2025-09-22T13:41:44,857 Created temporary directory: /tmp/pip-ephem-wheel-cache-h3tajzl0 2025-09-22T13:41:44,859 Created temporary directory: /tmp/pip-build-tracker-gsr1g1wb 2025-09-22T13:41:44,860 Initialized build tracking at /tmp/pip-build-tracker-gsr1g1wb 2025-09-22T13:41:44,860 Created build tracker: /tmp/pip-build-tracker-gsr1g1wb 2025-09-22T13:41:44,861 Entered build tracker: /tmp/pip-build-tracker-gsr1g1wb 2025-09-22T13:41:44,861 Created temporary directory: /tmp/pip-wheel-k34tlyx0 2025-09-22T13:41:44,865 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2025-09-22T13:41:44,867 Created temporary directory: /tmp/pip-ephem-wheel-cache-o1ces9ni 2025-09-22T13:41:44,889 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-22T13:41:44,892 2 location(s) to search for versions of pbiotools: 2025-09-22T13:41:44,892 * https://pypi.org/simple/pbiotools/ 2025-09-22T13:41:44,892 * https://www.piwheels.org/simple/pbiotools/ 2025-09-22T13:41:44,893 Fetching project page and analyzing links: https://pypi.org/simple/pbiotools/ 2025-09-22T13:41:44,894 Getting page https://pypi.org/simple/pbiotools/ 2025-09-22T13:41:44,895 Found index url https://pypi.org/simple 2025-09-22T13:41:45,106 Fetched page https://pypi.org/simple/pbiotools/ as application/vnd.pypi.simple.v1+json 2025-09-22T13:41:45,109 Skipping link: No binaries permitted for pbiotools: https://files.pythonhosted.org/packages/83/15/3a9d2181fdbd5914091d1293502ba952316da303c77acaeaaae4449178c1/pbiotools-2.0.0-py3-none-any.whl (from https://pypi.org/simple/pbiotools/) (requires-python:<3.10.0a0,>=3.6) 2025-09-22T13:41:45,110 Link requires a different Python (3.11.2 not in: '<3.10.0a0,>=3.6'): https://files.pythonhosted.org/packages/c9/25/5b8a312e4cdfa7171350114f86f57981d875c8a421e1e3b87a70f5048d31/pbiotools-2.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.10.0a0,>=3.6) 2025-09-22T13:41:45,111 Skipping link: 2.0.0 Requires-Python <3.10.0a0,>=3.6: https://files.pythonhosted.org/packages/c9/25/5b8a312e4cdfa7171350114f86f57981d875c8a421e1e3b87a70f5048d31/pbiotools-2.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.10.0a0,>=3.6) 2025-09-22T13:41:45,112 Skipping link: No binaries permitted for pbiotools: https://files.pythonhosted.org/packages/0d/20/ed3afb9550dee0195a390df4ea518e6c7e8a8f137989a68c85440997a05e/pbiotools-3.0.0-py3-none-any.whl (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.6) 2025-09-22T13:41:45,113 Link requires a different Python (3.11.2 not in: '<3.11,>=3.6'): https://files.pythonhosted.org/packages/2a/82/f1baf8c36ed40e8456c89c4b0502fc35ab74e5195be583fe7ac790a04830/pbiotools-3.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.6) 2025-09-22T13:41:45,113 Skipping link: 3.0.0 Requires-Python <3.11,>=3.6: https://files.pythonhosted.org/packages/2a/82/f1baf8c36ed40e8456c89c4b0502fc35ab74e5195be583fe7ac790a04830/pbiotools-3.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.6) 2025-09-22T13:41:45,114 Skipping link: No binaries permitted for pbiotools: https://files.pythonhosted.org/packages/c7/48/f226cedc06490bf8f65b40ac80daaf9cadbad704af58475df5f4a1510b1c/pbiotools-4.0.0-py3-none-any.whl (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,115 Link requires a different Python (3.11.2 not in: '<3.11,>=3.7'): https://files.pythonhosted.org/packages/40/25/65914736e1f90e42184816bd0a10b1a6e777b024a63cb1f84326f9643f4a/pbiotools-4.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,116 Skipping link: 4.0.0 Requires-Python <3.11,>=3.7: https://files.pythonhosted.org/packages/40/25/65914736e1f90e42184816bd0a10b1a6e777b024a63cb1f84326f9643f4a/pbiotools-4.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,116 Skipping link: No binaries permitted for pbiotools: https://files.pythonhosted.org/packages/d3/dd/ff112f68ecb0a511a50e437f96ae740629d83bc501b81beb3dbe8d960bb1/pbiotools-4.0.1-py3-none-any.whl (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,118 Link requires a different Python (3.11.2 not in: '<3.11,>=3.7'): https://files.pythonhosted.org/packages/34/9d/7f47c5cb936cc6b651021ef99cde58dd2c69074c49c1d0bba48f161933b5/pbiotools-4.0.1.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,118 Skipping link: 4.0.1 Requires-Python <3.11,>=3.7: https://files.pythonhosted.org/packages/34/9d/7f47c5cb936cc6b651021ef99cde58dd2c69074c49c1d0bba48f161933b5/pbiotools-4.0.1.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,119 Skipping link: No binaries permitted for pbiotools: https://files.pythonhosted.org/packages/43/bc/6364fa9fbb2361897154c314fdeedecbc02425b9941d57f8b9fb84faf924/pbiotools-4.0.2-py3-none-any.whl (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,120 Link requires a different Python (3.11.2 not in: '<3.11,>=3.7'): https://files.pythonhosted.org/packages/7d/1a/bdd88a4cb382e171749a3df8de2efcdfe8e3a8b99bbcd5d2b6c52c163fdb/pbiotools-4.0.2.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,120 Skipping link: 4.0.2 Requires-Python <3.11,>=3.7: https://files.pythonhosted.org/packages/7d/1a/bdd88a4cb382e171749a3df8de2efcdfe8e3a8b99bbcd5d2b6c52c163fdb/pbiotools-4.0.2.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,121 Skipping link: No binaries permitted for pbiotools: https://files.pythonhosted.org/packages/1c/5c/889517df6e8051b26c3f4f9d7b06ae89d968897f40d6037b569ea46b6fe4/pbiotools-5.0.0-py3-none-any.whl (from https://pypi.org/simple/pbiotools/) (requires-python:<3.14,>=3.11) 2025-09-22T13:41:45,122 Found link https://files.pythonhosted.org/packages/d7/1e/94483d6de177a8be36b618d2e9b2d550cd567ae38e7ad96a2a47af37d040/pbiotools-5.0.0.tar.gz (from https://pypi.org/simple/pbiotools/) (requires-python:<3.14,>=3.11), version: 5.0.0 2025-09-22T13:41:45,123 Fetching project page and analyzing links: https://www.piwheels.org/simple/pbiotools/ 2025-09-22T13:41:45,123 Getting page https://www.piwheels.org/simple/pbiotools/ 2025-09-22T13:41:45,125 Found index url https://www.piwheels.org/simple 2025-09-22T13:41:45,284 Fetched page https://www.piwheels.org/simple/pbiotools/ as text/html 2025-09-22T13:41:45,287 Skipping link: No binaries permitted for pbiotools: https://archive1.piwheels.org/simple/pbiotools/pbiotools-4.0.2-py3-none-any.whl#sha256=e2e0787efa8c800cc0848a25c6141d1590231fccdeb56dc506dc936e0983fe05 (from https://www.piwheels.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,287 Skipping link: No binaries permitted for pbiotools: https://archive1.piwheels.org/simple/pbiotools/pbiotools-4.0.1-py3-none-any.whl#sha256=60d1efcf0527e64363217a82b4bc156e05d433dacb240c38dca7e7f29b2d9d0d (from https://www.piwheels.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,288 Skipping link: No binaries permitted for pbiotools: https://archive1.piwheels.org/simple/pbiotools/pbiotools-4.0.0-py3-none-any.whl#sha256=c05a07240d056bc21294bcf39de0a3ff020f4c7519c8db6b1d1511c356927774 (from https://www.piwheels.org/simple/pbiotools/) (requires-python:<3.11,>=3.7) 2025-09-22T13:41:45,289 Skipping link: No binaries permitted for pbiotools: https://archive1.piwheels.org/simple/pbiotools/pbiotools-3.0.0-py3-none-any.whl#sha256=801de3aa8d710360620bf7d28cc88543f9d8158bf5152a0b7e12074ab99ebc41 (from https://www.piwheels.org/simple/pbiotools/) (requires-python:<3.11,>=3.6) 2025-09-22T13:41:45,289 Skipping link: No binaries permitted for pbiotools: https://archive1.piwheels.org/simple/pbiotools/pbiotools-2.0.0-py3-none-any.whl#sha256=95be136ed2cb9c33c8a278e694cf1ae8faffdcd35b85e1e44f5be6d0ab558183 (from https://www.piwheels.org/simple/pbiotools/) (requires-python:<3.10.0a0,>=3.6) 2025-09-22T13:41:45,290 Skipping link: not a file: https://www.piwheels.org/simple/pbiotools/ 2025-09-22T13:41:45,291 Skipping link: not a file: https://pypi.org/simple/pbiotools/ 2025-09-22T13:41:45,310 Given no hashes to check 1 links for project 'pbiotools': discarding no candidates 2025-09-22T13:41:45,328 Collecting pbiotools==5.0.0 2025-09-22T13:41:45,330 Created temporary directory: /tmp/pip-unpack-hrg76zft 2025-09-22T13:41:45,541 Downloading pbiotools-5.0.0.tar.gz (124 kB) 2025-09-22T13:41:45,755 Added pbiotools==5.0.0 from https://files.pythonhosted.org/packages/d7/1e/94483d6de177a8be36b618d2e9b2d550cd567ae38e7ad96a2a47af37d040/pbiotools-5.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-gsr1g1wb' 2025-09-22T13:41:45,762 Created temporary directory: /tmp/pip-build-env-9y2q_3af 2025-09-22T13:41:45,767 Installing build dependencies: started 2025-09-22T13:41:45,768 Running command pip subprocess to install build dependencies 2025-09-22T13:41:46,933 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2025-09-22T13:41:47,566 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2025-09-22T13:41:47,589 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-22T13:41:49,321 Collecting setuptools 2025-09-22T13:41:49,414 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2025-09-22T13:41:49,690 Collecting wheel 2025-09-22T13:41:49,707 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2025-09-22T13:41:52,725 Installing collected packages: wheel, setuptools 2025-09-22T13:41:52,973 Creating /tmp/pip-build-env-9y2q_3af/overlay/local/bin 2025-09-22T13:41:52,975 changing mode of /tmp/pip-build-env-9y2q_3af/overlay/local/bin/wheel to 755 2025-09-22T13:41:56,622 Successfully installed setuptools-80.9.0 wheel-0.45.1 2025-09-22T13:41:56,892 Installing build dependencies: finished with status 'done' 2025-09-22T13:41:56,898 Getting requirements to build wheel: started 2025-09-22T13:41:56,899 Running command Getting requirements to build wheel 2025-09-22T13:41:57,490 No `packages` or `py_modules` configuration, performing automatic discovery. 2025-09-22T13:41:57,490 `src-layout` detected -- analysing ./src 2025-09-22T13:41:57,496 discovered packages -- ['pbiotools', 'pbiotools.misc', 'pbiotools.utils', 'pbiotools.utils.pgrms'] 2025-09-22T13:41:57,496 discovered py_modules -- [] 2025-09-22T13:41:57,593 running egg_info 2025-09-22T13:41:57,600 writing src/pbiotools.egg-info/PKG-INFO 2025-09-22T13:41:57,606 writing dependency_links to src/pbiotools.egg-info/dependency_links.txt 2025-09-22T13:41:57,609 writing entry points to src/pbiotools.egg-info/entry_points.txt 2025-09-22T13:41:57,612 writing requirements to src/pbiotools.egg-info/requires.txt 2025-09-22T13:41:57,613 writing top-level names to src/pbiotools.egg-info/top_level.txt 2025-09-22T13:41:57,640 reading manifest file 'src/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:57,645 adding license file 'LICENSE' 2025-09-22T13:41:57,651 writing manifest file 'src/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:57,747 Getting requirements to build wheel: finished with status 'done' 2025-09-22T13:41:57,751 Created temporary directory: /tmp/pip-modern-metadata-w7fu_wrc 2025-09-22T13:41:57,753 Preparing metadata (pyproject.toml): started 2025-09-22T13:41:57,754 Running command Preparing metadata (pyproject.toml) 2025-09-22T13:41:58,307 No `packages` or `py_modules` configuration, performing automatic discovery. 2025-09-22T13:41:58,307 `src-layout` detected -- analysing ./src 2025-09-22T13:41:58,311 discovered packages -- ['pbiotools', 'pbiotools.misc', 'pbiotools.utils', 'pbiotools.utils.pgrms'] 2025-09-22T13:41:58,311 discovered py_modules -- [] 2025-09-22T13:41:58,401 running dist_info 2025-09-22T13:41:58,414 creating /tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info 2025-09-22T13:41:58,414 writing /tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/PKG-INFO 2025-09-22T13:41:58,420 writing dependency_links to /tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/dependency_links.txt 2025-09-22T13:41:58,423 writing entry points to /tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/entry_points.txt 2025-09-22T13:41:58,426 writing requirements to /tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/requires.txt 2025-09-22T13:41:58,427 writing top-level names to /tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/top_level.txt 2025-09-22T13:41:58,428 writing manifest file '/tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:58,452 reading manifest file '/tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:58,454 adding license file 'LICENSE' 2025-09-22T13:41:58,458 writing manifest file '/tmp/pip-modern-metadata-w7fu_wrc/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:58,459 creating '/tmp/pip-modern-metadata-w7fu_wrc/pbiotools-5.0.0.dist-info' 2025-09-22T13:41:58,583 Preparing metadata (pyproject.toml): finished with status 'done' 2025-09-22T13:41:58,587 Source in /tmp/pip-wheel-k34tlyx0/pbiotools_3b80d3a2c53d4252ac51e46114083e4e has version 5.0.0, which satisfies requirement pbiotools==5.0.0 from https://files.pythonhosted.org/packages/d7/1e/94483d6de177a8be36b618d2e9b2d550cd567ae38e7ad96a2a47af37d040/pbiotools-5.0.0.tar.gz 2025-09-22T13:41:58,588 Removed pbiotools==5.0.0 from https://files.pythonhosted.org/packages/d7/1e/94483d6de177a8be36b618d2e9b2d550cd567ae38e7ad96a2a47af37d040/pbiotools-5.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-gsr1g1wb' 2025-09-22T13:41:58,594 Created temporary directory: /tmp/pip-unpack-_4uqs1pp 2025-09-22T13:41:58,595 Building wheels for collected packages: pbiotools 2025-09-22T13:41:58,599 Created temporary directory: /tmp/pip-wheel-grfujch1 2025-09-22T13:41:58,600 Destination directory: /tmp/pip-wheel-grfujch1 2025-09-22T13:41:58,602 Building wheel for pbiotools (pyproject.toml): started 2025-09-22T13:41:58,603 Running command Building wheel for pbiotools (pyproject.toml) 2025-09-22T13:41:59,144 No `packages` or `py_modules` configuration, performing automatic discovery. 2025-09-22T13:41:59,144 `src-layout` detected -- analysing ./src 2025-09-22T13:41:59,148 discovered packages -- ['pbiotools', 'pbiotools.misc', 'pbiotools.utils', 'pbiotools.utils.pgrms'] 2025-09-22T13:41:59,148 discovered py_modules -- [] 2025-09-22T13:41:59,228 running bdist_wheel 2025-09-22T13:41:59,249 running build 2025-09-22T13:41:59,249 running build_py 2025-09-22T13:41:59,256 creating build/lib/pbiotools 2025-09-22T13:41:59,258 copying src/pbiotools/__init__.py -> build/lib/pbiotools 2025-09-22T13:41:59,260 creating build/lib/pbiotools/misc 2025-09-22T13:41:59,261 copying src/pbiotools/misc/math_utils.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,264 copying src/pbiotools/misc/suppress_stdout_stderr.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,266 copying src/pbiotools/misc/shell_utils.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,269 copying src/pbiotools/misc/pandas_utils.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,271 copying src/pbiotools/misc/mpl_utils.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,274 copying src/pbiotools/misc/__init__.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,276 copying src/pbiotools/misc/parallel.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,278 copying src/pbiotools/misc/slurm.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,281 copying src/pbiotools/misc/logging_utils.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,283 copying src/pbiotools/misc/utils.py -> build/lib/pbiotools/misc 2025-09-22T13:41:59,287 creating build/lib/pbiotools/utils 2025-09-22T13:41:59,288 copying src/pbiotools/utils/bam_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,290 copying src/pbiotools/utils/bed_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,294 copying src/pbiotools/utils/meme_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,296 copying src/pbiotools/utils/fastx_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,299 copying src/pbiotools/utils/gffread_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,301 copying src/pbiotools/utils/__init__.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,303 copying src/pbiotools/utils/bio.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,305 copying src/pbiotools/utils/pgrm_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,307 copying src/pbiotools/utils/mygene_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,309 copying src/pbiotools/utils/gtf_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,311 copying src/pbiotools/utils/metacyc_utils.py -> build/lib/pbiotools/utils 2025-09-22T13:41:59,315 creating build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,316 copying src/pbiotools/utils/pgrms/download_srr_files.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,318 copying src/pbiotools/utils/pgrms/fastq_pe_dedupe.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,320 copying src/pbiotools/utils/pgrms/remove_duplicate_sequences.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,322 copying src/pbiotools/utils/pgrms/convert_ccds_to_bed.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,324 copying src/pbiotools/utils/pgrms/subtract_bed.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,326 copying src/pbiotools/utils/pgrms/bam_to_wiggle.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,328 copying src/pbiotools/utils/pgrms/split_long_chromosomes.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,330 copying src/pbiotools/utils/pgrms/filter_bam_by_ids.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,332 copying src/pbiotools/utils/pgrms/create_mygene_report.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,334 copying src/pbiotools/utils/pgrms/bed12_to_gtf.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,336 copying src/pbiotools/utils/pgrms/fasta_to_fastq.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,338 copying src/pbiotools/utils/pgrms/extract_cds_coordinates.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,339 copying src/pbiotools/utils/pgrms/remove_duplicate_bed_entries.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,341 copying src/pbiotools/utils/pgrms/run_tmhmm.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,344 copying src/pbiotools/utils/pgrms/__init__.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,345 copying src/pbiotools/utils/pgrms/add_mygene_info_to_orfs.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,347 copying src/pbiotools/utils/pgrms/count_reads.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,349 copying src/pbiotools/utils/pgrms/extract_bed_sequences.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,351 copying src/pbiotools/utils/pgrms/split_bed12_blocks.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,353 copying src/pbiotools/utils/pgrms/fix_all_bed_files.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,355 copying src/pbiotools/utils/pgrms/run_signalp.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,357 copying src/pbiotools/utils/pgrms/reorder_fasta.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,359 copying src/pbiotools/utils/pgrms/run_bowtie.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,361 copying src/pbiotools/utils/pgrms/count_aligned_reads.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,363 copying src/pbiotools/utils/pgrms/bedx_to_bedy.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,364 copying src/pbiotools/utils/pgrms/merge_isoforms.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,367 copying src/pbiotools/utils/pgrms/get_all_utrs.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,368 copying src/pbiotools/utils/pgrms/dna_to_aa.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,370 copying src/pbiotools/utils/pgrms/join_long_chromosomes.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,372 copying src/pbiotools/utils/pgrms/gtf_to_bed12.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,374 copying src/pbiotools/utils/pgrms/remove_multimapping_reads.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,376 copying src/pbiotools/utils/pgrms/get_read_length_distribution.py -> build/lib/pbiotools/utils/pgrms 2025-09-22T13:41:59,378 running egg_info 2025-09-22T13:41:59,389 writing src/pbiotools.egg-info/PKG-INFO 2025-09-22T13:41:59,395 writing dependency_links to src/pbiotools.egg-info/dependency_links.txt 2025-09-22T13:41:59,397 writing entry points to src/pbiotools.egg-info/entry_points.txt 2025-09-22T13:41:59,400 writing requirements to src/pbiotools.egg-info/requires.txt 2025-09-22T13:41:59,401 writing top-level names to src/pbiotools.egg-info/top_level.txt 2025-09-22T13:41:59,415 reading manifest file 'src/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:59,420 adding license file 'LICENSE' 2025-09-22T13:41:59,425 writing manifest file 'src/pbiotools.egg-info/SOURCES.txt' 2025-09-22T13:41:59,442 installing to build/bdist.linux-armv7l/wheel 2025-09-22T13:41:59,443 running install 2025-09-22T13:41:59,466 running install_lib 2025-09-22T13:41:59,473 creating build/bdist.linux-armv7l/wheel 2025-09-22T13:41:59,474 creating build/bdist.linux-armv7l/wheel/pbiotools 2025-09-22T13:41:59,476 creating build/bdist.linux-armv7l/wheel/pbiotools/misc 2025-09-22T13:41:59,477 copying build/lib/pbiotools/misc/math_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,480 copying build/lib/pbiotools/misc/suppress_stdout_stderr.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,482 copying build/lib/pbiotools/misc/shell_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,484 copying build/lib/pbiotools/misc/pandas_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,487 copying build/lib/pbiotools/misc/mpl_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,489 copying build/lib/pbiotools/misc/__init__.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,491 copying build/lib/pbiotools/misc/parallel.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,493 copying build/lib/pbiotools/misc/slurm.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,495 copying build/lib/pbiotools/misc/logging_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,497 copying build/lib/pbiotools/misc/utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/misc 2025-09-22T13:41:59,501 creating build/bdist.linux-armv7l/wheel/pbiotools/utils 2025-09-22T13:41:59,502 copying build/lib/pbiotools/utils/bam_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,505 copying build/lib/pbiotools/utils/bed_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,508 copying build/lib/pbiotools/utils/meme_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,511 copying build/lib/pbiotools/utils/fastx_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,514 creating build/bdist.linux-armv7l/wheel/pbiotools/utils/pgrms 2025-09-22T13:41:59,515 copying build/lib/pbiotools/utils/pgrms/download_srr_files.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,518 copying build/lib/pbiotools/utils/pgrms/fastq_pe_dedupe.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,520 copying build/lib/pbiotools/utils/pgrms/remove_duplicate_sequences.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,522 copying build/lib/pbiotools/utils/pgrms/convert_ccds_to_bed.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,523 copying build/lib/pbiotools/utils/pgrms/subtract_bed.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,525 copying build/lib/pbiotools/utils/pgrms/bam_to_wiggle.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,528 copying build/lib/pbiotools/utils/pgrms/split_long_chromosomes.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,529 copying build/lib/pbiotools/utils/pgrms/filter_bam_by_ids.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,531 copying build/lib/pbiotools/utils/pgrms/create_mygene_report.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,533 copying build/lib/pbiotools/utils/pgrms/bed12_to_gtf.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,535 copying build/lib/pbiotools/utils/pgrms/fasta_to_fastq.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,537 copying build/lib/pbiotools/utils/pgrms/extract_cds_coordinates.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,538 copying build/lib/pbiotools/utils/pgrms/remove_duplicate_bed_entries.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,540 copying build/lib/pbiotools/utils/pgrms/run_tmhmm.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,543 copying build/lib/pbiotools/utils/pgrms/__init__.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,544 copying build/lib/pbiotools/utils/pgrms/add_mygene_info_to_orfs.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,547 copying build/lib/pbiotools/utils/pgrms/count_reads.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,549 copying build/lib/pbiotools/utils/pgrms/extract_bed_sequences.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,551 copying build/lib/pbiotools/utils/pgrms/split_bed12_blocks.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,553 copying build/lib/pbiotools/utils/pgrms/fix_all_bed_files.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,554 copying build/lib/pbiotools/utils/pgrms/run_signalp.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,557 copying build/lib/pbiotools/utils/pgrms/reorder_fasta.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,558 copying build/lib/pbiotools/utils/pgrms/run_bowtie.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,561 copying build/lib/pbiotools/utils/pgrms/count_aligned_reads.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,562 copying build/lib/pbiotools/utils/pgrms/bedx_to_bedy.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,564 copying build/lib/pbiotools/utils/pgrms/merge_isoforms.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,567 copying build/lib/pbiotools/utils/pgrms/get_all_utrs.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,568 copying build/lib/pbiotools/utils/pgrms/dna_to_aa.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,570 copying build/lib/pbiotools/utils/pgrms/join_long_chromosomes.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,572 copying build/lib/pbiotools/utils/pgrms/gtf_to_bed12.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,574 copying build/lib/pbiotools/utils/pgrms/remove_multimapping_reads.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,576 copying build/lib/pbiotools/utils/pgrms/get_read_length_distribution.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils/pgrms 2025-09-22T13:41:59,578 copying build/lib/pbiotools/utils/gffread_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,580 copying build/lib/pbiotools/utils/__init__.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,582 copying build/lib/pbiotools/utils/bio.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,584 copying build/lib/pbiotools/utils/pgrm_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,586 copying build/lib/pbiotools/utils/mygene_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,589 copying build/lib/pbiotools/utils/gtf_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,591 copying build/lib/pbiotools/utils/metacyc_utils.py -> build/bdist.linux-armv7l/wheel/./pbiotools/utils 2025-09-22T13:41:59,593 copying build/lib/pbiotools/__init__.py -> build/bdist.linux-armv7l/wheel/./pbiotools 2025-09-22T13:41:59,594 running install_egg_info 2025-09-22T13:41:59,600 Copying src/pbiotools.egg-info to build/bdist.linux-armv7l/wheel/./pbiotools-5.0.0-py3.11.egg-info 2025-09-22T13:41:59,612 running install_scripts 2025-09-22T13:41:59,624 creating build/bdist.linux-armv7l/wheel/pbiotools-5.0.0.dist-info/WHEEL 2025-09-22T13:41:59,627 creating '/tmp/pip-wheel-grfujch1/.tmp-cjyw0ix9/pbiotools-5.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-22T13:41:59,629 adding 'pbiotools/__init__.py' 2025-09-22T13:41:59,631 adding 'pbiotools/misc/__init__.py' 2025-09-22T13:41:59,633 adding 'pbiotools/misc/logging_utils.py' 2025-09-22T13:41:59,638 adding 'pbiotools/misc/math_utils.py' 2025-09-22T13:41:59,642 adding 'pbiotools/misc/mpl_utils.py' 2025-09-22T13:41:59,644 adding 'pbiotools/misc/pandas_utils.py' 2025-09-22T13:41:59,646 adding 'pbiotools/misc/parallel.py' 2025-09-22T13:41:59,649 adding 'pbiotools/misc/shell_utils.py' 2025-09-22T13:41:59,651 adding 'pbiotools/misc/slurm.py' 2025-09-22T13:41:59,653 adding 'pbiotools/misc/suppress_stdout_stderr.py' 2025-09-22T13:41:59,659 adding 'pbiotools/misc/utils.py' 2025-09-22T13:41:59,660 adding 'pbiotools/utils/__init__.py' 2025-09-22T13:41:59,663 adding 'pbiotools/utils/bam_utils.py' 2025-09-22T13:41:59,675 adding 'pbiotools/utils/bed_utils.py' 2025-09-22T13:41:59,677 adding 'pbiotools/utils/bio.py' 2025-09-22T13:41:59,680 adding 'pbiotools/utils/fastx_utils.py' 2025-09-22T13:41:59,682 adding 'pbiotools/utils/gffread_utils.py' 2025-09-22T13:41:59,684 adding 'pbiotools/utils/gtf_utils.py' 2025-09-22T13:41:59,687 adding 'pbiotools/utils/meme_utils.py' 2025-09-22T13:41:59,688 adding 'pbiotools/utils/metacyc_utils.py' 2025-09-22T13:41:59,690 adding 'pbiotools/utils/mygene_utils.py' 2025-09-22T13:41:59,692 adding 'pbiotools/utils/pgrm_utils.py' 2025-09-22T13:41:59,694 adding 'pbiotools/utils/pgrms/__init__.py' 2025-09-22T13:41:59,696 adding 'pbiotools/utils/pgrms/add_mygene_info_to_orfs.py' 2025-09-22T13:41:59,698 adding 'pbiotools/utils/pgrms/bam_to_wiggle.py' 2025-09-22T13:41:59,699 adding 'pbiotools/utils/pgrms/bed12_to_gtf.py' 2025-09-22T13:41:59,700 adding 'pbiotools/utils/pgrms/bedx_to_bedy.py' 2025-09-22T13:41:59,702 adding 'pbiotools/utils/pgrms/convert_ccds_to_bed.py' 2025-09-22T13:41:59,703 adding 'pbiotools/utils/pgrms/count_aligned_reads.py' 2025-09-22T13:41:59,704 adding 'pbiotools/utils/pgrms/count_reads.py' 2025-09-22T13:41:59,706 adding 'pbiotools/utils/pgrms/create_mygene_report.py' 2025-09-22T13:41:59,707 adding 'pbiotools/utils/pgrms/dna_to_aa.py' 2025-09-22T13:41:59,709 adding 'pbiotools/utils/pgrms/download_srr_files.py' 2025-09-22T13:41:59,710 adding 'pbiotools/utils/pgrms/extract_bed_sequences.py' 2025-09-22T13:41:59,712 adding 'pbiotools/utils/pgrms/extract_cds_coordinates.py' 2025-09-22T13:41:59,713 adding 'pbiotools/utils/pgrms/fasta_to_fastq.py' 2025-09-22T13:41:59,714 adding 'pbiotools/utils/pgrms/fastq_pe_dedupe.py' 2025-09-22T13:41:59,715 adding 'pbiotools/utils/pgrms/filter_bam_by_ids.py' 2025-09-22T13:41:59,716 adding 'pbiotools/utils/pgrms/fix_all_bed_files.py' 2025-09-22T13:41:59,718 adding 'pbiotools/utils/pgrms/get_all_utrs.py' 2025-09-22T13:41:59,719 adding 'pbiotools/utils/pgrms/get_read_length_distribution.py' 2025-09-22T13:41:59,721 adding 'pbiotools/utils/pgrms/gtf_to_bed12.py' 2025-09-22T13:41:59,722 adding 'pbiotools/utils/pgrms/join_long_chromosomes.py' 2025-09-22T13:41:59,724 adding 'pbiotools/utils/pgrms/merge_isoforms.py' 2025-09-22T13:41:59,725 adding 'pbiotools/utils/pgrms/remove_duplicate_bed_entries.py' 2025-09-22T13:41:59,726 adding 'pbiotools/utils/pgrms/remove_duplicate_sequences.py' 2025-09-22T13:41:59,728 adding 'pbiotools/utils/pgrms/remove_multimapping_reads.py' 2025-09-22T13:41:59,729 adding 'pbiotools/utils/pgrms/reorder_fasta.py' 2025-09-22T13:41:59,730 adding 'pbiotools/utils/pgrms/run_bowtie.py' 2025-09-22T13:41:59,732 adding 'pbiotools/utils/pgrms/run_signalp.py' 2025-09-22T13:41:59,734 adding 'pbiotools/utils/pgrms/run_tmhmm.py' 2025-09-22T13:41:59,735 adding 'pbiotools/utils/pgrms/split_bed12_blocks.py' 2025-09-22T13:41:59,736 adding 'pbiotools/utils/pgrms/split_long_chromosomes.py' 2025-09-22T13:41:59,738 adding 'pbiotools/utils/pgrms/subtract_bed.py' 2025-09-22T13:41:59,741 adding 'pbiotools-5.0.0.dist-info/licenses/LICENSE' 2025-09-22T13:41:59,742 adding 'pbiotools-5.0.0.dist-info/METADATA' 2025-09-22T13:41:59,743 adding 'pbiotools-5.0.0.dist-info/WHEEL' 2025-09-22T13:41:59,744 adding 'pbiotools-5.0.0.dist-info/entry_points.txt' 2025-09-22T13:41:59,745 adding 'pbiotools-5.0.0.dist-info/top_level.txt' 2025-09-22T13:41:59,746 adding 'pbiotools-5.0.0.dist-info/RECORD' 2025-09-22T13:41:59,749 removing build/bdist.linux-armv7l/wheel 2025-09-22T13:41:59,860 Building wheel for pbiotools (pyproject.toml): finished with status 'done' 2025-09-22T13:41:59,867 Created wheel for pbiotools: filename=pbiotools-5.0.0-py3-none-any.whl size=149141 sha256=d21390caadcd7881b839a6e461c564a0ea423dd6894e3eec5e662b6a9dffc680 2025-09-22T13:41:59,868 Stored in directory: /tmp/pip-ephem-wheel-cache-o1ces9ni/wheels/2f/85/b4/f87060a34afa13646861a9f3eef990e285595a06a6fd3667c0 2025-09-22T13:41:59,881 Successfully built pbiotools 2025-09-22T13:41:59,891 Removed build tracker: '/tmp/pip-build-tracker-gsr1g1wb'