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* Change SPAdes version * Add SPAdes v3.14.0 and remove v3.10.1 * Incorporate SPAdes --isolate option for estimated coverage >= 100x * Change MLST QA/QC * Samples with species known MLST scheme but for which it was not possible to find a scheme will now raise a warning instead of fail * Add more statistics * Save total number of reads and bp sequenced * Change Docker image * Change base image to perl:5.30-slim-stretch. This allows to use most recent Perl version but keeping an old Linux distribution for old kernels compatibility. * Install procps to provide free package to access memory usage * Do a JDK headless installation * Add any2fasta (_mlst_ dependency) * Minor changes * Add Docker image statistics to README * Minor fixes * Correct _mlst_ installation * Check if the _mlst_ novel alleles file exists before cleaning it * Catch subprocess error when program to run is not installed
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| FROM perl:5.30-slim-stretch | ||
| MAINTAINER Miguel Machado <[email protected]> | ||
| LABEL version="4.2.1-01" | ||
| LABEL version="4.2.2-01" | ||
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| WORKDIR /NGStools/ | ||
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@@ -46,6 +46,8 @@ ENV PATH="/NGStools/ncbi-blast-2.9.0+/bin:/NGStools/any2fasta:${PATH}" | |
| # --- mlst ---- | ||
| RUN git clone https://github.com/tseemann/mlst.git | ||
| ENV PATH="/NGStools/mlst/bin:${PATH}" | ||
| # Update Clostridium to Clostridioides | ||
| RUN echo -e 'cdifficile\tClostridioides\tdifficile' >> /NGStools/mlst/db/scheme_species_map.tab | ||
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| # --- ReMatCh --- | ||
| # TODO: to be used after converting INNUca do Python v3 | ||
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@@ -60,7 +62,7 @@ ENV PATH="/NGStools/ReMatCh/ReMatCh/src/samtools-1.3.1/bin:/NGStools/ReMatCh/ReM | |
| # --- INNUca --- | ||
| RUN git clone https://github.com/B-UMMI/INNUca.git && \ | ||
| pip install setuptools | ||
| ENV PATH="/NGStools/INNUca/src/fastqc_v0.11.5:/NGStools/INNUca/src/pilon_v1.23:/NGStools/INNUca/src/SPAdes-3.13.0-Linux/bin:/NGStools/INNUca/src/Trimmomatic-0.38:/NGStools/INNUca:${PATH}" | ||
| ENV PATH="/NGStools/INNUca/src/fastqc_v0.11.5:/NGStools/INNUca/src/pilon_v1.23:/NGStools/INNUca/src/SPAdes-3.14.0-Linux/bin:/NGStools/INNUca/src/Trimmomatic-0.38:/NGStools/INNUca:${PATH}" | ||
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| # fixing permissions for MLST update | ||
| RUN chmod +x /NGStools/INNUca/Docker/update_mlst_db.sh && chmod o+wr /NGStools/mlst/scripts/ && chmod -R o+wr /NGStools/mlst/db/ && sed -i "s#OUTDIR=pubmlst#OUTDIR=/NGStools/mlst/scripts/pubmlst#1" /NGStools/mlst/scripts/mlst-download_pub_mlst | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -11,7 +11,7 @@ | |
| Copyright (C) 2018 Miguel Machado <[email protected]> | ||
| Last modified: November 25, 2019 | ||
| Last modified: February 05, 2020 | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
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@@ -91,7 +91,7 @@ def include_rematch_dependencies_path(do_not_use_provided_software): | |
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| def main(): | ||
| version = '4.2.1' | ||
| version = '4.2.2' | ||
| args = utils.parseArguments(version) | ||
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| general_start_time = time.time() | ||
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@@ -138,12 +138,12 @@ def main(): | |
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| # Check programms | ||
| programs_version_dictionary = {} | ||
| programs_version_dictionary['gunzip'] = ['--version', '>=', '1.6'] | ||
| programs_version_dictionary['gunzip'] = {'required': ['--version', '>=', '1.6']} | ||
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| # Java check first for java dependents check next | ||
| if not (args.skipFastQC and args.skipTrimmomatic and (args.skipPilon or args.skipSPAdes)): | ||
| # programs_version_dictionary['java'] = ['-version', '>=', '1.8'] | ||
| programs_version_dictionary['java'] = [None, '>=', '1.8'] # For OpenJDK compatibility | ||
| programs_version_dictionary['java'] = {'required': [None, '>=', '1.8']} # For OpenJDK compatibility | ||
| missingPrograms, programs_version_dictionary = utils.checkPrograms(programs_version_dictionary) | ||
| if len(missingPrograms) > 0: | ||
| sys.exit('\n' + 'Errors:' + '\n' + '\n'.join(missingPrograms)) | ||
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@@ -154,35 +154,35 @@ def main(): | |
| global version_kraken_global | ||
| version_kraken_global = kraken_version() | ||
| if version_kraken_global == 2: | ||
| programs_version_dictionary['kraken2'] = ['--version', '>=', '2.0.6'] | ||
| programs_version_dictionary['kraken2'] = {'required': ['--version', '>=', '2.0.6']} | ||
| else: | ||
| programs_version_dictionary['kraken'] = ['--version', '>=', '0.10.6'] | ||
| programs_version_dictionary['kraken-repor'] = ['--version', '>=', '0.10.6'] | ||
| programs_version_dictionary['kraken'] = {'required': ['--version', '>=', '0.10.6']} | ||
| programs_version_dictionary['kraken-repor'] = {'required': ['--version', '>=', '0.10.6']} | ||
| if not args.skipTrueCoverage and trueCoverage_config is not None: | ||
| rematch_script = include_rematch_dependencies_path(args.doNotUseProvidedSoftware) | ||
| programs_version_dictionary['rematch.py'] = ['--version', '>=', '4.0.1'] | ||
| programs_version_dictionary['bcftools'] = ['--version', '==', '1.3.1'] | ||
| programs_version_dictionary['rematch.py'] = {'required': ['--version', '>=', '4.0.1']} | ||
| programs_version_dictionary['bcftools'] = {'required': ['--version', '==', '1.3.1']} | ||
| if not (args.skipTrueCoverage and ((args.skipAssemblyMapping and args.skipPilon) or args.skipSPAdes)): | ||
| programs_version_dictionary['bowtie2'] = ['--version', '>=', '2.2.9'] | ||
| programs_version_dictionary['samtools'] = ['--version', '==', '1.3.1'] | ||
| programs_version_dictionary['bowtie2'] = {'required': ['--version', '>=', '2.2.9']} | ||
| programs_version_dictionary['samtools'] = {'required': ['--version', '==', '1.3.1']} | ||
| if not args.skipFastQC: | ||
| programs_version_dictionary['fastqc'] = ['--version', '==', '0.11.5'] | ||
| programs_version_dictionary['fastqc'] = {'required': ['--version', '==', '0.11.5']} | ||
| if not args.skipTrimmomatic: | ||
| programs_version_dictionary['trimmomatic-{version}.jar'.format(version=args.trimVersion)] = ['-version', '==', | ||
| args.trimVersion] | ||
| programs_version_dictionary['trimmomatic-{version}.jar'.format(version=args.trimVersion)] = \ | ||
| {'required': ['-version', '==', args.trimVersion]} | ||
| if args.runPear: | ||
| programs_version_dictionary['pear'] = ['--version', '>=', '0.9.10'] | ||
| programs_version_dictionary['pear'] = {'required': ['--version', '>=', '0.9.10']} | ||
| if not args.skipSPAdes: | ||
| programs_version_dictionary['spades.py'] = ['--version', '>=', '3.9.0'] | ||
| programs_version_dictionary['spades.py'] = {'required': ['--version', '>=', '3.9.0']} | ||
| if not (args.skipPilon or args.skipSPAdes): | ||
| programs_version_dictionary['pilon-{version}.jar'.format(version=args.pilonVersion)] = ['--version', '==', | ||
| args.pilonVersion] | ||
| programs_version_dictionary['pilon-{version}.jar'.format(version=args.pilonVersion)] = \ | ||
| {'required': ['--version', '==', args.pilonVersion]} | ||
| if not (args.skipMLST or args.skipSPAdes): | ||
| programs_version_dictionary['mlst'] = ['--version', '>=', '2.4'] | ||
| programs_version_dictionary['mlst'] = {'required': ['--version', '>=', '2.4']} | ||
| if args.runInsertSize and not args.skipSPAdes: | ||
| if args.skipAssemblyMapping and args.skipPilon: | ||
| programs_version_dictionary['bowtie2'] = ['--version', '>=', '2.2.9'] | ||
| programs_version_dictionary['samtools'] = ['--version', '==', '1.3.1'] | ||
| programs_version_dictionary['bowtie2'] = {'required': ['--version', '>=', '2.2.9']} | ||
| programs_version_dictionary['samtools'] = {'required': ['--version', '==', '1.3.1']} | ||
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| # Set and print PATH variable | ||
| utils.setPATHvariable(args, script_path) | ||
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@@ -195,19 +195,25 @@ def main(): | |
| jar_path_trimmomatic = None | ||
| if not args.skipTrimmomatic: | ||
| jar_path_trimmomatic = \ | ||
| programs_version_dictionary['trimmomatic-{version}.jar'.format(version=args.trimVersion)][3] | ||
| programs_version_dictionary['trimmomatic-{version}.jar'.format(version=args.trimVersion)]['found']['path'] | ||
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| jar_path_pilon = None | ||
| if not args.skipPilon and not args.skipSPAdes: | ||
| jar_path_pilon = programs_version_dictionary['pilon-{version}.jar'.format(version=args.pilonVersion)][3] | ||
| jar_path_pilon = \ | ||
| programs_version_dictionary['pilon-{version}.jar'.format(version=args.pilonVersion)]['found']['path'] | ||
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| # Get SPAdes version | ||
| spades_version = None | ||
| if not args.skipSPAdes: | ||
| spades_version = programs_version_dictionary['spades.py']['found']['version'] | ||
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| # pairEnd_filesSeparation_list = args.pairEnd_filesSeparation | ||
| pairEnd_filesSeparation_list = None | ||
| samples, inputDirectory, removeCreatedSamplesDirectories, indir_same_outdir = \ | ||
| get_samples(args.inputDirectory, args.fastq, outdir, pairEnd_filesSeparation_list) | ||
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| # Start running the analysis | ||
| print '\n' + 'RUNNING INNUca.py' | ||
| print('\n' + 'RUNNING INNUca.py') | ||
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| # Prepare run report file | ||
| samples_report_path = os.path.join(outdir, 'samples_report.' + time_str + '.tab') | ||
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@@ -230,20 +236,20 @@ def main(): | |
| # Determine SPAdes maximum memory | ||
| spadesMaxMemory = None | ||
| if not args.skipSPAdes: | ||
| print '' | ||
| print('') | ||
| spadesMaxMemory = spades.define_memory(args.spadesMaxMemory, args.threads, available_memory_GB) | ||
| # Determine .jar maximum memory | ||
| jarMaxMemory = 'off' | ||
| if not (args.skipTrimmomatic and (args.skipSPAdes or args.skipPilon)): | ||
| print '' | ||
| print('') | ||
| jarMaxMemory = utils.define_jar_max_memory(args.jarMaxMemory, args.threads, available_memory_GB) | ||
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| # Run INNUca for each sample | ||
| sample_report_json = {} | ||
| for sample in samples: | ||
| sample_start_time = time.time() | ||
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| print '\n' + 'Sample: ' + sample + '\n' | ||
| print('\n' + 'Sample: ' + sample + '\n') | ||
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| # Create sample outdir | ||
| sample_outdir = os.path.abspath(os.path.join(outdir, sample, '')) | ||
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@@ -253,21 +259,21 @@ def main(): | |
| # Get fastq files | ||
| fastq_files = utils.searchFastqFiles(os.path.join(inputDirectory, sample, ''), pairEnd_filesSeparation_list, False) | ||
| if len(fastq_files) == 1: | ||
| print 'Only one fastq file was found: ' + str(fastq_files) | ||
| print 'Pair-End sequencing is required. Moving to the next sample' | ||
| print('Only one fastq file was found: ' + str(fastq_files)) | ||
| print('Pair-End sequencing is required. Moving to the next sample') | ||
| continue | ||
| elif len(fastq_files) == 0: | ||
| print 'No compressed fastq files were found. Continue to the next sample' | ||
| print('No compressed fastq files were found. Continue to the next sample') | ||
| continue | ||
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| print 'The following files will be used:' | ||
| print str(fastq_files) + '\n' | ||
| print('The following files will be used:') | ||
| print(str(fastq_files) + '\n') | ||
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| # Run INNUca.py analysis | ||
| run_successfully, pass_qc, run_report = \ | ||
| run_innuca(sample, sample_outdir, fastq_files, args, script_path, scheme, spadesMaxMemory, | ||
| jar_path_trimmomatic, jar_path_pilon, jarMaxMemory, trueCoverage_config, rematch_script, | ||
| species_genus, mlst_scheme_genus) | ||
| species_genus, mlst_scheme_genus, spades_version=spades_version) | ||
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| # Save sample fail report | ||
| utils.write_fail_report(os.path.join(sample_outdir, 'fail_report.txt'), run_report) | ||
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@@ -286,7 +292,7 @@ def main(): | |
| if args.fastq is not None: | ||
| utils.removeDirectory(os.path.join(outdir, 'reads', '')) | ||
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| print 'END ' + sample + ' analysis' | ||
| print('END ' + sample + ' analysis') | ||
| time_taken = utils.runTime(sample_start_time) | ||
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| # Save run report | ||
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@@ -389,7 +395,8 @@ def get_samples(args_input_directory, args_fastq, outdir, pair_end_files_separat | |
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| def run_innuca(sample_name, outdir, fastq_files, args, script_path, scheme, spades_max_memory, jar_path_trimmomatic, | ||
| jar_path_pilon, jar_max_memory, true_coverage_config, rematch_script, species_genus, mlst_scheme_genus): | ||
| jar_path_pilon, jar_max_memory, true_coverage_config, rematch_script, species_genus, mlst_scheme_genus, | ||
| spades_version=None): | ||
| threads = args.threads | ||
| adapters_fasta = args.adapters | ||
| if adapters_fasta is not None: | ||
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@@ -624,7 +631,9 @@ def run_innuca(sample_name, outdir, fastq_files, args, script_path, scheme, spad | |
| args.spadesMinCoverageAssembly, args.spadesMinContigsLength, genome_size, | ||
| args.spadesKmers, max_reads_length, args.spadesDefaultKmers, | ||
| args.spadesMinKmerCovContigs, assembled_se_reads, args.saveExcludedContigs, | ||
| args.maxNumberContigs, args.keepSPAdesScaffolds) | ||
| args.maxNumberContigs, args.keepSPAdesScaffolds, spades_version=spades_version, | ||
| estimated_coverage=estimated_coverage, | ||
| spades_not_use_isolate=args.spadesNotUseIsolate) | ||
| runs['SPAdes'] = [run_successfully, pass_qc, time_taken, failing, warning, 'NA'] | ||
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| if run_successfully: | ||
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