2024-02-13T22:04:43,998 Created temporary directory: /tmp/pip-build-tracker-o31_du1l 2024-02-13T22:04:43,999 Initialized build tracking at /tmp/pip-build-tracker-o31_du1l 2024-02-13T22:04:43,999 Created build tracker: /tmp/pip-build-tracker-o31_du1l 2024-02-13T22:04:44,000 Entered build tracker: /tmp/pip-build-tracker-o31_du1l 2024-02-13T22:04:44,001 Created temporary directory: /tmp/pip-wheel-b240ql53 2024-02-13T22:04:44,004 Created temporary directory: /tmp/pip-ephem-wheel-cache-qy_m75s3 2024-02-13T22:04:44,026 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-13T22:04:44,029 2 location(s) to search for versions of somaticseq: 2024-02-13T22:04:44,029 * https://pypi.org/simple/somaticseq/ 2024-02-13T22:04:44,029 * https://www.piwheels.org/simple/somaticseq/ 2024-02-13T22:04:44,030 Fetching project page and analyzing links: https://pypi.org/simple/somaticseq/ 2024-02-13T22:04:44,031 Getting page https://pypi.org/simple/somaticseq/ 2024-02-13T22:04:44,032 Found index url https://pypi.org/simple/ 2024-02-13T22:04:44,249 Fetched page https://pypi.org/simple/somaticseq/ as application/vnd.pypi.simple.v1+json 2024-02-13T22:04:44,250 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 2024-02-13T22:04:44,251 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 2024-02-13T22:04:44,252 Fetching project page and analyzing links: https://www.piwheels.org/simple/somaticseq/ 2024-02-13T22:04:44,252 Getting page https://www.piwheels.org/simple/somaticseq/ 2024-02-13T22:04:44,253 Found index url https://www.piwheels.org/simple/ 2024-02-13T22:04:44,415 Fetched page https://www.piwheels.org/simple/somaticseq/ as text/html 2024-02-13T22:04:44,416 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/) 2024-02-13T22:04:44,417 Skipping link: not a file: https://www.piwheels.org/simple/somaticseq/ 2024-02-13T22:04:44,417 Skipping link: not a file: https://pypi.org/simple/somaticseq/ 2024-02-13T22:04:44,436 Given no hashes to check 1 links for project 'somaticseq': discarding no candidates 2024-02-13T22:04:44,454 Collecting somaticseq==3.7.4 2024-02-13T22:04:44,456 Created temporary directory: /tmp/pip-unpack-t133jdc7 2024-02-13T22:04:44,671 Downloading somaticseq-3.7.4.tar.gz (129 kB) 2024-02-13T22:04:44,943 Added somaticseq==3.7.4 from https://files.pythonhosted.org/packages/17/b0/17d3cb01fae1f469ac27f88b2094e0918704cc402b4d0194ea6f1e32b800/somaticseq-3.7.4.tar.gz to build tracker '/tmp/pip-build-tracker-o31_du1l' 2024-02-13T22:04:44,945 Running setup.py (path:/tmp/pip-wheel-b240ql53/somaticseq_a80d72505e344d57926ba8ad6328bd20/setup.py) egg_info for package somaticseq 2024-02-13T22:04:44,945 Created temporary directory: /tmp/pip-pip-egg-info-jytd2dwg 2024-02-13T22:04:44,946 Preparing metadata (setup.py): started 2024-02-13T22:04:44,947 Running command python setup.py egg_info 2024-02-13T22:04:45,434 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-02-13T22:04:45,435 !! 2024-02-13T22:04:45,436 ******************************************************************************** 2024-02-13T22:04:45,436 Usage of dash-separated 'description-file' will not be supported in future 2024-02-13T22:04:45,437 versions. Please use the underscore name 'description_file' instead. 2024-02-13T22:04:45,438 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-02-13T22:04:45,439 or your builds will no longer be supported. 2024-02-13T22:04:45,440 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-02-13T22:04:45,441 ******************************************************************************** 2024-02-13T22:04:45,442 !! 2024-02-13T22:04:45,442 opt = self.warn_dash_deprecation(opt, section) 2024-02-13T22:04:45,950 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-02-13T22:04:45,950 !! 2024-02-13T22:04:45,951 ******************************************************************************** 2024-02-13T22:04:45,952 Usage of dash-separated 'description-file' will not be supported in future 2024-02-13T22:04:45,952 versions. Please use the underscore name 'description_file' instead. 2024-02-13T22:04:45,953 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-02-13T22:04:45,953 or your builds will no longer be supported. 2024-02-13T22:04:45,954 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-02-13T22:04:45,955 ******************************************************************************** 2024-02-13T22:04:45,955 !! 2024-02-13T22:04:45,956 opt = self.warn_dash_deprecation(opt, section) 2024-02-13T22:04:45,989 3.7.4 2024-02-13T22:04:45,989 running egg_info 2024-02-13T22:04:45,990 creating /tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info 2024-02-13T22:04:46,014 writing /tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/PKG-INFO 2024-02-13T22:04:46,018 writing dependency_links to /tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/dependency_links.txt 2024-02-13T22:04:46,019 writing requirements to /tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/requires.txt 2024-02-13T22:04:46,020 writing top-level names to /tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/top_level.txt 2024-02-13T22:04:46,022 writing manifest file '/tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/SOURCES.txt' 2024-02-13T22:04:46,133 reading manifest file '/tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/SOURCES.txt' 2024-02-13T22:04:46,134 adding license file 'LICENSE.txt' 2024-02-13T22:04:46,138 writing manifest file '/tmp/pip-pip-egg-info-jytd2dwg/somaticseq.egg-info/SOURCES.txt' 2024-02-13T22:04:46,246 Preparing metadata (setup.py): finished with status 'done' 2024-02-13T22:04:46,253 Source in /tmp/pip-wheel-b240ql53/somaticseq_a80d72505e344d57926ba8ad6328bd20 has version 3.7.4, which satisfies requirement somaticseq==3.7.4 from https://files.pythonhosted.org/packages/17/b0/17d3cb01fae1f469ac27f88b2094e0918704cc402b4d0194ea6f1e32b800/somaticseq-3.7.4.tar.gz 2024-02-13T22:04:46,254 Removed somaticseq==3.7.4 from https://files.pythonhosted.org/packages/17/b0/17d3cb01fae1f469ac27f88b2094e0918704cc402b4d0194ea6f1e32b800/somaticseq-3.7.4.tar.gz from build tracker '/tmp/pip-build-tracker-o31_du1l' 2024-02-13T22:04:46,260 Created temporary directory: /tmp/pip-unpack-ahhng_tf 2024-02-13T22:04:46,261 Created temporary directory: /tmp/pip-unpack-ke42r7t6 2024-02-13T22:04:46,269 Building wheels for collected packages: somaticseq 2024-02-13T22:04:46,273 Created temporary directory: /tmp/pip-wheel-ash_gb_8 2024-02-13T22:04:46,274 Building wheel for somaticseq (setup.py): started 2024-02-13T22:04:46,275 Destination directory: /tmp/pip-wheel-ash_gb_8 2024-02-13T22:04:46,276 Running command python setup.py bdist_wheel 2024-02-13T22:04:46,685 3.7.4 2024-02-13T22:04:46,722 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-02-13T22:04:46,723 !! 2024-02-13T22:04:46,724 ******************************************************************************** 2024-02-13T22:04:46,724 Usage of dash-separated 'description-file' will not be supported in future 2024-02-13T22:04:46,725 versions. Please use the underscore name 'description_file' instead. 2024-02-13T22:04:46,726 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-02-13T22:04:46,726 or your builds will no longer be supported. 2024-02-13T22:04:46,728 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-02-13T22:04:46,728 ******************************************************************************** 2024-02-13T22:04:46,729 !! 2024-02-13T22:04:46,729 opt = self.warn_dash_deprecation(opt, section) 2024-02-13T22:04:47,246 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:472: SetuptoolsDeprecationWarning: Invalid dash-separated options 2024-02-13T22:04:47,246 !! 2024-02-13T22:04:47,247 ******************************************************************************** 2024-02-13T22:04:47,248 Usage of dash-separated 'description-file' will not be supported in future 2024-02-13T22:04:47,248 versions. Please use the underscore name 'description_file' instead. 2024-02-13T22:04:47,249 By 2024-Sep-26, you need to update your project and remove deprecated calls 2024-02-13T22:04:47,249 or your builds will no longer be supported. 2024-02-13T22:04:47,251 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2024-02-13T22:04:47,251 ******************************************************************************** 2024-02-13T22:04:47,252 !! 2024-02-13T22:04:47,253 opt = self.warn_dash_deprecation(opt, section) 2024-02-13T22:04:47,278 running bdist_wheel 2024-02-13T22:04:47,373 running build 2024-02-13T22:04:47,374 running build_py 2024-02-13T22:04:47,400 creating build 2024-02-13T22:04:47,401 creating build/lib 2024-02-13T22:04:47,402 creating build/lib/r_scripts 2024-02-13T22:04:47,403 copying r_scripts/__init__.py -> build/lib/r_scripts 2024-02-13T22:04:47,405 creating build/lib/somaticseq 2024-02-13T22:04:47,406 copying somaticseq/ntchange_type.py -> build/lib/somaticseq 2024-02-13T22:04:47,408 copying somaticseq/annotate_caller.py -> build/lib/somaticseq 2024-02-13T22:04:47,411 copying somaticseq/run_somaticseq.py -> build/lib/somaticseq 2024-02-13T22:04:47,413 copying somaticseq/somatic_xgboost.py -> build/lib/somaticseq 2024-02-13T22:04:47,416 copying somaticseq/SSeq_tsv2vcf.py -> build/lib/somaticseq 2024-02-13T22:04:47,418 copying somaticseq/_version.py -> build/lib/somaticseq 2024-02-13T22:04:47,420 copying somaticseq/combine_callers.py -> build/lib/somaticseq 2024-02-13T22:04:47,423 copying somaticseq/somaticseq_parallel.py -> build/lib/somaticseq 2024-02-13T22:04:47,425 copying somaticseq/somatic_vcf2tsv.py -> build/lib/somaticseq 2024-02-13T22:04:47,428 copying somaticseq/sequencing_features.py -> build/lib/somaticseq 2024-02-13T22:04:47,431 copying somaticseq/__init__.py -> build/lib/somaticseq 2024-02-13T22:04:47,432 copying somaticseq/tsv2vcf.py -> build/lib/somaticseq 2024-02-13T22:04:47,435 copying somaticseq/single_sample_vcf2tsv.py -> build/lib/somaticseq 2024-02-13T22:04:47,439 creating build/lib/somaticseq/utilities 2024-02-13T22:04:47,440 copying somaticseq/utilities/bamQC.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,442 copying somaticseq/utilities/split_Bed_into_equal_regions.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,445 copying somaticseq/utilities/filter_SomaticSeq_VCF.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,447 copying somaticseq/utilities/linguistic_sequence_complexity.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,448 copying somaticseq/utilities/bedFileHandler.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,450 copying somaticseq/utilities/BAM_filter.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,452 copying somaticseq/utilities/reformat_VCF2SEQC2.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,454 copying somaticseq/utilities/attach_pileupVAF.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,457 copying somaticseq/utilities/trimSoftClippedReads.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,459 copying somaticseq/utilities/multi-nucleotide_phaser.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,461 copying somaticseq/utilities/plot_TPvsFP.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,463 copying somaticseq/utilities/paired_end_bam2fastq.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,465 copying somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,467 copying somaticseq/utilities/combo_callers_evaluator.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,468 copying somaticseq/utilities/lociCounterWithLabels.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,471 copying somaticseq/utilities/variant_annotation.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,472 copying somaticseq/utilities/tally_MyVCF_vs_Truth.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,475 copying somaticseq/utilities/__init__.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,476 copying somaticseq/utilities/lociCounters.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,478 copying somaticseq/utilities/split_mergedBed.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,480 copying somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/lib/somaticseq/utilities 2024-02-13T22:04:47,483 creating build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,484 copying somaticseq/vcfModifier/modify_VarDict.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,487 copying somaticseq/vcfModifier/modify_JointSNVMix2.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,488 copying somaticseq/vcfModifier/copy_TextFile.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,490 copying somaticseq/vcfModifier/getUniqueVcfPositions.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,492 copying somaticseq/vcfModifier/modify_MuTect2.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,494 copying somaticseq/vcfModifier/modify_ssMuTect2.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,496 copying somaticseq/vcfModifier/vcfIntersector.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,498 copying somaticseq/vcfModifier/splitVcf.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,500 copying somaticseq/vcfModifier/modify_SomaticSniper.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,502 copying somaticseq/vcfModifier/modify_ssStrelka.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,504 copying somaticseq/vcfModifier/leftAlign.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,506 copying somaticseq/vcfModifier/complex2indel.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,507 copying somaticseq/vcfModifier/modify_Strelka.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,509 copying somaticseq/vcfModifier/modify_MuTect.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,511 copying somaticseq/vcfModifier/modify_VarScan2.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,513 copying somaticseq/vcfModifier/__init__.py -> build/lib/somaticseq/vcfModifier 2024-02-13T22:04:47,515 creating build/lib/somaticseq/genomicFileHandler 2024-02-13T22:04:47,516 copying somaticseq/genomicFileHandler/read_info_extractor.py -> build/lib/somaticseq/genomicFileHandler 2024-02-13T22:04:47,518 copying somaticseq/genomicFileHandler/genomic_file_handlers.py -> build/lib/somaticseq/genomicFileHandler 2024-02-13T22:04:47,521 copying somaticseq/genomicFileHandler/pileup_reader.py -> build/lib/somaticseq/genomicFileHandler 2024-02-13T22:04:47,523 copying somaticseq/genomicFileHandler/concat.py -> build/lib/somaticseq/genomicFileHandler 2024-02-13T22:04:47,525 copying somaticseq/genomicFileHandler/__init__.py -> build/lib/somaticseq/genomicFileHandler 2024-02-13T22:04:47,528 creating build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,529 copying somaticseq/utilities/dockered_pipelines/container_option.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,531 copying somaticseq/utilities/dockered_pipelines/tumor_only_run.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,534 copying somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,536 copying somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,538 copying somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,541 copying somaticseq/utilities/dockered_pipelines/tumor_normal_run.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,543 copying somaticseq/utilities/dockered_pipelines/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,545 creating build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,546 copying somaticseq/utilities/dockered_pipelines/alignments/markdup.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,548 copying somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,550 copying somaticseq/utilities/dockered_pipelines/alignments/trim.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,553 copying somaticseq/utilities/dockered_pipelines/alignments/align.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,555 copying somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,557 copying somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,559 copying somaticseq/utilities/dockered_pipelines/alignments/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,561 creating build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,562 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,564 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,567 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,569 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,571 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,574 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,577 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,580 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,582 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,585 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,594 copying r_scripts/ada_cross_validation.R -> build/lib/r_scripts 2024-02-13T22:04:47,597 copying r_scripts/xgboost_model_builder_ntChange.R -> build/lib/r_scripts 2024-02-13T22:04:47,599 copying r_scripts/xgboost_model_predictor.R -> build/lib/r_scripts 2024-02-13T22:04:47,601 copying r_scripts/ada_model_builder.R -> build/lib/r_scripts 2024-02-13T22:04:47,603 copying r_scripts/ada_model_predictor.R -> build/lib/r_scripts 2024-02-13T22:04:47,605 copying r_scripts/ada_model_builder_ntChange.R -> build/lib/r_scripts 2024-02-13T22:04:47,612 running build_scripts 2024-02-13T22:04:47,613 creating build/scripts-3.11 2024-02-13T22:04:47,614 copying and adjusting somaticseq/somaticseq_parallel.py -> build/scripts-3.11 2024-02-13T22:04:47,616 copying and adjusting somaticseq/run_somaticseq.py -> build/scripts-3.11 2024-02-13T22:04:47,619 copying and adjusting somaticseq/single_sample_vcf2tsv.py -> build/scripts-3.11 2024-02-13T22:04:47,623 copying and adjusting somaticseq/somatic_vcf2tsv.py -> build/scripts-3.11 2024-02-13T22:04:47,626 copying and adjusting somaticseq/somatic_xgboost.py -> build/scripts-3.11 2024-02-13T22:04:47,628 copying and adjusting somaticseq/SSeq_tsv2vcf.py -> build/scripts-3.11 2024-02-13T22:04:47,631 copying and adjusting somaticseq/genomicFileHandler/concat.py -> build/scripts-3.11 2024-02-13T22:04:47,633 copying and adjusting somaticseq/utilities/linguistic_sequence_complexity.py -> build/scripts-3.11 2024-02-13T22:04:47,635 copying and adjusting somaticseq/utilities/lociCounterWithLabels.py -> build/scripts-3.11 2024-02-13T22:04:47,637 copying and adjusting somaticseq/utilities/paired_end_bam2fastq.py -> build/scripts-3.11 2024-02-13T22:04:47,639 copying and adjusting somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/scripts-3.11 2024-02-13T22:04:47,640 copying and adjusting somaticseq/utilities/split_Bed_into_equal_regions.py -> build/scripts-3.11 2024-02-13T22:04:47,642 copying and adjusting somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/scripts-3.11 2024-02-13T22:04:47,644 copying and adjusting somaticseq/utilities/variant_annotation.py -> build/scripts-3.11 2024-02-13T22:04:47,646 copying somaticseq/utilities/vcfsorter.pl -> build/scripts-3.11 2024-02-13T22:04:47,648 copying and adjusting somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/scripts-3.11 2024-02-13T22:04:47,651 copying and adjusting somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/scripts-3.11 2024-02-13T22:04:47,653 copying and adjusting somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/scripts-3.11 2024-02-13T22:04:47,655 copying and adjusting somaticseq/vcfModifier/splitVcf.py -> build/scripts-3.11 2024-02-13T22:04:47,658 copying r_scripts/ada_model_builder_ntChange.R -> build/scripts-3.11 2024-02-13T22:04:47,660 copying r_scripts/ada_model_predictor.R -> build/scripts-3.11 2024-02-13T22:04:47,661 changing mode of build/scripts-3.11/somaticseq_parallel.py from 644 to 755 2024-02-13T22:04:47,662 changing mode of build/scripts-3.11/run_somaticseq.py from 644 to 755 2024-02-13T22:04:47,662 changing mode of build/scripts-3.11/single_sample_vcf2tsv.py from 644 to 755 2024-02-13T22:04:47,663 changing mode of build/scripts-3.11/somatic_vcf2tsv.py from 644 to 755 2024-02-13T22:04:47,663 changing mode of build/scripts-3.11/somatic_xgboost.py from 644 to 755 2024-02-13T22:04:47,664 changing mode of build/scripts-3.11/SSeq_tsv2vcf.py from 644 to 755 2024-02-13T22:04:47,664 changing mode of build/scripts-3.11/concat.py from 644 to 755 2024-02-13T22:04:47,665 changing mode of build/scripts-3.11/linguistic_sequence_complexity.py from 644 to 755 2024-02-13T22:04:47,665 changing mode of build/scripts-3.11/lociCounterWithLabels.py from 644 to 755 2024-02-13T22:04:47,666 changing mode of build/scripts-3.11/paired_end_bam2fastq.py from 644 to 755 2024-02-13T22:04:47,667 changing mode of build/scripts-3.11/remove_callers_from_somaticseq_tsv.py from 644 to 755 2024-02-13T22:04:47,667 changing mode of build/scripts-3.11/split_Bed_into_equal_regions.py from 644 to 755 2024-02-13T22:04:47,668 changing mode of build/scripts-3.11/tally_variants_from_multiple_vcfs.py from 644 to 755 2024-02-13T22:04:47,669 changing mode of build/scripts-3.11/variant_annotation.py from 644 to 755 2024-02-13T22:04:47,669 changing mode of build/scripts-3.11/makeAlignmentScripts.py from 644 to 755 2024-02-13T22:04:47,670 changing mode of build/scripts-3.11/makeSomaticScripts.py from 644 to 755 2024-02-13T22:04:47,670 changing mode of build/scripts-3.11/run_workflows.py from 644 to 755 2024-02-13T22:04:47,671 changing mode of build/scripts-3.11/splitVcf.py from 644 to 755 2024-02-13T22:04:47,695 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-02-13T22:04:47,695 !! 2024-02-13T22:04:47,696 ******************************************************************************** 2024-02-13T22:04:47,697 Please avoid running ``setup.py`` directly. 2024-02-13T22:04:47,697 Instead, use pypa/build, pypa/installer or other 2024-02-13T22:04:47,698 standards-based tools. 2024-02-13T22:04:47,699 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-02-13T22:04:47,699 ******************************************************************************** 2024-02-13T22:04:47,700 !! 2024-02-13T22:04:47,700 self.initialize_options() 2024-02-13T22:04:47,722 installing to build/bdist.linux-armv7l/wheel 2024-02-13T22:04:47,723 running install 2024-02-13T22:04:47,746 running install_lib 2024-02-13T22:04:47,771 creating build/bdist.linux-armv7l 2024-02-13T22:04:47,771 creating build/bdist.linux-armv7l/wheel 2024-02-13T22:04:47,773 creating build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,774 copying build/lib/r_scripts/ada_cross_validation.R -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,776 copying build/lib/r_scripts/xgboost_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,778 copying build/lib/r_scripts/xgboost_model_predictor.R -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,780 copying build/lib/r_scripts/ada_model_builder.R -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,782 copying build/lib/r_scripts/ada_model_predictor.R -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,783 copying build/lib/r_scripts/__init__.py -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,785 copying build/lib/r_scripts/ada_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/r_scripts 2024-02-13T22:04:47,787 creating build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,789 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,790 copying build/lib/somaticseq/utilities/bamQC.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,793 copying build/lib/somaticseq/utilities/split_Bed_into_equal_regions.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,795 copying build/lib/somaticseq/utilities/filter_SomaticSeq_VCF.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,798 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,799 copying build/lib/somaticseq/utilities/dockered_pipelines/container_option.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,801 copying build/lib/somaticseq/utilities/dockered_pipelines/tumor_only_run.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,804 copying build/lib/somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,806 copying build/lib/somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,809 copying build/lib/somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,812 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,813 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/markdup.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,816 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,817 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/trim.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,820 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/align.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,822 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,824 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,826 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2024-02-13T22:04:47,828 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,829 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,831 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,833 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,836 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,838 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,840 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,843 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,845 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,847 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,850 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2024-02-13T22:04:47,851 copying build/lib/somaticseq/utilities/dockered_pipelines/tumor_normal_run.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,854 copying build/lib/somaticseq/utilities/dockered_pipelines/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2024-02-13T22:04:47,856 copying build/lib/somaticseq/utilities/linguistic_sequence_complexity.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,858 copying build/lib/somaticseq/utilities/bedFileHandler.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,859 copying build/lib/somaticseq/utilities/BAM_filter.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,861 copying build/lib/somaticseq/utilities/reformat_VCF2SEQC2.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,863 copying build/lib/somaticseq/utilities/attach_pileupVAF.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,865 copying build/lib/somaticseq/utilities/trimSoftClippedReads.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,867 copying build/lib/somaticseq/utilities/multi-nucleotide_phaser.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,869 copying build/lib/somaticseq/utilities/plot_TPvsFP.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,872 copying build/lib/somaticseq/utilities/paired_end_bam2fastq.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,873 copying build/lib/somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,875 copying build/lib/somaticseq/utilities/combo_callers_evaluator.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,877 copying build/lib/somaticseq/utilities/lociCounterWithLabels.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,879 copying build/lib/somaticseq/utilities/variant_annotation.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,881 copying build/lib/somaticseq/utilities/tally_MyVCF_vs_Truth.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,883 copying build/lib/somaticseq/utilities/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,885 copying build/lib/somaticseq/utilities/lociCounters.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,887 copying build/lib/somaticseq/utilities/split_mergedBed.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,889 copying build/lib/somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/bdist.linux-armv7l/wheel/somaticseq/utilities 2024-02-13T22:04:47,891 copying build/lib/somaticseq/ntchange_type.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,894 creating build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,895 copying build/lib/somaticseq/vcfModifier/modify_VarDict.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,898 copying build/lib/somaticseq/vcfModifier/modify_JointSNVMix2.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,900 copying build/lib/somaticseq/vcfModifier/copy_TextFile.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,902 copying build/lib/somaticseq/vcfModifier/getUniqueVcfPositions.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,904 copying build/lib/somaticseq/vcfModifier/modify_MuTect2.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,906 copying build/lib/somaticseq/vcfModifier/modify_ssMuTect2.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,909 copying build/lib/somaticseq/vcfModifier/vcfIntersector.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,910 copying build/lib/somaticseq/vcfModifier/splitVcf.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,912 copying build/lib/somaticseq/vcfModifier/modify_SomaticSniper.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,914 copying build/lib/somaticseq/vcfModifier/modify_ssStrelka.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,916 copying build/lib/somaticseq/vcfModifier/leftAlign.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,918 copying build/lib/somaticseq/vcfModifier/complex2indel.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,919 copying build/lib/somaticseq/vcfModifier/modify_Strelka.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,921 copying build/lib/somaticseq/vcfModifier/modify_MuTect.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,923 copying build/lib/somaticseq/vcfModifier/modify_VarScan2.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,925 copying build/lib/somaticseq/vcfModifier/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq/vcfModifier 2024-02-13T22:04:47,927 copying build/lib/somaticseq/annotate_caller.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,929 copying build/lib/somaticseq/run_somaticseq.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,932 copying build/lib/somaticseq/somatic_xgboost.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,934 copying build/lib/somaticseq/SSeq_tsv2vcf.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,937 copying build/lib/somaticseq/_version.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,939 creating build/bdist.linux-armv7l/wheel/somaticseq/genomicFileHandler 2024-02-13T22:04:47,940 copying build/lib/somaticseq/genomicFileHandler/read_info_extractor.py -> build/bdist.linux-armv7l/wheel/somaticseq/genomicFileHandler 2024-02-13T22:04:47,942 copying build/lib/somaticseq/genomicFileHandler/genomic_file_handlers.py -> build/bdist.linux-armv7l/wheel/somaticseq/genomicFileHandler 2024-02-13T22:04:47,945 copying build/lib/somaticseq/genomicFileHandler/pileup_reader.py -> build/bdist.linux-armv7l/wheel/somaticseq/genomicFileHandler 2024-02-13T22:04:47,947 copying build/lib/somaticseq/genomicFileHandler/concat.py -> build/bdist.linux-armv7l/wheel/somaticseq/genomicFileHandler 2024-02-13T22:04:47,949 copying build/lib/somaticseq/genomicFileHandler/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq/genomicFileHandler 2024-02-13T22:04:47,951 copying build/lib/somaticseq/combine_callers.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,954 copying build/lib/somaticseq/somaticseq_parallel.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,956 copying build/lib/somaticseq/somatic_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,959 copying build/lib/somaticseq/sequencing_features.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,961 copying build/lib/somaticseq/__init__.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,963 copying build/lib/somaticseq/tsv2vcf.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,966 copying build/lib/somaticseq/single_sample_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq 2024-02-13T22:04:47,968 running install_egg_info 2024-02-13T22:04:48,027 running egg_info 2024-02-13T22:04:48,051 writing somaticseq.egg-info/PKG-INFO 2024-02-13T22:04:48,055 writing dependency_links to somaticseq.egg-info/dependency_links.txt 2024-02-13T22:04:48,057 writing requirements to somaticseq.egg-info/requires.txt 2024-02-13T22:04:48,058 writing top-level names to somaticseq.egg-info/top_level.txt 2024-02-13T22:04:48,095 reading manifest file 'somaticseq.egg-info/SOURCES.txt' 2024-02-13T22:04:48,098 adding license file 'LICENSE.txt' 2024-02-13T22:04:48,104 writing manifest file 'somaticseq.egg-info/SOURCES.txt' 2024-02-13T22:04:48,106 Copying somaticseq.egg-info to build/bdist.linux-armv7l/wheel/somaticseq-3.7.4-py3.11.egg-info 2024-02-13T22:04:48,118 running install_scripts 2024-02-13T22:04:48,120 creating build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data 2024-02-13T22:04:48,121 creating build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,122 copying build/scripts-3.11/run_workflows.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,124 copying build/scripts-3.11/splitVcf.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,127 copying build/scripts-3.11/split_Bed_into_equal_regions.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,130 copying build/scripts-3.11/makeAlignmentScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,133 copying build/scripts-3.11/run_somaticseq.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,136 copying build/scripts-3.11/linguistic_sequence_complexity.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,139 copying build/scripts-3.11/somatic_xgboost.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,142 copying build/scripts-3.11/SSeq_tsv2vcf.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,145 copying build/scripts-3.11/paired_end_bam2fastq.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,147 copying build/scripts-3.11/makeSomaticScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,151 copying build/scripts-3.11/somaticseq_parallel.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,154 copying build/scripts-3.11/remove_callers_from_somaticseq_tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,156 copying build/scripts-3.11/somatic_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,159 copying build/scripts-3.11/ada_model_predictor.R -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,162 copying build/scripts-3.11/concat.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,164 copying build/scripts-3.11/lociCounterWithLabels.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,167 copying build/scripts-3.11/variant_annotation.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,169 copying build/scripts-3.11/vcfsorter.pl -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,171 copying build/scripts-3.11/ada_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,173 copying build/scripts-3.11/tally_variants_from_multiple_vcfs.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,176 copying build/scripts-3.11/single_sample_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts 2024-02-13T22:04:48,179 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/run_workflows.py to 755 2024-02-13T22:04:48,180 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/splitVcf.py to 755 2024-02-13T22:04:48,181 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/split_Bed_into_equal_regions.py to 755 2024-02-13T22:04:48,181 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/makeAlignmentScripts.py to 755 2024-02-13T22:04:48,182 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/run_somaticseq.py to 755 2024-02-13T22:04:48,183 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/linguistic_sequence_complexity.py to 755 2024-02-13T22:04:48,183 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/somatic_xgboost.py to 755 2024-02-13T22:04:48,184 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/SSeq_tsv2vcf.py to 755 2024-02-13T22:04:48,185 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/paired_end_bam2fastq.py to 755 2024-02-13T22:04:48,186 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/makeSomaticScripts.py to 755 2024-02-13T22:04:48,186 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/somaticseq_parallel.py to 755 2024-02-13T22:04:48,187 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/remove_callers_from_somaticseq_tsv.py to 755 2024-02-13T22:04:48,187 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/somatic_vcf2tsv.py to 755 2024-02-13T22:04:48,188 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/ada_model_predictor.R to 755 2024-02-13T22:04:48,188 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/concat.py to 755 2024-02-13T22:04:48,189 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/lociCounterWithLabels.py to 755 2024-02-13T22:04:48,189 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/variant_annotation.py to 755 2024-02-13T22:04:48,190 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/vcfsorter.pl to 755 2024-02-13T22:04:48,191 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/ada_model_builder_ntChange.R to 755 2024-02-13T22:04:48,191 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/tally_variants_from_multiple_vcfs.py to 755 2024-02-13T22:04:48,192 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.data/scripts/single_sample_vcf2tsv.py to 755 2024-02-13T22:04:48,208 creating build/bdist.linux-armv7l/wheel/somaticseq-3.7.4.dist-info/WHEEL 2024-02-13T22:04:48,211 creating '/tmp/pip-wheel-ash_gb_8/somaticseq-3.7.4-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-02-13T22:04:48,213 adding 'r_scripts/__init__.py' 2024-02-13T22:04:48,214 adding 'r_scripts/ada_cross_validation.R' 2024-02-13T22:04:48,216 adding 'r_scripts/ada_model_builder.R' 2024-02-13T22:04:48,217 adding 'r_scripts/ada_model_builder_ntChange.R' 2024-02-13T22:04:48,218 adding 'r_scripts/ada_model_predictor.R' 2024-02-13T22:04:48,220 adding 'r_scripts/xgboost_model_builder_ntChange.R' 2024-02-13T22:04:48,221 adding 'r_scripts/xgboost_model_predictor.R' 2024-02-13T22:04:48,225 adding 'somaticseq/SSeq_tsv2vcf.py' 2024-02-13T22:04:48,226 adding 'somaticseq/__init__.py' 2024-02-13T22:04:48,227 adding 'somaticseq/_version.py' 2024-02-13T22:04:48,229 adding 'somaticseq/annotate_caller.py' 2024-02-13T22:04:48,232 adding 'somaticseq/combine_callers.py' 2024-02-13T22:04:48,233 adding 'somaticseq/ntchange_type.py' 2024-02-13T22:04:48,236 adding 'somaticseq/run_somaticseq.py' 2024-02-13T22:04:48,238 adding 'somaticseq/sequencing_features.py' 2024-02-13T22:04:48,242 adding 'somaticseq/single_sample_vcf2tsv.py' 2024-02-13T22:04:48,246 adding 'somaticseq/somatic_vcf2tsv.py' 2024-02-13T22:04:48,248 adding 'somaticseq/somatic_xgboost.py' 2024-02-13T22:04:48,250 adding 'somaticseq/somaticseq_parallel.py' 2024-02-13T22:04:48,253 adding 'somaticseq/tsv2vcf.py' 2024-02-13T22:04:48,254 adding 'somaticseq/genomicFileHandler/__init__.py' 2024-02-13T22:04:48,256 adding 'somaticseq/genomicFileHandler/concat.py' 2024-02-13T22:04:48,258 adding 'somaticseq/genomicFileHandler/genomic_file_handlers.py' 2024-02-13T22:04:48,260 adding 'somaticseq/genomicFileHandler/pileup_reader.py' 2024-02-13T22:04:48,262 adding 'somaticseq/genomicFileHandler/read_info_extractor.py' 2024-02-13T22:04:48,264 adding 'somaticseq/utilities/BAM_filter.py' 2024-02-13T22:04:48,265 adding 'somaticseq/utilities/__init__.py' 2024-02-13T22:04:48,267 adding 'somaticseq/utilities/attach_pileupVAF.py' 2024-02-13T22:04:48,269 adding 'somaticseq/utilities/bamQC.py' 2024-02-13T22:04:48,270 adding 'somaticseq/utilities/bedFileHandler.py' 2024-02-13T22:04:48,271 adding 'somaticseq/utilities/combo_callers_evaluator.py' 2024-02-13T22:04:48,273 adding 'somaticseq/utilities/filter_SomaticSeq_VCF.py' 2024-02-13T22:04:48,274 adding 'somaticseq/utilities/linguistic_sequence_complexity.py' 2024-02-13T22:04:48,276 adding 'somaticseq/utilities/lociCounterWithLabels.py' 2024-02-13T22:04:48,277 adding 'somaticseq/utilities/lociCounters.py' 2024-02-13T22:04:48,279 adding 'somaticseq/utilities/multi-nucleotide_phaser.py' 2024-02-13T22:04:48,280 adding 'somaticseq/utilities/paired_end_bam2fastq.py' 2024-02-13T22:04:48,282 adding 'somaticseq/utilities/plot_TPvsFP.py' 2024-02-13T22:04:48,284 adding 'somaticseq/utilities/reformat_VCF2SEQC2.py' 2024-02-13T22:04:48,285 adding 'somaticseq/utilities/remove_callers_from_somaticseq_tsv.py' 2024-02-13T22:04:48,287 adding 'somaticseq/utilities/split_Bed_into_equal_regions.py' 2024-02-13T22:04:48,288 adding 'somaticseq/utilities/split_mergedBed.py' 2024-02-13T22:04:48,290 adding 'somaticseq/utilities/tally_MyVCF_vs_Truth.py' 2024-02-13T22:04:48,292 adding 'somaticseq/utilities/tally_variants_from_multiple_vcfs.py' 2024-02-13T22:04:48,293 adding 'somaticseq/utilities/trimSoftClippedReads.py' 2024-02-13T22:04:48,295 adding 'somaticseq/utilities/variant_annotation.py' 2024-02-13T22:04:48,296 adding 'somaticseq/utilities/dockered_pipelines/__init__.py' 2024-02-13T22:04:48,298 adding 'somaticseq/utilities/dockered_pipelines/container_option.py' 2024-02-13T22:04:48,300 adding 'somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py' 2024-02-13T22:04:48,302 adding 'somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py' 2024-02-13T22:04:48,304 adding 'somaticseq/utilities/dockered_pipelines/run_workflows.py' 2024-02-13T22:04:48,306 adding 'somaticseq/utilities/dockered_pipelines/tumor_normal_run.py' 2024-02-13T22:04:48,309 adding 'somaticseq/utilities/dockered_pipelines/tumor_only_run.py' 2024-02-13T22:04:48,310 adding 'somaticseq/utilities/dockered_pipelines/alignments/__init__.py' 2024-02-13T22:04:48,312 adding 'somaticseq/utilities/dockered_pipelines/alignments/align.py' 2024-02-13T22:04:48,314 adding 'somaticseq/utilities/dockered_pipelines/alignments/markdup.py' 2024-02-13T22:04:48,315 adding 'somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py' 2024-02-13T22:04:48,317 adding 'somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py' 2024-02-13T22:04:48,318 adding 'somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py' 2024-02-13T22:04:48,320 adding 'somaticseq/utilities/dockered_pipelines/alignments/trim.py' 2024-02-13T22:04:48,322 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py' 2024-02-13T22:04:48,323 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py' 2024-02-13T22:04:48,325 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py' 2024-02-13T22:04:48,326 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py' 2024-02-13T22:04:48,328 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py' 2024-02-13T22:04:48,329 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py' 2024-02-13T22:04:48,331 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py' 2024-02-13T22:04:48,332 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py' 2024-02-13T22:04:48,334 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py' 2024-02-13T22:04:48,335 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py' 2024-02-13T22:04:48,337 adding 'somaticseq/vcfModifier/__init__.py' 2024-02-13T22:04:48,338 adding 'somaticseq/vcfModifier/complex2indel.py' 2024-02-13T22:04:48,339 adding 'somaticseq/vcfModifier/copy_TextFile.py' 2024-02-13T22:04:48,341 adding 'somaticseq/vcfModifier/getUniqueVcfPositions.py' 2024-02-13T22:04:48,342 adding 'somaticseq/vcfModifier/leftAlign.py' 2024-02-13T22:04:48,343 adding 'somaticseq/vcfModifier/modify_JointSNVMix2.py' 2024-02-13T22:04:48,345 adding 'somaticseq/vcfModifier/modify_MuTect.py' 2024-02-13T22:04:48,346 adding 'somaticseq/vcfModifier/modify_MuTect2.py' 2024-02-13T22:04:48,348 adding 'somaticseq/vcfModifier/modify_SomaticSniper.py' 2024-02-13T22:04:48,349 adding 'somaticseq/vcfModifier/modify_Strelka.py' 2024-02-13T22:04:48,350 adding 'somaticseq/vcfModifier/modify_VarDict.py' 2024-02-13T22:04:48,352 adding 'somaticseq/vcfModifier/modify_VarScan2.py' 2024-02-13T22:04:48,353 adding 'somaticseq/vcfModifier/modify_ssMuTect2.py' 2024-02-13T22:04:48,355 adding 'somaticseq/vcfModifier/modify_ssStrelka.py' 2024-02-13T22:04:48,356 adding 'somaticseq/vcfModifier/splitVcf.py' 2024-02-13T22:04:48,357 adding 'somaticseq/vcfModifier/vcfIntersector.py' 2024-02-13T22:04:48,361 adding 'somaticseq-3.7.4.data/scripts/SSeq_tsv2vcf.py' 2024-02-13T22:04:48,362 adding 'somaticseq-3.7.4.data/scripts/ada_model_builder_ntChange.R' 2024-02-13T22:04:48,364 adding 'somaticseq-3.7.4.data/scripts/ada_model_predictor.R' 2024-02-13T22:04:48,365 adding 'somaticseq-3.7.4.data/scripts/concat.py' 2024-02-13T22:04:48,367 adding 'somaticseq-3.7.4.data/scripts/linguistic_sequence_complexity.py' 2024-02-13T22:04:48,368 adding 'somaticseq-3.7.4.data/scripts/lociCounterWithLabels.py' 2024-02-13T22:04:48,370 adding 'somaticseq-3.7.4.data/scripts/makeAlignmentScripts.py' 2024-02-13T22:04:48,373 adding 'somaticseq-3.7.4.data/scripts/makeSomaticScripts.py' 2024-02-13T22:04:48,374 adding 'somaticseq-3.7.4.data/scripts/paired_end_bam2fastq.py' 2024-02-13T22:04:48,376 adding 'somaticseq-3.7.4.data/scripts/remove_callers_from_somaticseq_tsv.py' 2024-02-13T22:04:48,379 adding 'somaticseq-3.7.4.data/scripts/run_somaticseq.py' 2024-02-13T22:04:48,381 adding 'somaticseq-3.7.4.data/scripts/run_workflows.py' 2024-02-13T22:04:48,384 adding 'somaticseq-3.7.4.data/scripts/single_sample_vcf2tsv.py' 2024-02-13T22:04:48,389 adding 'somaticseq-3.7.4.data/scripts/somatic_vcf2tsv.py' 2024-02-13T22:04:48,391 adding 'somaticseq-3.7.4.data/scripts/somatic_xgboost.py' 2024-02-13T22:04:48,392 adding 'somaticseq-3.7.4.data/scripts/somaticseq_parallel.py' 2024-02-13T22:04:48,394 adding 'somaticseq-3.7.4.data/scripts/splitVcf.py' 2024-02-13T22:04:48,396 adding 'somaticseq-3.7.4.data/scripts/split_Bed_into_equal_regions.py' 2024-02-13T22:04:48,398 adding 'somaticseq-3.7.4.data/scripts/tally_variants_from_multiple_vcfs.py' 2024-02-13T22:04:48,399 adding 'somaticseq-3.7.4.data/scripts/variant_annotation.py' 2024-02-13T22:04:48,401 adding 'somaticseq-3.7.4.data/scripts/vcfsorter.pl' 2024-02-13T22:04:48,403 adding 'somaticseq-3.7.4.dist-info/LICENSE.txt' 2024-02-13T22:04:48,405 adding 'somaticseq-3.7.4.dist-info/METADATA' 2024-02-13T22:04:48,406 adding 'somaticseq-3.7.4.dist-info/WHEEL' 2024-02-13T22:04:48,407 adding 'somaticseq-3.7.4.dist-info/top_level.txt' 2024-02-13T22:04:48,409 adding 'somaticseq-3.7.4.dist-info/RECORD' 2024-02-13T22:04:48,414 removing build/bdist.linux-armv7l/wheel 2024-02-13T22:04:48,549 Building wheel for somaticseq (setup.py): finished with status 'done' 2024-02-13T22:04:48,554 Created wheel for somaticseq: filename=somaticseq-3.7.4-py3-none-any.whl size=236061 sha256=2ab6487255fe614e97cf1e771576df0f07771a923286483c3f16a551897d9294 2024-02-13T22:04:48,555 Stored in directory: /tmp/pip-ephem-wheel-cache-qy_m75s3/wheels/0a/1e/3b/fd6fe8d1a4e4ecf3d9a1e321e3854ee124ee0ed7d1a67b717c 2024-02-13T22:04:48,571 Successfully built somaticseq 2024-02-13T22:04:48,583 Removed build tracker: '/tmp/pip-build-tracker-o31_du1l'