debruijn/datasets.info $1 ---- a/assembler/src/tools/estimation/run_real.sh -+++ b/assembler/src/tools/estimation/run_real.sh +--- spades.orig/assembler/src/tools/estimation/run_real.sh ++++ spades/assembler/src/tools/estimation/run_real.sh @@ -1,3 +1,4 @@ +#!/bin/sh ############################################################################ @@ -1418,14 +1410,14 @@ Description: Make sure Python3 interpret -python real_cumulative.py ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_before_enlarge.fasta 0.5 ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_final.fasta 0.5 ../quality/velvet_paired55.fa 1 ../quality/velvet_unpaired55.fa +python3 real_cumulative.py ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_before_enlarge.fasta 0.5 ~/algorithmic-biology/assembler/data/debruijn/latest/contigs_final.fasta 0.5 ../quality/velvet_paired55.fa 1 ../quality/velvet_unpaired55.fa ---- a/assembler/src/tools/estimation_deprecated/Nx_plot.py -+++ b/assembler/src/tools/estimation_deprecated/Nx_plot.py +--- spades.orig/assembler/src/tools/estimation_deprecated/Nx_plot.py ++++ spades/assembler/src/tools/estimation_deprecated/Nx_plot.py @@ -1,3 +1,4 @@ +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University # Copyright (c) 2011-2014 Saint Petersburg Academic University -@@ -18,9 +19,9 @@ import fastaparser +@@ -18,9 +19,9 @@ if len(sys.argv) < 2: print "Draws Nx plot (from N00 through N50 to N100)" print @@ -1437,536 +1429,536 @@ Description: Make sure Python3 interpret exit(0) for filename in sys.argv[1:]: ---- a/assembler/src/tools/estimation_deprecated/README -+++ b/assembler/src/tools/estimation_deprecated/README +--- spades.orig/assembler/src/tools/estimation_deprecated/README ++++ spades/assembler/src/tools/estimation_deprecated/README @@ -1,3 +1,3 @@ Prerequisites: - sudo apt-get install python python-matplotlib python-numpy + sudo apt-get install python3 python3-matplotlib python3-numpy ---- a/assembler/src/tools/fastafix/fastafix.py -+++ b/assembler/src/tools/fastafix/fastafix.py +--- spades.orig/assembler/src/tools/fastafix/fastafix.py ++++ spades/assembler/src/tools/fastafix/fastafix.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/loc_pic.py -+++ b/assembler/src/tools/loc_pic.py +--- spades.orig/assembler/src/tools/loc_pic.py ++++ spades/assembler/src/tools/loc_pic.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/mapreads/mapreads.py -+++ b/assembler/src/tools/mapreads/mapreads.py +--- spades.orig/assembler/src/tools/mapreads/mapreads.py ++++ spades/assembler/src/tools/mapreads/mapreads.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/assembler_runner/runner.py -+++ b/assembler/src/tools/misc/assembler_runner/runner.py +--- spades.orig/assembler/src/tools/misc/assembler_runner/runner.py ++++ spades/assembler/src/tools/misc/assembler_runner/runner.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/copyrighter.py -+++ b/assembler/src/tools/misc/copyrighter.py +--- spades.orig/assembler/src/tools/misc/copyrighter.py ++++ spades/assembler/src/tools/misc/copyrighter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/datasets_converter.py -+++ b/assembler/src/tools/misc/datasets_converter.py +--- spades.orig/assembler/src/tools/misc/datasets_converter.py ++++ spades/assembler/src/tools/misc/datasets_converter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/datasets_info2yaml_converter.py -+++ b/assembler/src/tools/misc/datasets_info2yaml_converter.py +--- spades.orig/assembler/src/tools/misc/datasets_info2yaml_converter.py ++++ spades/assembler/src/tools/misc/datasets_info2yaml_converter.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/datasets_info_cleaner.py -+++ b/assembler/src/tools/misc/datasets_info_cleaner.py +--- spades.orig/assembler/src/tools/misc/datasets_info_cleaner.py ++++ spades/assembler/src/tools/misc/datasets_info_cleaner.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/gcc_version_check.py -+++ b/assembler/src/tools/misc/gcc_version_check.py +--- spades.orig/assembler/src/tools/misc/gcc_version_check.py ++++ spades/assembler/src/tools/misc/gcc_version_check.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/sam_analysis_sorter.py -+++ b/assembler/src/tools/misc/sam_analysis_sorter.py +--- spades.orig/assembler/src/tools/misc/sam_analysis_sorter.py ++++ spades/assembler/src/tools/misc/sam_analysis_sorter.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/sam_analyzer.py -+++ b/assembler/src/tools/misc/sam_analyzer.py +--- spades.orig/assembler/src/tools/misc/sam_analyzer.py ++++ spades/assembler/src/tools/misc/sam_analyzer.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/sam_analyzer_2.py -+++ b/assembler/src/tools/misc/sam_analyzer_2.py +--- spades.orig/assembler/src/tools/misc/sam_analyzer_2.py ++++ spades/assembler/src/tools/misc/sam_analyzer_2.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/sv_simulator.py -+++ b/assembler/src/tools/misc/sv_simulator.py +--- spades.orig/assembler/src/tools/misc/sv_simulator.py ++++ spades/assembler/src/tools/misc/sv_simulator.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/misc/txt2gff.py -+++ b/assembler/src/tools/misc/txt2gff.py +--- spades.orig/assembler/src/tools/misc/txt2gff.py ++++ spades/assembler/src/tools/misc/txt2gff.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/broken_fastq_filter.py -+++ b/assembler/src/tools/reads_utils/conversion/broken_fastq_filter.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/broken_fastq_filter.py ++++ spades/assembler/src/tools/reads_utils/conversion/broken_fastq_filter.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/fasta_merge_repeated_nucleotides.py -+++ b/assembler/src/tools/reads_utils/conversion/fasta_merge_repeated_nucleotides.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/fasta_merge_repeated_nucleotides.py ++++ spades/assembler/src/tools/reads_utils/conversion/fasta_merge_repeated_nucleotides.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/fasta_to_fastq.py -+++ b/assembler/src/tools/reads_utils/conversion/fasta_to_fastq.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/fasta_to_fastq.py ++++ spades/assembler/src/tools/reads_utils/conversion/fasta_to_fastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/fastq_crop_read_length.py -+++ b/assembler/src/tools/reads_utils/conversion/fastq_crop_read_length.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/fastq_crop_read_length.py ++++ spades/assembler/src/tools/reads_utils/conversion/fastq_crop_read_length.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/fastq_merge_repeated_nucleotides.py -+++ b/assembler/src/tools/reads_utils/conversion/fastq_merge_repeated_nucleotides.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/fastq_merge_repeated_nucleotides.py ++++ spades/assembler/src/tools/reads_utils/conversion/fastq_merge_repeated_nucleotides.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/join.py -+++ b/assembler/src/tools/reads_utils/conversion/join.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/join.py ++++ spades/assembler/src/tools/reads_utils/conversion/join.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/meraculus_to_fastq.py -+++ b/assembler/src/tools/reads_utils/conversion/meraculus_to_fastq.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/meraculus_to_fastq.py ++++ spades/assembler/src/tools/reads_utils/conversion/meraculus_to_fastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/multiline_to_oneline_reads.py -+++ b/assembler/src/tools/reads_utils/conversion/multiline_to_oneline_reads.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/multiline_to_oneline_reads.py ++++ spades/assembler/src/tools/reads_utils/conversion/multiline_to_oneline_reads.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/rf_to_fr.py -+++ b/assembler/src/tools/reads_utils/conversion/rf_to_fr.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/rf_to_fr.py ++++ spades/assembler/src/tools/reads_utils/conversion/rf_to_fr.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/single_fastq_to_paired.py -+++ b/assembler/src/tools/reads_utils/conversion/single_fastq_to_paired.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/single_fastq_to_paired.py ++++ spades/assembler/src/tools/reads_utils/conversion/single_fastq_to_paired.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/split_2_fasts_any_format.py -+++ b/assembler/src/tools/reads_utils/conversion/split_2_fasts_any_format.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/split_2_fasts_any_format.py ++++ spades/assembler/src/tools/reads_utils/conversion/split_2_fasts_any_format.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/split_any_fasta_or_fastq.py -+++ b/assembler/src/tools/reads_utils/conversion/split_any_fasta_or_fastq.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/split_any_fasta_or_fastq.py ++++ spades/assembler/src/tools/reads_utils/conversion/split_any_fasta_or_fastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/split_fastq.py -+++ b/assembler/src/tools/reads_utils/conversion/split_fastq.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/split_fastq.py ++++ spades/assembler/src/tools/reads_utils/conversion/split_fastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/to_meraculus.py -+++ b/assembler/src/tools/reads_utils/conversion/to_meraculus.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/to_meraculus.py ++++ spades/assembler/src/tools/reads_utils/conversion/to_meraculus.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/conversion/trim_ns.py -+++ b/assembler/src/tools/reads_utils/conversion/trim_ns.py +--- spades.orig/assembler/src/tools/reads_utils/conversion/trim_ns.py ++++ spades/assembler/src/tools/reads_utils/conversion/trim_ns.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/crop/crop_bfaecium.py -+++ b/assembler/src/tools/reads_utils/crop/crop_bfaecium.py +--- spades.orig/assembler/src/tools/reads_utils/crop/crop_bfaecium.py ++++ spades/assembler/src/tools/reads_utils/crop/crop_bfaecium.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/crop/crop_genome.py -+++ b/assembler/src/tools/reads_utils/crop/crop_genome.py +--- spades.orig/assembler/src/tools/reads_utils/crop/crop_genome.py ++++ spades/assembler/src/tools/reads_utils/crop/crop_genome.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/crop/crop_reads.py -+++ b/assembler/src/tools/reads_utils/crop/crop_reads.py +--- spades.orig/assembler/src/tools/reads_utils/crop/crop_reads.py ++++ spades/assembler/src/tools/reads_utils/crop/crop_reads.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/crop/paired_crop.py -+++ b/assembler/src/tools/reads_utils/crop/paired_crop.py +--- spades.orig/assembler/src/tools/reads_utils/crop/paired_crop.py ++++ spades/assembler/src/tools/reads_utils/crop/paired_crop.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/crop/single_crop.py -+++ b/assembler/src/tools/reads_utils/crop/single_crop.py +--- spades.orig/assembler/src/tools/reads_utils/crop/single_crop.py ++++ spades/assembler/src/tools/reads_utils/crop/single_crop.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/filter/filter_contigs.py -+++ b/assembler/src/tools/reads_utils/filter/filter_contigs.py +--- spades.orig/assembler/src/tools/reads_utils/filter/filter_contigs.py ++++ spades/assembler/src/tools/reads_utils/filter/filter_contigs.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/filter/filter_reads.py -+++ b/assembler/src/tools/reads_utils/filter/filter_reads.py +--- spades.orig/assembler/src/tools/reads_utils/filter/filter_reads.py ++++ spades/assembler/src/tools/reads_utils/filter/filter_reads.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/filter/filter_reads_by_fastq.py -+++ b/assembler/src/tools/reads_utils/filter/filter_reads_by_fastq.py +--- spades.orig/assembler/src/tools/reads_utils/filter/filter_reads_by_fastq.py ++++ spades/assembler/src/tools/reads_utils/filter/filter_reads_by_fastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/filter/filter_reads_by_paired.py -+++ b/assembler/src/tools/reads_utils/filter/filter_reads_by_paired.py +--- spades.orig/assembler/src/tools/reads_utils/filter/filter_reads_by_paired.py ++++ spades/assembler/src/tools/reads_utils/filter/filter_reads_by_paired.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/filter/filter_single_reads.py -+++ b/assembler/src/tools/reads_utils/filter/filter_single_reads.py +--- spades.orig/assembler/src/tools/reads_utils/filter/filter_single_reads.py ++++ spades/assembler/src/tools/reads_utils/filter/filter_single_reads.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/ideal_by_fasta.py -+++ b/assembler/src/tools/reads_utils/ideal_by_fasta.py +--- spades.orig/assembler/src/tools/reads_utils/ideal_by_fasta.py ++++ spades/assembler/src/tools/reads_utils/ideal_by_fasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/ideal_sim.py -+++ b/assembler/src/tools/reads_utils/ideal_sim.py +--- spades.orig/assembler/src/tools/reads_utils/ideal_sim.py ++++ spades/assembler/src/tools/reads_utils/ideal_sim.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/identical_contigs_stats.py -+++ b/assembler/src/tools/reads_utils/identical_contigs_stats.py +--- spades.orig/assembler/src/tools/reads_utils/identical_contigs_stats.py ++++ spades/assembler/src/tools/reads_utils/identical_contigs_stats.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/meta/mixin_contamination.py -+++ b/assembler/src/tools/reads_utils/meta/mixin_contamination.py +--- spades.orig/assembler/src/tools/reads_utils/meta/mixin_contamination.py ++++ spades/assembler/src/tools/reads_utils/meta/mixin_contamination.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/paired_reads_quality.py -+++ b/assembler/src/tools/reads_utils/paired_reads_quality.py +--- spades.orig/assembler/src/tools/reads_utils/paired_reads_quality.py ++++ spades/assembler/src/tools/reads_utils/paired_reads_quality.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/read_stat.py -+++ b/assembler/src/tools/reads_utils/read_stat.py +--- spades.orig/assembler/src/tools/reads_utils/read_stat.py ++++ spades/assembler/src/tools/reads_utils/read_stat.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/reads_quality.py -+++ b/assembler/src/tools/reads_utils/reads_quality.py +--- spades.orig/assembler/src/tools/reads_utils/reads_quality.py ++++ spades/assembler/src/tools/reads_utils/reads_quality.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/simulate_ideal_by_dataset.py -+++ b/assembler/src/tools/reads_utils/simulate_ideal_by_dataset.py +--- spades.orig/assembler/src/tools/reads_utils/simulate_ideal_by_dataset.py ++++ spades/assembler/src/tools/reads_utils/simulate_ideal_by_dataset.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/simulate_ideal_by_fasta.py -+++ b/assembler/src/tools/reads_utils/simulate_ideal_by_fasta.py +--- spades.orig/assembler/src/tools/reads_utils/simulate_ideal_by_fasta.py ++++ spades/assembler/src/tools/reads_utils/simulate_ideal_by_fasta.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/coverage_hist.py -+++ b/assembler/src/tools/reads_utils/stat/coverage_hist.py +--- spades.orig/assembler/src/tools/reads_utils/stat/coverage_hist.py ++++ spades/assembler/src/tools/reads_utils/stat/coverage_hist.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/gc.py -+++ b/assembler/src/tools/reads_utils/stat/gc.py +--- spades.orig/assembler/src/tools/reads_utils/stat/gc.py ++++ spades/assembler/src/tools/reads_utils/stat/gc.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/is.py -+++ b/assembler/src/tools/reads_utils/stat/is.py +--- spades.orig/assembler/src/tools/reads_utils/stat/is.py ++++ spades/assembler/src/tools/reads_utils/stat/is.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/is_from_single_log.py -+++ b/assembler/src/tools/reads_utils/stat/is_from_single_log.py +--- spades.orig/assembler/src/tools/reads_utils/stat/is_from_single_log.py ++++ spades/assembler/src/tools/reads_utils/stat/is_from_single_log.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/is_genome.py -+++ b/assembler/src/tools/reads_utils/stat/is_genome.py +--- spades.orig/assembler/src/tools/reads_utils/stat/is_genome.py ++++ spades/assembler/src/tools/reads_utils/stat/is_genome.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/mean_is.py -+++ b/assembler/src/tools/reads_utils/stat/mean_is.py +--- spades.orig/assembler/src/tools/reads_utils/stat/mean_is.py ++++ spades/assembler/src/tools/reads_utils/stat/mean_is.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/overlaps.py -+++ b/assembler/src/tools/reads_utils/stat/overlaps.py +--- spades.orig/assembler/src/tools/reads_utils/stat/overlaps.py ++++ spades/assembler/src/tools/reads_utils/stat/overlaps.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/raw.py -+++ b/assembler/src/tools/reads_utils/stat/raw.py +--- spades.orig/assembler/src/tools/reads_utils/stat/raw.py ++++ spades/assembler/src/tools/reads_utils/stat/raw.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/raw_single.py -+++ b/assembler/src/tools/reads_utils/stat/raw_single.py +--- spades.orig/assembler/src/tools/reads_utils/stat/raw_single.py ++++ spades/assembler/src/tools/reads_utils/stat/raw_single.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/raw_w_gc.py -+++ b/assembler/src/tools/reads_utils/stat/raw_w_gc.py +--- spades.orig/assembler/src/tools/reads_utils/stat/raw_w_gc.py ++++ spades/assembler/src/tools/reads_utils/stat/raw_w_gc.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/raws_w_orientation.py -+++ b/assembler/src/tools/reads_utils/stat/raws_w_orientation.py +--- spades.orig/assembler/src/tools/reads_utils/stat/raws_w_orientation.py ++++ spades/assembler/src/tools/reads_utils/stat/raws_w_orientation.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/reads_length.py -+++ b/assembler/src/tools/reads_utils/stat/reads_length.py +--- spades.orig/assembler/src/tools/reads_utils/stat/reads_length.py ++++ spades/assembler/src/tools/reads_utils/stat/reads_length.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/rf_to_fr.py -+++ b/assembler/src/tools/reads_utils/stat/rf_to_fr.py +--- spades.orig/assembler/src/tools/reads_utils/stat/rf_to_fr.py ++++ spades/assembler/src/tools/reads_utils/stat/rf_to_fr.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/shift.py -+++ b/assembler/src/tools/reads_utils/stat/shift.py +--- spades.orig/assembler/src/tools/reads_utils/stat/shift.py ++++ spades/assembler/src/tools/reads_utils/stat/shift.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/single_log_to_paired.py -+++ b/assembler/src/tools/reads_utils/stat/single_log_to_paired.py +--- spades.orig/assembler/src/tools/reads_utils/stat/single_log_to_paired.py ++++ spades/assembler/src/tools/reads_utils/stat/single_log_to_paired.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/reads_utils/stat/trim.py -+++ b/assembler/src/tools/reads_utils/stat/trim.py +--- spades.orig/assembler/src/tools/reads_utils/stat/trim.py ++++ spades/assembler/src/tools/reads_utils/stat/trim.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -O +#!/usr/bin/python3 -O ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/res_counter/mem_checker.py -+++ b/assembler/src/tools/res_counter/mem_checker.py +--- spades.orig/assembler/src/tools/res_counter/mem_checker.py ++++ spades/assembler/src/tools/res_counter/mem_checker.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/res_counter/run.pl -+++ b/assembler/src/tools/res_counter/run.pl -@@ -14,7 +14,7 @@ print "started...\n"; +--- spades.orig/assembler/src/tools/res_counter/run.pl ++++ spades/assembler/src/tools/res_counter/run.pl +@@ -14,7 +14,7 @@ my $stat_proc = fork; if ($stat_proc == 0) { @@ -1975,49 +1967,49 @@ Description: Make sure Python3 interpret } waitpid($child, 0); ---- a/assembler/src/tools/res_counter/stats_counter.py -+++ b/assembler/src/tools/res_counter/stats_counter.py +--- spades.orig/assembler/src/tools/res_counter/stats_counter.py ++++ spades/assembler/src/tools/res_counter/stats_counter.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/sequenceDistanceMeter/main.py -+++ b/assembler/src/tools/sequenceDistanceMeter/main.py +--- spades.orig/assembler/src/tools/sequenceDistanceMeter/main.py ++++ spades/assembler/src/tools/sequenceDistanceMeter/main.py @@ -1,4 +1,4 @@ -#!/usr/bin/python -OO +#!/usr/bin/python3 -OO ############################################################################ # Copyright (c) 2015 Saint Petersburg State University # Copyright (c) 2011-2014 Saint Petersburg Academic University ---- a/assembler/src/tools/spades_download_stats/filter.py -+++ b/assembler/src/tools/spades_download_stats/filter.py +--- spades.orig/assembler/src/tools/spades_download_stats/filter.py ++++ spades/assembler/src/tools/spades_download_stats/filter.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 #*************************************************************************** ##* Copyright (c) 2011-2014 Saint-Petersburg Academic University ---- a/assembler/src/tools/spades_pipeline/spades_download_binary.py -+++ b/assembler/src/tools/spades_pipeline/spades_download_binary.py +--- spades.orig/assembler/src/tools/spades_pipeline/spades_download_binary.py ++++ spades/assembler/src/tools/spades_pipeline/spades_download_binary.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/truseq/quast_all.py -+++ b/assembler/src/tools/truseq/quast_all.py +--- spades.orig/assembler/src/tools/truseq/quast_all.py ++++ spades/assembler/src/tools/truseq/quast_all.py @@ -1,4 +1,4 @@ -#! /usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University ---- a/assembler/src/tools/truseq/quast_all.sh -+++ b/assembler/src/tools/truseq/quast_all.sh -@@ -14,7 +14,7 @@ mkdir $3/tmp +--- spades.orig/assembler/src/tools/truseq/quast_all.sh ++++ spades/assembler/src/tools/truseq/quast_all.sh +@@ -14,7 +14,7 @@ mkdir $3/all_reports ls $1 | xargs -P $4 -I {} -t quast --min-contig 1000 --contig-thresholds 5000,8000,12000 -e -R $2/{}.fasta $1/{}/scaffolds.fasta -o $3/tmp/{} ls $1 | xargs -P $4 -I {} -t cp $3/tmp/{}/report.tsv $3/all_reports/{}.tsv @@ -2026,15 +2018,15 @@ Description: Make sure Python3 interpret grep "( inversion )" $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/inversions.txt grep "( translocation )" $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/translocations.txt grep "( relocation," $3/tmp/*/contigs_reports/contigs_report_*.stdout > $3/relocations.txt ---- a/assembler/src/tools/ukonnen/ukonnen.py -+++ b/assembler/src/tools/ukonnen/ukonnen.py +--- spades.orig/assembler/src/tools/ukonnen/ukonnen.py ++++ spades/assembler/src/tools/ukonnen/ukonnen.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University -@@ -14,7 +14,7 @@ import itertools +@@ -14,7 +14,7 @@ if len(sys.argv) < 5: print 'Prepare reads for Ukonnen\'s scaffolder' @@ -2043,15 +2035,15 @@ Description: Make sure Python3 interpret exit() inf1 = open(sys.argv[1]); ---- a/assembler/truspades.py -+++ b/assembler/truspades.py +--- spades.orig/assembler/truspades.py ++++ spades/assembler/truspades.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 ############################################################################ # Copyright (c) 2015 Saint Petersburg State University -@@ -53,9 +53,9 @@ def reads_line(libs): +@@ -53,9 +53,9 @@ def command_line(barcode, output_dir, params, continue_launch): # logfile = os.path.join(output_dir, "logs", barcode.id + ".out") if continue_launch and os.path.exists(os.path.join(output_dir, barcode.id, "params.txt")): diff -pruN 3.15.4+dfsg-3/debian/patches/yaml_load.patch 3.15.5+dfsg-1/debian/patches/yaml_load.patch --- 3.15.4+dfsg-3/debian/patches/yaml_load.patch 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/patches/yaml_load.patch 2022-08-01 19:11:59.000000000 +0000 @@ -45,7 +45,7 @@ Description: Specify yaml loader continue --- spades.orig/assembler/src/spades_pipeline/options_parser.py +++ spades/assembler/src/spades_pipeline/options_parser.py -@@ -1062,14 +1062,14 @@ +@@ -1073,14 +1073,14 @@ if load_processed_dataset: if os.path.isfile(processed_dataset_fpath): try: @@ -95,7 +95,7 @@ Description: Specify yaml loader python_modules_home = abspath(dirname(realpath(__file__))) --- spades.orig/assembler/src/spades_pipeline/stages/correction_stage.py +++ spades/assembler/src/spades_pipeline/stages/correction_stage.py -@@ -25,7 +25,7 @@ +@@ -24,7 +24,7 @@ import pyyaml2 as pyyaml elif sys.version.startswith("3."): import pyyaml3 as pyyaml @@ -106,7 +106,7 @@ Description: Specify yaml loader data["work_dir"] = cfg.tmp_dir --- spades.orig/assembler/src/spades_pipeline/stages/spades_stage.py +++ spades/assembler/src/spades_pipeline/stages/spades_stage.py -@@ -30,7 +30,7 @@ +@@ -29,7 +29,7 @@ import pyyaml2 as pyyaml elif sys.version.startswith("3."): import pyyaml3 as pyyaml diff -pruN 3.15.4+dfsg-3/debian/salsa-ci.yml 3.15.5+dfsg-1/debian/salsa-ci.yml --- 3.15.4+dfsg-3/debian/salsa-ci.yml 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/salsa-ci.yml 2022-08-01 19:11:59.000000000 +0000 @@ -2,3 +2,6 @@ include: - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml + +variables: + SALSA_CI_DISABLE_BUILD_PACKAGE_I386: "true" diff -pruN 3.15.4+dfsg-3/debian/tests/run-upstreams-tests 3.15.5+dfsg-1/debian/tests/run-upstreams-tests --- 3.15.4+dfsg-3/debian/tests/run-upstreams-tests 2022-06-25 15:41:51.000000000 +0000 +++ 3.15.5+dfsg-1/debian/tests/run-upstreams-tests 2022-08-01 19:11:59.000000000 +0000 @@ -8,6 +8,17 @@ trap "rm -rf $WORKDIR" 0 INT QUIT ABRT P cd $WORKDIR spades --test -truspades --test +coronaspades --test metaspades --test +plasmidspades --test rnaspades --test + +# truspades is deprecated in v3.15 and may fail its own test suite. +if command -v truspades > /dev/null +then + if ! truspades --test + then echo 'W: truspades failed its self-test suite.' + fi +else + echo 'W: truspades is not provided upstream anymore.' +fi diff -pruN 3.15.4+dfsg-3/README.md 3.15.5+dfsg-1/README.md --- 3.15.4+dfsg-3/README.md 2022-02-01 11:36:35.000000000 +0000 +++ 3.15.5+dfsg-1/README.md 2022-07-16 09:53:26.000000000 +0000 @@ -6,7 +6,7 @@ [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](code_of_conduct.md) -__SPAdes 3.15.4 Manual__ +__SPAdes 3.15.5 Manual__ 1. [About SPAdes](#sec1)
        1.1. [Supported data types](#sec1.1)
        @@ -42,7 +42,7 @@ # About SPAdes -SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.4 was released under GPLv2 on February 1, 2021 and can be downloaded from . +SPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. This manual will help you to install and run SPAdes. SPAdes version 3.15.5 was released under GPLv2 on July 14th, 2022 and can be downloaded from . The latest SPAdes paper describing various pipelines in a protocol format is available [here](https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.102). @@ -51,11 +51,11 @@ The latest SPAdes paper describing vario The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads. -Version 3.15.4 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk. +Version 3.15.5 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk. If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use [`--isolate`](#isolate) option. -SPAdes 3.15.4 includes the following additional pipelines: +SPAdes 3.15.5 includes the following additional pipelines: - metaSPAdes - a pipeline for metagenomic data sets (see [metaSPAdes options](#meta)). - plasmidSPAdes - a pipeline for extracting and assembling plasmids from WGS data sets (see [plasmid options](#plasmid)). @@ -187,13 +187,13 @@ In case of successful installation the f ## Downloading SPAdes Linux binaries -To download [SPAdes Linux binaries](http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz) and extract them, go to the directory in which you wish SPAdes to be installed and run: +To download [SPAdes Linux binaries](http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Linux.tar.gz) and extract them, go to the directory in which you wish SPAdes to be installed and run: ``` bash - wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Linux.tar.gz - tar -xzf SPAdes-3.15.4-Linux.tar.gz - cd SPAdes-3.15.4-Linux/bin/ + wget http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Linux.tar.gz + tar -xzf SPAdes-3.15.5-Linux.tar.gz + cd SPAdes-3.15.5-Linux/bin/ ``` In this case you do not need to run any installation scripts - SPAdes is ready to use. We also suggest adding SPAdes installation directory to the `PATH` variable. []() @@ -203,13 +203,13 @@ Note, that pre-build binaries do not wor ## Downloading SPAdes binaries for Mac -To obtain [SPAdes binaries for Mac](http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Darwin.tar.gz), go to the directory in which you wish SPAdes to be installed and run: +To obtain [SPAdes binaries for Mac](http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Darwin.tar.gz), go to the directory in which you wish SPAdes to be installed and run: ``` bash - curl http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Darwin.tar.gz -o SPAdes-3.15.4-Darwin.tar.gz - tar -zxf SPAdes-3.15.4-Darwin.tar.gz - cd SPAdes-3.15.4-Darwin/bin/ + curl http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5-Darwin.tar.gz -o SPAdes-3.15.5-Darwin.tar.gz + tar -zxf SPAdes-3.15.5-Darwin.tar.gz + cd SPAdes-3.15.5-Darwin/bin/ ``` Just as in Linux, SPAdes is ready to use and no further installation steps are required. We also suggest adding SPAdes installation directory to the `PATH` variable. []() @@ -224,13 +224,13 @@ If you wish to compile SPAdes by yoursel - zlib - libbz2 -If you meet these requirements, you can download the [SPAdes source code](http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4.tar.gz): +If you meet these requirements, you can download the [SPAdes source code](http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5.tar.gz): ``` bash - wget http://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4.tar.gz - tar -xzf SPAdes-3.15.4.tar.gz - cd SPAdes-3.15.4 + wget http://cab.spbu.ru/files/release3.15.5/SPAdes-3.15.5.tar.gz + tar -xzf SPAdes-3.15.5.tar.gz + cd SPAdes-3.15.5 ``` and build it with the following script: @@ -309,7 +309,7 @@ Thank you for using SPAdes! SPAdes takes as input paired-end reads, mate-pairs and single (unpaired) reads in FASTA and FASTQ. For IonTorrent data SPAdes also supports unpaired reads in unmapped BAM format (like the one produced by Torrent Server). However, in order to run read error correction, reads should be in FASTQ or BAM format. Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data. -To run SPAdes 3.15.4 you need at least one library of the following types: +To run SPAdes 3.15.5 you need at least one library of the following types: - Illumina paired-end/high-quality mate-pairs/unpaired reads - IonTorrent paired-end/high-quality mate-pairs/unpaired reads