2024-09-24T18:01:32,472 Created temporary directory: /tmp/pip-build-tracker-tledervy 2024-09-24T18:01:32,473 Initialized build tracking at /tmp/pip-build-tracker-tledervy 2024-09-24T18:01:32,473 Created build tracker: /tmp/pip-build-tracker-tledervy 2024-09-24T18:01:32,474 Entered build tracker: /tmp/pip-build-tracker-tledervy 2024-09-24T18:01:32,475 Created temporary directory: /tmp/pip-wheel-i2mmt_fc 2024-09-24T18:01:32,479 Created temporary directory: /tmp/pip-ephem-wheel-cache-widg8wga 2024-09-24T18:01:32,521 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-09-24T18:01:32,524 2 location(s) to search for versions of somaticseq: 2024-09-24T18:01:32,524 * https://pypi.org/simple/somaticseq/ 2024-09-24T18:01:32,524 * https://www.piwheels.org/simple/somaticseq/ 2024-09-24T18:01:32,525 Fetching project page and analyzing links: https://pypi.org/simple/somaticseq/ 2024-09-24T18:01:32,525 Getting page https://pypi.org/simple/somaticseq/ 2024-09-24T18:01:32,527 Found index url https://pypi.org/simple/ 2024-09-24T18:01:32,752 Fetched page https://pypi.org/simple/somaticseq/ as application/vnd.pypi.simple.v1+json 2024-09-24T18:01:32,754 Found link https://files.pythonhosted.org/packages/66/a1/52de812952b5ebc3df0b945d88d8c72a15fde3a6d44c7761042a4704cdc3/somaticseq-3.7.3.tar.gz (from https://pypi.org/simple/somaticseq/), version: 3.7.3 2024-09-24T18:01:32,754 Found link https://files.pythonhosted.org/packages/17/b0/17d3cb01fae1f469ac27f88b2094e0918704cc402b4d0194ea6f1e32b800/somaticseq-3.7.4.tar.gz (from https://pypi.org/simple/somaticseq/), version: 3.7.4 2024-09-24T18:01:32,755 Found link https://files.pythonhosted.org/packages/53/d3/ae6ee18a759498f405592c94c0499842faa0603b6c23b607e3e66c22d7a4/somaticseq-3.8.0.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.10.0), version: 3.8.0 2024-09-24T18:01:32,756 Fetching project page and analyzing links: https://www.piwheels.org/simple/somaticseq/ 2024-09-24T18:01:32,757 Getting page https://www.piwheels.org/simple/somaticseq/ 2024-09-24T18:01:32,758 Found index url https://www.piwheels.org/simple/ 2024-09-24T18:01:32,935 Fetched page https://www.piwheels.org/simple/somaticseq/ as text/html 2024-09-24T18:01:32,936 Skipping link: No binaries permitted for somaticseq: https://www.piwheels.org/simple/somaticseq/somaticseq-3.7.4-py3-none-any.whl#sha256=2ab6487255fe614e97cf1e771576df0f07771a923286483c3f16a551897d9294 (from https://www.piwheels.org/simple/somaticseq/) 2024-09-24T18:01:32,937 Skipping link: No binaries permitted for somaticseq: https://www.piwheels.org/simple/somaticseq/somaticseq-3.7.3-py3-none-any.whl#sha256=ffd2a113ca4746e6d200ae746559246271776a2dd38b2af16327199d91bf9ea1 (from https://www.piwheels.org/simple/somaticseq/) 2024-09-24T18:01:32,938 Skipping link: not a file: https://www.piwheels.org/simple/somaticseq/ 2024-09-24T18:01:32,939 Skipping link: not a file: https://pypi.org/simple/somaticseq/ 2024-09-24T18:01:32,957 Given no hashes to check 1 links for project 'somaticseq': discarding no candidates 2024-09-24T18:01:32,958 Collecting somaticseq==3.8.0 2024-09-24T18:01:32,961 Created temporary directory: /tmp/pip-unpack-4fvxuk59 2024-09-24T18:01:33,267 Downloading somaticseq-3.8.0.tar.gz (133 kB) 2024-09-24T18:01:33,542 Added somaticseq==3.8.0 from https://files.pythonhosted.org/packages/53/d3/ae6ee18a759498f405592c94c0499842faa0603b6c23b607e3e66c22d7a4/somaticseq-3.8.0.tar.gz to build tracker '/tmp/pip-build-tracker-tledervy' 2024-09-24T18:01:33,546 Running setup.py (path:/tmp/pip-wheel-i2mmt_fc/somaticseq_5e8ebfa7cc91413482b69c862d16320c/setup.py) egg_info for package somaticseq 2024-09-24T18:01:33,547 Created temporary directory: /tmp/pip-pip-egg-info-_q1cts46 2024-09-24T18:01:33,547 Preparing metadata (setup.py): started 2024-09-24T18:01:33,549 Running command python setup.py egg_info 2024-09-24T18:01:34,205 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-09-24T18:01:34,205 !! 2024-09-24T18:01:34,207 ******************************************************************************** 2024-09-24T18:01:34,207 Usage of dash-separated 'description-file' will not be supported in future 2024-09-24T18:01:34,208 versions. Please use the underscore name 'description_file' instead. 2024-09-24T18:01:34,209 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-09-24T18:01:34,210 or your builds will no longer be supported. 2024-09-24T18:01:34,210 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-09-24T18:01:34,211 ******************************************************************************** 2024-09-24T18:01:34,212 !! 2024-09-24T18:01:34,212 opt = self.warn_dash_deprecation(opt, section) 2024-09-24T18:01:34,904 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-09-24T18:01:34,905 !! 2024-09-24T18:01:34,906 ******************************************************************************** 2024-09-24T18:01:34,906 Usage of dash-separated 'description-file' will not be supported in future 2024-09-24T18:01:34,907 versions. Please use the underscore name 'description_file' instead. 2024-09-24T18:01:34,908 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-09-24T18:01:34,908 or your builds will no longer be supported. 2024-09-24T18:01:34,909 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-09-24T18:01:34,910 ******************************************************************************** 2024-09-24T18:01:34,911 !! 2024-09-24T18:01:34,911 opt = self.warn_dash_deprecation(opt, section) 2024-09-24T18:01:34,955 3.8.0 2024-09-24T18:01:34,956 running egg_info 2024-09-24T18:01:34,957 creating /tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info 2024-09-24T18:01:34,984 writing /tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/PKG-INFO 2024-09-24T18:01:34,987 writing dependency_links to /tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/dependency_links.txt 2024-09-24T18:01:34,990 writing requirements to /tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/requires.txt 2024-09-24T18:01:34,991 writing top-level names to /tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/top_level.txt 2024-09-24T18:01:34,992 writing manifest file '/tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/SOURCES.txt' 2024-09-24T18:01:35,119 reading manifest file '/tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/SOURCES.txt' 2024-09-24T18:01:35,121 adding license file 'LICENSE.txt' 2024-09-24T18:01:35,126 writing manifest file '/tmp/pip-pip-egg-info-_q1cts46/somaticseq.egg-info/SOURCES.txt' 2024-09-24T18:01:35,238 Preparing metadata (setup.py): finished with status 'done' 2024-09-24T18:01:35,242 Source in /tmp/pip-wheel-i2mmt_fc/somaticseq_5e8ebfa7cc91413482b69c862d16320c has version 3.8.0, which satisfies requirement somaticseq==3.8.0 from https://files.pythonhosted.org/packages/53/d3/ae6ee18a759498f405592c94c0499842faa0603b6c23b607e3e66c22d7a4/somaticseq-3.8.0.tar.gz 2024-09-24T18:01:35,243 Removed somaticseq==3.8.0 from https://files.pythonhosted.org/packages/53/d3/ae6ee18a759498f405592c94c0499842faa0603b6c23b607e3e66c22d7a4/somaticseq-3.8.0.tar.gz from build tracker '/tmp/pip-build-tracker-tledervy' 2024-09-24T18:01:35,251 Created temporary directory: /tmp/pip-unpack-x6uswxaz 2024-09-24T18:01:35,252 Created temporary directory: /tmp/pip-unpack-2cuvjkrb 2024-09-24T18:01:35,253 Building wheels for collected packages: somaticseq 2024-09-24T18:01:35,257 Created temporary directory: /tmp/pip-wheel-z9ia5ngx 2024-09-24T18:01:35,258 Building wheel for somaticseq (setup.py): started 2024-09-24T18:01:35,259 Destination directory: /tmp/pip-wheel-z9ia5ngx 2024-09-24T18:01:35,260 Running command python setup.py bdist_wheel 2024-09-24T18:01:35,708 3.8.0 2024-09-24T18:01:35,749 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-09-24T18:01:35,750 !! 2024-09-24T18:01:35,751 ******************************************************************************** 2024-09-24T18:01:35,752 Usage of dash-separated 'description-file' will not be supported in future 2024-09-24T18:01:35,752 versions. Please use the underscore name 'description_file' instead. 2024-09-24T18:01:35,753 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-09-24T18:01:35,754 or your builds will no longer be supported. 2024-09-24T18:01:35,755 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-09-24T18:01:35,755 ******************************************************************************** 2024-09-24T18:01:35,756 !! 2024-09-24T18:01:35,756 opt = self.warn_dash_deprecation(opt, section) 2024-09-24T18:01:36,283 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:452: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-09-24T18:01:36,284 !! 2024-09-24T18:01:36,285 ******************************************************************************** 2024-09-24T18:01:36,285 Usage of dash-separated 'description-file' will not be supported in future 2024-09-24T18:01:36,286 versions. Please use the underscore name 'description_file' instead. 2024-09-24T18:01:36,287 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-09-24T18:01:36,288 or your builds will no longer be supported. 2024-09-24T18:01:36,289 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-09-24T18:01:36,289 ******************************************************************************** 2024-09-24T18:01:36,291 !! 2024-09-24T18:01:36,291 opt = self.warn_dash_deprecation(opt, section) 2024-09-24T18:01:36,302 running bdist_wheel 2024-09-24T18:01:36,437 running build 2024-09-24T18:01:36,438 running build_py 2024-09-24T18:01:36,469 creating build/lib/somaticseq 2024-09-24T18:01:36,471 copying somaticseq/ntchange_type.py -> build/lib/somaticseq 2024-09-24T18:01:36,473 copying somaticseq/_version.py -> build/lib/somaticseq 2024-09-24T18:01:36,475 copying somaticseq/somaticseq_parallel.py -> build/lib/somaticseq 2024-09-24T18:01:36,478 copying somaticseq/bam_features.py -> build/lib/somaticseq 2024-09-24T18:01:36,481 copying somaticseq/annotate_caller.py -> build/lib/somaticseq 2024-09-24T18:01:36,483 copying somaticseq/__init__.py -> build/lib/somaticseq 2024-09-24T18:01:36,485 copying somaticseq/run_somaticseq.py -> build/lib/somaticseq 2024-09-24T18:01:36,488 copying somaticseq/somatic_tsv2vcf.py -> build/lib/somaticseq 2024-09-24T18:01:36,491 copying somaticseq/defaults.py -> build/lib/somaticseq 2024-09-24T18:01:36,493 copying somaticseq/somatic_vcf2tsv.py -> build/lib/somaticseq 2024-09-24T18:01:36,496 copying somaticseq/somatic_xgboost.py -> build/lib/somaticseq 2024-09-24T18:01:36,498 copying somaticseq/sequencing_features.py -> build/lib/somaticseq 2024-09-24T18:01:36,501 copying somaticseq/tsv2vcf.py -> build/lib/somaticseq 2024-09-24T18:01:36,503 copying somaticseq/combine_callers.py -> build/lib/somaticseq 2024-09-24T18:01:36,506 copying somaticseq/single_sample_vcf2tsv.py -> build/lib/somaticseq 2024-09-24T18:01:36,509 creating build/lib/r_scripts 2024-09-24T18:01:36,510 copying r_scripts/__init__.py -> build/lib/r_scripts 2024-09-24T18:01:36,513 creating build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,514 copying somaticseq/vcf_modifier/vcfIntersector.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,516 copying somaticseq/vcf_modifier/modify_JointSNVMix2.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,518 copying somaticseq/vcf_modifier/modify_MuTect2.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,521 copying somaticseq/vcf_modifier/modify_VarDict.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,523 copying somaticseq/vcf_modifier/modify_MuTect.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,525 copying somaticseq/vcf_modifier/modify_Strelka.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,527 copying somaticseq/vcf_modifier/__init__.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,529 copying somaticseq/vcf_modifier/modify_ssMuTect2.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,531 copying somaticseq/vcf_modifier/modify_SomaticSniper.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,533 copying somaticseq/vcf_modifier/complex2indel.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,535 copying somaticseq/vcf_modifier/leftAlign.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,536 copying somaticseq/vcf_modifier/modify_VarScan2.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,539 copying somaticseq/vcf_modifier/copy_TextFile.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,541 copying somaticseq/vcf_modifier/splitVcf.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,543 copying somaticseq/vcf_modifier/getUniqueVcfPositions.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,545 copying somaticseq/vcf_modifier/modify_ssStrelka.py -> build/lib/somaticseq/vcf_modifier 2024-09-24T18:01:36,548 creating build/lib/somaticseq/utilities 2024-09-24T18:01:36,549 copying somaticseq/utilities/combo_callers_evaluator.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,551 copying somaticseq/utilities/bamQC.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,553 copying somaticseq/utilities/multi-nucleotide_phaser.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,555 copying somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,557 copying somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,560 copying somaticseq/utilities/attach_pileupVAF.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,562 copying somaticseq/utilities/reformat_VCF2SEQC2.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,564 copying somaticseq/utilities/filter_SomaticSeq_VCF.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,567 copying somaticseq/utilities/lociCounters.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,569 copying somaticseq/utilities/__init__.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,570 copying somaticseq/utilities/bedFileHandler.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,573 copying somaticseq/utilities/tally_MyVCF_vs_Truth.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,575 copying somaticseq/utilities/plot_TPvsFP.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,577 copying somaticseq/utilities/BAM_filter.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,579 copying somaticseq/utilities/split_mergedBed.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,581 copying somaticseq/utilities/paired_end_bam2fastq.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,583 copying somaticseq/utilities/linguistic_sequence_complexity.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,585 copying somaticseq/utilities/split_bed_into_equal_regions.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,587 copying somaticseq/utilities/trimSoftClippedReads.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,589 copying somaticseq/utilities/lociCounterWithLabels.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,591 copying somaticseq/utilities/variant_annotation.py -> build/lib/somaticseq/utilities 2024-09-24T18:01:36,594 creating build/lib/somaticseq/genomic_file_parsers 2024-09-24T18:01:36,595 copying somaticseq/genomic_file_parsers/concat.py -> build/lib/somaticseq/genomic_file_parsers 2024-09-24T18:01:36,598 copying somaticseq/genomic_file_parsers/genomic_file_handlers.py -> build/lib/somaticseq/genomic_file_parsers 2024-09-24T18:01:36,601 copying somaticseq/genomic_file_parsers/pileup_reader.py -> build/lib/somaticseq/genomic_file_parsers 2024-09-24T18:01:36,603 copying somaticseq/genomic_file_parsers/__init__.py -> build/lib/somaticseq/genomic_file_parsers 2024-09-24T18:01:36,605 copying somaticseq/genomic_file_parsers/read_info_extractor.py -> build/lib/somaticseq/genomic_file_parsers 2024-09-24T18:01:36,607 creating build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,609 copying somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,611 copying somaticseq/utilities/dockered_pipelines/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,613 copying somaticseq/utilities/dockered_pipelines/container_option.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,614 copying somaticseq/utilities/dockered_pipelines/tumor_normal_run.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,617 copying somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,619 copying somaticseq/utilities/dockered_pipelines/tumor_only_run.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,622 copying somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,626 creating build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,627 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,630 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,632 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,634 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,635 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,638 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,640 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,643 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,645 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,648 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,651 creating build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,652 copying somaticseq/utilities/dockered_pipelines/alignments/align.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,654 copying somaticseq/utilities/dockered_pipelines/alignments/markdup.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,657 copying somaticseq/utilities/dockered_pipelines/alignments/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,658 copying somaticseq/utilities/dockered_pipelines/alignments/trim.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,661 copying somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,663 copying somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,665 copying somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,674 copying r_scripts/ada_model_builder.R -> build/lib/r_scripts 2024-09-24T18:01:36,676 copying r_scripts/ada_model_predictor.R -> build/lib/r_scripts 2024-09-24T18:01:36,678 copying r_scripts/ada_model_builder_ntChange.R -> build/lib/r_scripts 2024-09-24T18:01:36,680 copying r_scripts/ada_cross_validation.R -> build/lib/r_scripts 2024-09-24T18:01:36,687 running build_scripts 2024-09-24T18:01:36,688 creating build/scripts-3.11 2024-09-24T18:01:36,689 copying and adjusting somaticseq/somaticseq_parallel.py -> build/scripts-3.11 2024-09-24T18:01:36,692 copying and adjusting somaticseq/run_somaticseq.py -> build/scripts-3.11 2024-09-24T18:01:36,695 copying and adjusting somaticseq/single_sample_vcf2tsv.py -> build/scripts-3.11 2024-09-24T18:01:36,698 copying and adjusting somaticseq/somatic_vcf2tsv.py -> build/scripts-3.11 2024-09-24T18:01:36,701 copying and adjusting somaticseq/somatic_xgboost.py -> build/scripts-3.11 2024-09-24T18:01:36,703 copying and adjusting somaticseq/somatic_tsv2vcf.py -> build/scripts-3.11 2024-09-24T18:01:36,706 copying and adjusting somaticseq/genomic_file_parsers/concat.py -> build/scripts-3.11 2024-09-24T18:01:36,709 copying and adjusting somaticseq/utilities/linguistic_sequence_complexity.py -> build/scripts-3.11 2024-09-24T18:01:36,711 copying and adjusting somaticseq/utilities/lociCounterWithLabels.py -> build/scripts-3.11 2024-09-24T18:01:36,713 copying and adjusting somaticseq/utilities/paired_end_bam2fastq.py -> build/scripts-3.11 2024-09-24T18:01:36,714 copying and adjusting somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/scripts-3.11 2024-09-24T18:01:36,716 copying and adjusting somaticseq/utilities/split_bed_into_equal_regions.py -> build/scripts-3.11 2024-09-24T18:01:36,718 copying and adjusting somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/scripts-3.11 2024-09-24T18:01:36,721 copying and adjusting somaticseq/utilities/variant_annotation.py -> build/scripts-3.11 2024-09-24T18:01:36,723 copying somaticseq/utilities/vcfsorter.pl -> build/scripts-3.11 2024-09-24T18:01:36,725 copying and adjusting somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/scripts-3.11 2024-09-24T18:01:36,728 copying and adjusting somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/scripts-3.11 2024-09-24T18:01:36,731 copying and adjusting somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/scripts-3.11 2024-09-24T18:01:36,733 copying and adjusting somaticseq/vcf_modifier/splitVcf.py -> build/scripts-3.11 2024-09-24T18:01:36,735 copying r_scripts/ada_model_builder_ntChange.R -> build/scripts-3.11 2024-09-24T18:01:36,737 copying r_scripts/ada_model_predictor.R -> build/scripts-3.11 2024-09-24T18:01:36,739 changing mode of build/scripts-3.11/somaticseq_parallel.py from 644 to 755 2024-09-24T18:01:36,740 changing mode of build/scripts-3.11/run_somaticseq.py from 644 to 755 2024-09-24T18:01:36,740 changing mode of build/scripts-3.11/single_sample_vcf2tsv.py from 644 to 755 2024-09-24T18:01:36,741 changing mode of build/scripts-3.11/somatic_vcf2tsv.py from 644 to 755 2024-09-24T18:01:36,741 changing mode of build/scripts-3.11/somatic_xgboost.py from 644 to 755 2024-09-24T18:01:36,742 changing mode of build/scripts-3.11/somatic_tsv2vcf.py from 644 to 755 2024-09-24T18:01:36,742 changing mode of build/scripts-3.11/concat.py from 644 to 755 2024-09-24T18:01:36,743 changing mode of build/scripts-3.11/linguistic_sequence_complexity.py from 644 to 755 2024-09-24T18:01:36,744 changing mode of build/scripts-3.11/lociCounterWithLabels.py from 644 to 755 2024-09-24T18:01:36,744 changing mode of build/scripts-3.11/paired_end_bam2fastq.py from 644 to 755 2024-09-24T18:01:36,745 changing mode of build/scripts-3.11/remove_callers_from_somaticseq_tsv.py from 644 to 755 2024-09-24T18:01:36,745 changing mode of build/scripts-3.11/split_bed_into_equal_regions.py from 644 to 755 2024-09-24T18:01:36,746 changing mode of build/scripts-3.11/tally_variants_from_multiple_vcfs.py from 644 to 755 2024-09-24T18:01:36,746 changing mode of build/scripts-3.11/variant_annotation.py from 644 to 755 2024-09-24T18:01:36,747 changing mode of build/scripts-3.11/makeAlignmentScripts.py from 644 to 755 2024-09-24T18:01:36,747 changing mode of build/scripts-3.11/makeSomaticScripts.py from 644 to 755 2024-09-24T18:01:36,748 changing mode of build/scripts-3.11/run_workflows.py from 644 to 755 2024-09-24T18:01:36,748 changing mode of build/scripts-3.11/splitVcf.py from 644 to 755 2024-09-24T18:01:36,774 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-09-24T18:01:36,775 !! 2024-09-24T18:01:36,776 ******************************************************************************** 2024-09-24T18:01:36,777 Please avoid running ``setup.py`` directly. 2024-09-24T18:01:36,777 Instead, use pypa/build, pypa/installer or other 2024-09-24T18:01:36,778 standards-based tools. 2024-09-24T18:01:36,779 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-09-24T18:01:36,779 ******************************************************************************** 2024-09-24T18:01:36,781 !! 2024-09-24T18:01:36,781 self.initialize_options() 2024-09-24T18:01:36,803 installing to build/bdist.linux-armv7l/wheel 2024-09-24T18:01:36,804 running install 2024-09-24T18:01:36,831 running install_lib 2024-09-24T18:01:36,857 creating build/bdist.linux-armv7l/wheel 2024-09-24T18:01:36,859 creating build/bdist.linux-armv7l/wheel/somaticseq 2024-09-24T18:01:36,861 copying build/lib/somaticseq/ntchange_type.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,863 copying build/lib/somaticseq/_version.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,864 copying build/lib/somaticseq/somaticseq_parallel.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,867 creating build/bdist.linux-armv7l/wheel/somaticseq/vcf_modifier 2024-09-24T18:01:36,869 copying build/lib/somaticseq/vcf_modifier/vcfIntersector.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,871 copying build/lib/somaticseq/vcf_modifier/modify_JointSNVMix2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,873 copying build/lib/somaticseq/vcf_modifier/modify_MuTect2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,875 copying build/lib/somaticseq/vcf_modifier/modify_VarDict.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,877 copying build/lib/somaticseq/vcf_modifier/modify_MuTect.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,880 copying build/lib/somaticseq/vcf_modifier/modify_Strelka.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,881 copying build/lib/somaticseq/vcf_modifier/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,883 copying build/lib/somaticseq/vcf_modifier/modify_ssMuTect2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,885 copying build/lib/somaticseq/vcf_modifier/modify_SomaticSniper.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,887 copying build/lib/somaticseq/vcf_modifier/complex2indel.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,889 copying build/lib/somaticseq/vcf_modifier/leftAlign.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,891 copying build/lib/somaticseq/vcf_modifier/modify_VarScan2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,893 copying build/lib/somaticseq/vcf_modifier/copy_TextFile.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,894 copying build/lib/somaticseq/vcf_modifier/splitVcf.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,897 copying build/lib/somaticseq/vcf_modifier/getUniqueVcfPositions.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,898 copying build/lib/somaticseq/vcf_modifier/modify_ssStrelka.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2024-09-24T18:01:36,900 copying build/lib/somaticseq/bam_features.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,903 copying build/lib/somaticseq/annotate_caller.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,905 copying build/lib/somaticseq/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,906 copying build/lib/somaticseq/run_somaticseq.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,909 copying build/lib/somaticseq/somatic_tsv2vcf.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,912 copying build/lib/somaticseq/defaults.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:36,914 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-09-24T18:01:36,915 copying build/lib/somaticseq/utilities/combo_callers_evaluator.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,918 copying build/lib/somaticseq/utilities/bamQC.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,920 copying build/lib/somaticseq/utilities/multi-nucleotide_phaser.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,922 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,924 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,925 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,928 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,930 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,933 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,934 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,936 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,939 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,941 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,943 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,946 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-09-24T18:01:36,948 copying build/lib/somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,950 copying build/lib/somaticseq/utilities/dockered_pipelines/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,952 copying build/lib/somaticseq/utilities/dockered_pipelines/container_option.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,954 copying build/lib/somaticseq/utilities/dockered_pipelines/tumor_normal_run.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,957 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,958 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/align.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,960 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/markdup.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,964 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,965 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/trim.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,967 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,969 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,971 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2024-09-24T18:01:36,973 copying build/lib/somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,976 copying build/lib/somaticseq/utilities/dockered_pipelines/tumor_only_run.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,978 copying build/lib/somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2024-09-24T18:01:36,981 copying build/lib/somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,983 copying build/lib/somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,985 copying build/lib/somaticseq/utilities/attach_pileupVAF.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,988 copying build/lib/somaticseq/utilities/reformat_VCF2SEQC2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,990 copying build/lib/somaticseq/utilities/filter_SomaticSeq_VCF.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,992 copying build/lib/somaticseq/utilities/lociCounters.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,994 copying build/lib/somaticseq/utilities/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,996 copying build/lib/somaticseq/utilities/bedFileHandler.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:36,998 copying build/lib/somaticseq/utilities/tally_MyVCF_vs_Truth.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,000 copying build/lib/somaticseq/utilities/plot_TPvsFP.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,003 copying build/lib/somaticseq/utilities/BAM_filter.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,004 copying build/lib/somaticseq/utilities/split_mergedBed.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,006 copying build/lib/somaticseq/utilities/paired_end_bam2fastq.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,008 copying build/lib/somaticseq/utilities/linguistic_sequence_complexity.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,010 copying build/lib/somaticseq/utilities/split_bed_into_equal_regions.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,012 copying build/lib/somaticseq/utilities/trimSoftClippedReads.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,014 copying build/lib/somaticseq/utilities/lociCounterWithLabels.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,016 copying build/lib/somaticseq/utilities/variant_annotation.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2024-09-24T18:01:37,018 copying build/lib/somaticseq/somatic_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:37,021 copying build/lib/somaticseq/somatic_xgboost.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:37,024 creating build/bdist.linux-armv7l/wheel/somaticseq/genomic_file_parsers 2024-09-24T18:01:37,025 copying build/lib/somaticseq/genomic_file_parsers/concat.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2024-09-24T18:01:37,027 copying build/lib/somaticseq/genomic_file_parsers/genomic_file_handlers.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2024-09-24T18:01:37,030 copying build/lib/somaticseq/genomic_file_parsers/pileup_reader.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2024-09-24T18:01:37,032 copying build/lib/somaticseq/genomic_file_parsers/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2024-09-24T18:01:37,034 copying build/lib/somaticseq/genomic_file_parsers/read_info_extractor.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2024-09-24T18:01:37,036 copying build/lib/somaticseq/sequencing_features.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:37,039 copying build/lib/somaticseq/tsv2vcf.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:37,041 copying build/lib/somaticseq/combine_callers.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:37,044 copying build/lib/somaticseq/single_sample_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2024-09-24T18:01:37,048 creating build/bdist.linux-armv7l/wheel/r_scripts 2024-09-24T18:01:37,049 copying build/lib/r_scripts/ada_model_builder.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2024-09-24T18:01:37,051 copying build/lib/r_scripts/ada_model_predictor.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2024-09-24T18:01:37,053 copying build/lib/r_scripts/ada_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2024-09-24T18:01:37,055 copying build/lib/r_scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./r_scripts 2024-09-24T18:01:37,056 copying build/lib/r_scripts/ada_cross_validation.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2024-09-24T18:01:37,058 running install_egg_info 2024-09-24T18:01:37,095 running egg_info 2024-09-24T18:01:37,123 writing somaticseq.egg-info/PKG-INFO 2024-09-24T18:01:37,127 writing dependency_links to somaticseq.egg-info/dependency_links.txt 2024-09-24T18:01:37,129 writing requirements to somaticseq.egg-info/requires.txt 2024-09-24T18:01:37,130 writing top-level names to somaticseq.egg-info/top_level.txt 2024-09-24T18:01:37,171 reading manifest file 'somaticseq.egg-info/SOURCES.txt' 2024-09-24T18:01:37,178 adding license file 'LICENSE.txt' 2024-09-24T18:01:37,184 writing manifest file 'somaticseq.egg-info/SOURCES.txt' 2024-09-24T18:01:37,186 Copying somaticseq.egg-info to build/bdist.linux-armv7l/wheel/./somaticseq-3.8.0-py3.11.egg-info 2024-09-24T18:01:37,197 running install_scripts 2024-09-24T18:01:37,198 creating build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,199 copying build/scripts-3.11/concat.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,202 copying build/scripts-3.11/remove_callers_from_somaticseq_tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,204 copying build/scripts-3.11/tally_variants_from_multiple_vcfs.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,206 copying build/scripts-3.11/ada_model_predictor.R -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,208 copying build/scripts-3.11/somaticseq_parallel.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,210 copying build/scripts-3.11/ada_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,212 copying build/scripts-3.11/run_workflows.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,214 copying build/scripts-3.11/vcfsorter.pl -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,217 copying build/scripts-3.11/run_somaticseq.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,220 copying build/scripts-3.11/somatic_tsv2vcf.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,223 copying build/scripts-3.11/somatic_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,226 copying build/scripts-3.11/somatic_xgboost.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,229 copying build/scripts-3.11/paired_end_bam2fastq.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,231 copying build/scripts-3.11/linguistic_sequence_complexity.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,234 copying build/scripts-3.11/split_bed_into_equal_regions.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,236 copying build/scripts-3.11/lociCounterWithLabels.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,238 copying build/scripts-3.11/single_sample_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,241 copying build/scripts-3.11/splitVcf.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,243 copying build/scripts-3.11/makeAlignmentScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,246 copying build/scripts-3.11/variant_annotation.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,248 copying build/scripts-3.11/makeSomaticScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts 2024-09-24T18:01:37,251 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/concat.py to 755 2024-09-24T18:01:37,251 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/remove_callers_from_somaticseq_tsv.py to 755 2024-09-24T18:01:37,252 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/tally_variants_from_multiple_vcfs.py to 755 2024-09-24T18:01:37,253 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/ada_model_predictor.R to 755 2024-09-24T18:01:37,253 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/somaticseq_parallel.py to 755 2024-09-24T18:01:37,254 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/ada_model_builder_ntChange.R to 755 2024-09-24T18:01:37,254 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/run_workflows.py to 755 2024-09-24T18:01:37,255 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/vcfsorter.pl to 755 2024-09-24T18:01:37,255 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/run_somaticseq.py to 755 2024-09-24T18:01:37,256 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/somatic_tsv2vcf.py to 755 2024-09-24T18:01:37,257 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/somatic_vcf2tsv.py to 755 2024-09-24T18:01:37,257 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/somatic_xgboost.py to 755 2024-09-24T18:01:37,258 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/paired_end_bam2fastq.py to 755 2024-09-24T18:01:37,258 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/linguistic_sequence_complexity.py to 755 2024-09-24T18:01:37,259 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/split_bed_into_equal_regions.py to 755 2024-09-24T18:01:37,260 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/lociCounterWithLabels.py to 755 2024-09-24T18:01:37,260 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/single_sample_vcf2tsv.py to 755 2024-09-24T18:01:37,261 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/splitVcf.py to 755 2024-09-24T18:01:37,262 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/makeAlignmentScripts.py to 755 2024-09-24T18:01:37,262 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/variant_annotation.py to 755 2024-09-24T18:01:37,263 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.data/scripts/makeSomaticScripts.py to 755 2024-09-24T18:01:37,279 creating build/bdist.linux-armv7l/wheel/somaticseq-3.8.0.dist-info/WHEEL 2024-09-24T18:01:37,282 creating '/tmp/pip-wheel-z9ia5ngx/somaticseq-3.8.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-09-24T18:01:37,284 adding 'r_scripts/__init__.py' 2024-09-24T18:01:37,286 adding 'r_scripts/ada_cross_validation.R' 2024-09-24T18:01:37,287 adding 'r_scripts/ada_model_builder.R' 2024-09-24T18:01:37,289 adding 'r_scripts/ada_model_builder_ntChange.R' 2024-09-24T18:01:37,290 adding 'r_scripts/ada_model_predictor.R' 2024-09-24T18:01:37,292 adding 'somaticseq/__init__.py' 2024-09-24T18:01:37,294 adding 'somaticseq/_version.py' 2024-09-24T18:01:37,296 adding 'somaticseq/annotate_caller.py' 2024-09-24T18:01:37,298 adding 'somaticseq/bam_features.py' 2024-09-24T18:01:37,300 adding 'somaticseq/combine_callers.py' 2024-09-24T18:01:37,301 adding 'somaticseq/defaults.py' 2024-09-24T18:01:37,302 adding 'somaticseq/ntchange_type.py' 2024-09-24T18:01:37,306 adding 'somaticseq/run_somaticseq.py' 2024-09-24T18:01:37,308 adding 'somaticseq/sequencing_features.py' 2024-09-24T18:01:37,312 adding 'somaticseq/single_sample_vcf2tsv.py' 2024-09-24T18:01:37,315 adding 'somaticseq/somatic_tsv2vcf.py' 2024-09-24T18:01:37,319 adding 'somaticseq/somatic_vcf2tsv.py' 2024-09-24T18:01:37,321 adding 'somaticseq/somatic_xgboost.py' 2024-09-24T18:01:37,324 adding 'somaticseq/somaticseq_parallel.py' 2024-09-24T18:01:37,327 adding 'somaticseq/tsv2vcf.py' 2024-09-24T18:01:37,329 adding 'somaticseq/genomic_file_parsers/__init__.py' 2024-09-24T18:01:37,331 adding 'somaticseq/genomic_file_parsers/concat.py' 2024-09-24T18:01:37,334 adding 'somaticseq/genomic_file_parsers/genomic_file_handlers.py' 2024-09-24T18:01:37,336 adding 'somaticseq/genomic_file_parsers/pileup_reader.py' 2024-09-24T18:01:37,337 adding 'somaticseq/genomic_file_parsers/read_info_extractor.py' 2024-09-24T18:01:37,339 adding 'somaticseq/utilities/BAM_filter.py' 2024-09-24T18:01:37,340 adding 'somaticseq/utilities/__init__.py' 2024-09-24T18:01:37,342 adding 'somaticseq/utilities/attach_pileupVAF.py' 2024-09-24T18:01:37,344 adding 'somaticseq/utilities/bamQC.py' 2024-09-24T18:01:37,345 adding 'somaticseq/utilities/bedFileHandler.py' 2024-09-24T18:01:37,346 adding 'somaticseq/utilities/combo_callers_evaluator.py' 2024-09-24T18:01:37,348 adding 'somaticseq/utilities/filter_SomaticSeq_VCF.py' 2024-09-24T18:01:37,349 adding 'somaticseq/utilities/linguistic_sequence_complexity.py' 2024-09-24T18:01:37,351 adding 'somaticseq/utilities/lociCounterWithLabels.py' 2024-09-24T18:01:37,353 adding 'somaticseq/utilities/lociCounters.py' 2024-09-24T18:01:37,354 adding 'somaticseq/utilities/multi-nucleotide_phaser.py' 2024-09-24T18:01:37,356 adding 'somaticseq/utilities/paired_end_bam2fastq.py' 2024-09-24T18:01:37,357 adding 'somaticseq/utilities/plot_TPvsFP.py' 2024-09-24T18:01:37,359 adding 'somaticseq/utilities/reformat_VCF2SEQC2.py' 2024-09-24T18:01:37,360 adding 'somaticseq/utilities/remove_callers_from_somaticseq_tsv.py' 2024-09-24T18:01:37,362 adding 'somaticseq/utilities/split_bed_into_equal_regions.py' 2024-09-24T18:01:37,364 adding 'somaticseq/utilities/split_mergedBed.py' 2024-09-24T18:01:37,365 adding 'somaticseq/utilities/tally_MyVCF_vs_Truth.py' 2024-09-24T18:01:37,367 adding 'somaticseq/utilities/tally_variants_from_multiple_vcfs.py' 2024-09-24T18:01:37,369 adding 'somaticseq/utilities/trimSoftClippedReads.py' 2024-09-24T18:01:37,370 adding 'somaticseq/utilities/variant_annotation.py' 2024-09-24T18:01:37,372 adding 'somaticseq/utilities/dockered_pipelines/__init__.py' 2024-09-24T18:01:37,374 adding 'somaticseq/utilities/dockered_pipelines/container_option.py' 2024-09-24T18:01:37,376 adding 'somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py' 2024-09-24T18:01:37,378 adding 'somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py' 2024-09-24T18:01:37,380 adding 'somaticseq/utilities/dockered_pipelines/run_workflows.py' 2024-09-24T18:01:37,382 adding 'somaticseq/utilities/dockered_pipelines/tumor_normal_run.py' 2024-09-24T18:01:37,385 adding 'somaticseq/utilities/dockered_pipelines/tumor_only_run.py' 2024-09-24T18:01:37,387 adding 'somaticseq/utilities/dockered_pipelines/alignments/__init__.py' 2024-09-24T18:01:37,388 adding 'somaticseq/utilities/dockered_pipelines/alignments/align.py' 2024-09-24T18:01:37,390 adding 'somaticseq/utilities/dockered_pipelines/alignments/markdup.py' 2024-09-24T18:01:37,392 adding 'somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py' 2024-09-24T18:01:37,393 adding 'somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py' 2024-09-24T18:01:37,394 adding 'somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py' 2024-09-24T18:01:37,396 adding 'somaticseq/utilities/dockered_pipelines/alignments/trim.py' 2024-09-24T18:01:37,399 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py' 2024-09-24T18:01:37,400 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py' 2024-09-24T18:01:37,402 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py' 2024-09-24T18:01:37,403 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py' 2024-09-24T18:01:37,405 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py' 2024-09-24T18:01:37,406 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py' 2024-09-24T18:01:37,408 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py' 2024-09-24T18:01:37,409 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py' 2024-09-24T18:01:37,411 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py' 2024-09-24T18:01:37,413 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py' 2024-09-24T18:01:37,415 adding 'somaticseq/vcf_modifier/__init__.py' 2024-09-24T18:01:37,416 adding 'somaticseq/vcf_modifier/complex2indel.py' 2024-09-24T18:01:37,417 adding 'somaticseq/vcf_modifier/copy_TextFile.py' 2024-09-24T18:01:37,418 adding 'somaticseq/vcf_modifier/getUniqueVcfPositions.py' 2024-09-24T18:01:37,419 adding 'somaticseq/vcf_modifier/leftAlign.py' 2024-09-24T18:01:37,421 adding 'somaticseq/vcf_modifier/modify_JointSNVMix2.py' 2024-09-24T18:01:37,422 adding 'somaticseq/vcf_modifier/modify_MuTect.py' 2024-09-24T18:01:37,424 adding 'somaticseq/vcf_modifier/modify_MuTect2.py' 2024-09-24T18:01:37,425 adding 'somaticseq/vcf_modifier/modify_SomaticSniper.py' 2024-09-24T18:01:37,426 adding 'somaticseq/vcf_modifier/modify_Strelka.py' 2024-09-24T18:01:37,428 adding 'somaticseq/vcf_modifier/modify_VarDict.py' 2024-09-24T18:01:37,429 adding 'somaticseq/vcf_modifier/modify_VarScan2.py' 2024-09-24T18:01:37,431 adding 'somaticseq/vcf_modifier/modify_ssMuTect2.py' 2024-09-24T18:01:37,432 adding 'somaticseq/vcf_modifier/modify_ssStrelka.py' 2024-09-24T18:01:37,434 adding 'somaticseq/vcf_modifier/splitVcf.py' 2024-09-24T18:01:37,435 adding 'somaticseq/vcf_modifier/vcfIntersector.py' 2024-09-24T18:01:37,437 adding 'somaticseq-3.8.0.data/scripts/ada_model_builder_ntChange.R' 2024-09-24T18:01:37,439 adding 'somaticseq-3.8.0.data/scripts/ada_model_predictor.R' 2024-09-24T18:01:37,440 adding 'somaticseq-3.8.0.data/scripts/concat.py' 2024-09-24T18:01:37,441 adding 'somaticseq-3.8.0.data/scripts/linguistic_sequence_complexity.py' 2024-09-24T18:01:37,443 adding 'somaticseq-3.8.0.data/scripts/lociCounterWithLabels.py' 2024-09-24T18:01:37,445 adding 'somaticseq-3.8.0.data/scripts/makeAlignmentScripts.py' 2024-09-24T18:01:37,448 adding 'somaticseq-3.8.0.data/scripts/makeSomaticScripts.py' 2024-09-24T18:01:37,450 adding 'somaticseq-3.8.0.data/scripts/paired_end_bam2fastq.py' 2024-09-24T18:01:37,451 adding 'somaticseq-3.8.0.data/scripts/remove_callers_from_somaticseq_tsv.py' 2024-09-24T18:01:37,455 adding 'somaticseq-3.8.0.data/scripts/run_somaticseq.py' 2024-09-24T18:01:37,457 adding 'somaticseq-3.8.0.data/scripts/run_workflows.py' 2024-09-24T18:01:37,460 adding 'somaticseq-3.8.0.data/scripts/single_sample_vcf2tsv.py' 2024-09-24T18:01:37,463 adding 'somaticseq-3.8.0.data/scripts/somatic_tsv2vcf.py' 2024-09-24T18:01:37,467 adding 'somaticseq-3.8.0.data/scripts/somatic_vcf2tsv.py' 2024-09-24T18:01:37,469 adding 'somaticseq-3.8.0.data/scripts/somatic_xgboost.py' 2024-09-24T18:01:37,472 adding 'somaticseq-3.8.0.data/scripts/somaticseq_parallel.py' 2024-09-24T18:01:37,473 adding 'somaticseq-3.8.0.data/scripts/splitVcf.py' 2024-09-24T18:01:37,475 adding 'somaticseq-3.8.0.data/scripts/split_bed_into_equal_regions.py' 2024-09-24T18:01:37,477 adding 'somaticseq-3.8.0.data/scripts/tally_variants_from_multiple_vcfs.py' 2024-09-24T18:01:37,479 adding 'somaticseq-3.8.0.data/scripts/variant_annotation.py' 2024-09-24T18:01:37,480 adding 'somaticseq-3.8.0.data/scripts/vcfsorter.pl' 2024-09-24T18:01:37,482 adding 'somaticseq-3.8.0.dist-info/LICENSE.txt' 2024-09-24T18:01:37,484 adding 'somaticseq-3.8.0.dist-info/METADATA' 2024-09-24T18:01:37,486 adding 'somaticseq-3.8.0.dist-info/WHEEL' 2024-09-24T18:01:37,486 adding 'somaticseq-3.8.0.dist-info/top_level.txt' 2024-09-24T18:01:37,489 adding 'somaticseq-3.8.0.dist-info/RECORD' 2024-09-24T18:01:37,494 removing build/bdist.linux-armv7l/wheel 2024-09-24T18:01:37,633 Building wheel for somaticseq (setup.py): finished with status 'done' 2024-09-24T18:01:37,638 Created wheel for somaticseq: filename=somaticseq-3.8.0-py3-none-any.whl size=240613 sha256=02cf9678ebe683363a38a2bb89a4645fdc408e8c2f079693a2682e067e85523f 2024-09-24T18:01:37,639 Stored in directory: /tmp/pip-ephem-wheel-cache-widg8wga/wheels/a9/ac/0b/6abb6e8578eed4622aecd69499517ab6b6befce7462204f524 2024-09-24T18:01:37,654 Successfully built somaticseq 2024-09-24T18:01:37,665 Removed build tracker: '/tmp/pip-build-tracker-tledervy'