2025-05-30T19:18:37,852 Created temporary directory: /tmp/pip-build-tracker-db4ftzve 2025-05-30T19:18:37,853 Initialized build tracking at /tmp/pip-build-tracker-db4ftzve 2025-05-30T19:18:37,854 Created build tracker: /tmp/pip-build-tracker-db4ftzve 2025-05-30T19:18:37,854 Entered build tracker: /tmp/pip-build-tracker-db4ftzve 2025-05-30T19:18:37,855 Created temporary directory: /tmp/pip-wheel-owxyj8ci 2025-05-30T19:18:37,859 Created temporary directory: /tmp/pip-ephem-wheel-cache-he0n4yzn 2025-05-30T19:18:37,912 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-05-30T19:18:37,914 2 location(s) to search for versions of kneaddata: 2025-05-30T19:18:37,914 * https://pypi.org/simple/kneaddata/ 2025-05-30T19:18:37,914 * https://www.piwheels.org/simple/kneaddata/ 2025-05-30T19:18:37,915 Fetching project page and analyzing links: https://pypi.org/simple/kneaddata/ 2025-05-30T19:18:37,915 Getting page https://pypi.org/simple/kneaddata/ 2025-05-30T19:18:37,917 Found index url https://pypi.org/simple/ 2025-05-30T19:18:38,147 Fetched page https://pypi.org/simple/kneaddata/ as application/vnd.pypi.simple.v1+json 2025-05-30T19:18:38,153 Found link https://files.pythonhosted.org/packages/91/19/62d9ecf0db18cd94089bc4115fa1b2cb4c3ffc79c652385e4c3f7e03ceef/kneaddata-0.5.2.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.5.2 2025-05-30T19:18:38,154 Found link https://files.pythonhosted.org/packages/6d/50/dd20a862b2532a476b4837a2b1fe4f9e8131cf554751adb6fd7186ee33e3/kneaddata-0.5.4.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.5.4 2025-05-30T19:18:38,155 Found link https://files.pythonhosted.org/packages/f8/6a/3c8f200d3088c5bc0dd2c85b74d5199e3ca1f2fb7d8baae44708f5b1b928/kneaddata-0.6.1.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.6.1 2025-05-30T19:18:38,156 Found link https://files.pythonhosted.org/packages/40/31/eeace9b4a9e40060da156a930043c0fc32ed454381cef39e8e3176aced48/kneaddata-0.7.2.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.2 2025-05-30T19:18:38,157 Found link https://files.pythonhosted.org/packages/a4/6a/4176eee7a83b80ac12ca6727df6cb9dd3fec2051cca8a707ccbebc5962d3/kneaddata-0.7.3.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.3 2025-05-30T19:18:38,158 Found link https://files.pythonhosted.org/packages/11/2c/cd13c0bf0fa2b7906ac4d7004d2f6965e24253f416fa568bd8971562feca/kneaddata-0.7.5.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.5 2025-05-30T19:18:38,160 Found link https://files.pythonhosted.org/packages/c4/19/aa5f38b94b7d6bc86f6ad0352a84ce1bc77ebdbd81fcce8d01eecaac398f/kneaddata-0.7.6.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.6 2025-05-30T19:18:38,161 Found link https://files.pythonhosted.org/packages/97/18/94837e3387b344d089fbe29b009bc199ac9a9e915d31ed63927ed7465f1c/kneaddata-0.7.8.1.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.8.1 2025-05-30T19:18:38,162 Found link https://files.pythonhosted.org/packages/ae/d7/e5ba98f255eb5f11b0b4b7b789191e44d582f95d3e705d30099a895ad3e6/kneaddata-0.7.9.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.9 2025-05-30T19:18:38,163 Found link https://files.pythonhosted.org/packages/42/d3/ed2ec7741a8b33fb490bfd164f7a13f108e64d2d2e2cb4b2cedff24a5734/kneaddata-0.7.10.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.7.10 2025-05-30T19:18:38,164 Found link https://files.pythonhosted.org/packages/5c/c0/5b2d9b1b9a006b48bbf02cb6f189fc9c14feb10b71c0ebcbe038f716a362/kneaddata-0.9.0.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.9.0 2025-05-30T19:18:38,165 Found link https://files.pythonhosted.org/packages/0d/6b/993dd8066f06fbeb6d1e6eae163976fff9b41ab6b7cc13f61615ef8b5b0b/kneaddata-0.10.0.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.10.0 2025-05-30T19:18:38,166 Found link https://files.pythonhosted.org/packages/63/b8/5d380501db6bc6b35ec6aace96fbbf57e653e4ef0a74c3821665a96f7a63/kneaddata-0.12.0.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.12.0 2025-05-30T19:18:38,167 Skipping link: No binaries permitted for kneaddata: https://files.pythonhosted.org/packages/41/42/b247974ab722c5833ab3905a865c724a951d1105e3a7f722d6de09126b93/kneaddata-0.12.1-py3-none-any.whl (from https://pypi.org/simple/kneaddata/) 2025-05-30T19:18:38,167 Found link https://files.pythonhosted.org/packages/f3/78/2cc05ac66640eba0b647350fc020ffcc84d870e9d813150e80f26b126089/kneaddata-0.12.1.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.12.1 2025-05-30T19:18:38,168 Skipping link: No binaries permitted for kneaddata: https://files.pythonhosted.org/packages/89/e9/6f374f5629771ee9a7599ed73ef90071f08e381fd1d627c3f5e51ef4b194/kneaddata-0.12.2-py3-none-any.whl (from https://pypi.org/simple/kneaddata/) 2025-05-30T19:18:38,169 Found link https://files.pythonhosted.org/packages/98/90/2f334311d1e1cce204706f91d9f380cfb85201061eb3e0c703d374790bf8/kneaddata-0.12.2.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.12.2 2025-05-30T19:18:38,169 Skipping link: No binaries permitted for kneaddata: https://files.pythonhosted.org/packages/da/ac/a785339ea32f4e75049e87f0578203f9ca64964528e0051ede18b3857ec7/kneaddata-0.12.3-py3-none-any.whl (from https://pypi.org/simple/kneaddata/) 2025-05-30T19:18:38,170 Found link https://files.pythonhosted.org/packages/30/84/725452fdb0003bb6aa31c61a57308b3bd374de1f21a04e1cbc0679a561fa/kneaddata-0.12.3.tar.gz (from https://pypi.org/simple/kneaddata/), version: 0.12.3 2025-05-30T19:18:38,171 Fetching project page and analyzing links: https://www.piwheels.org/simple/kneaddata/ 2025-05-30T19:18:38,171 Getting page https://www.piwheels.org/simple/kneaddata/ 2025-05-30T19:18:38,173 Found index url https://www.piwheels.org/simple/ 2025-05-30T19:18:38,330 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kneaddata/ 2025-05-30T19:18:38,990 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kneaddata/ 2025-05-30T19:18:40,161 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kneaddata/ 2025-05-30T19:18:42,329 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kneaddata/ 2025-05-30T19:18:46,497 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/kneaddata/ 2025-05-30T19:18:46,665 Could not fetch URL https://www.piwheels.org/simple/kneaddata/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/kneaddata/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping 2025-05-30T19:18:46,667 Skipping link: not a file: https://www.piwheels.org/simple/kneaddata/ 2025-05-30T19:18:46,668 Skipping link: not a file: https://pypi.org/simple/kneaddata/ 2025-05-30T19:18:46,692 Given no hashes to check 1 links for project 'kneaddata': discarding no candidates 2025-05-30T19:18:46,694 Collecting kneaddata==0.12.3 2025-05-30T19:18:46,696 Created temporary directory: /tmp/pip-unpack-8263yvvr 2025-05-30T19:18:46,935 Downloading kneaddata-0.12.3.tar.gz (658 kB) 2025-05-30T19:18:47,758 Added kneaddata==0.12.3 from https://files.pythonhosted.org/packages/30/84/725452fdb0003bb6aa31c61a57308b3bd374de1f21a04e1cbc0679a561fa/kneaddata-0.12.3.tar.gz to build tracker '/tmp/pip-build-tracker-db4ftzve' 2025-05-30T19:18:47,761 Running setup.py (path:/tmp/pip-wheel-owxyj8ci/kneaddata_6e0fa76b592a4463922e0f07e7619d84/setup.py) egg_info for package kneaddata 2025-05-30T19:18:47,762 Created temporary directory: /tmp/pip-pip-egg-info-iopntpgt 2025-05-30T19:18:47,762 Preparing metadata (setup.py): started 2025-05-30T19:18:47,764 Running command python setup.py egg_info 2025-05-30T19:18:50,192 Downloading https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/TruSeq2-PE.fa 2025-05-30T19:18:50,192 Downloading file of size: 0.00 MB 2025-05-30T19:18:50,193 0.01 MB 1519.85 % 1.53 MB/sec 0 min -0 sec 2025-05-30T19:18:50,194 Downloading https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/TruSeq2-SE.fa 2025-05-30T19:18:50,194 Downloading file of size: 0.00 MB 2025-05-30T19:18:50,195 0.01 MB 5728.67 % 1.56 MB/sec 0 min -0 sec 2025-05-30T19:18:50,196 Downloading https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/TruSeq3-PE.fa 2025-05-30T19:18:50,196 Downloading file of size: 0.00 MB 2025-05-30T19:18:50,198 0.01 MB 8808.60 % 1.55 MB/sec 0 min -0 sec 2025-05-30T19:18:50,198 Downloading https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/TruSeq3-SE.fa 2025-05-30T19:18:50,198 Downloading file of size: 0.00 MB 2025-05-30T19:18:50,199 0.01 MB 6884.03 % 1.47 MB/sec 0 min -0 sec 2025-05-30T19:18:50,200 Downloading https://raw.githubusercontent.com/timflutre/trimmomatic/master/adapters/NexteraPE-PE.fa 2025-05-30T19:18:50,201 Downloading file of size: 0.00 MB 2025-05-30T19:18:50,202 0.01 MB 3427.62 % 1.51 MB/sec 0 min -0 sec 2025-05-30T19:18:50,202 running egg_info 2025-05-30T19:18:50,224 creating /tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info 2025-05-30T19:18:50,225 writing /tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/PKG-INFO 2025-05-30T19:18:50,229 writing dependency_links to /tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/dependency_links.txt 2025-05-30T19:18:50,231 writing entry points to /tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/entry_points.txt 2025-05-30T19:18:50,232 writing top-level names to /tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/top_level.txt 2025-05-30T19:18:50,234 writing manifest file '/tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/SOURCES.txt' 2025-05-30T19:18:50,332 reading manifest file '/tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/SOURCES.txt' 2025-05-30T19:18:50,334 reading manifest template 'MANIFEST.in' 2025-05-30T19:18:50,377 adding license file 'LICENSE' 2025-05-30T19:18:50,381 writing manifest file '/tmp/pip-pip-egg-info-iopntpgt/kneaddata.egg-info/SOURCES.txt' 2025-05-30T19:18:50,493 Preparing metadata (setup.py): finished with status 'done' 2025-05-30T19:18:50,497 Source in /tmp/pip-wheel-owxyj8ci/kneaddata_6e0fa76b592a4463922e0f07e7619d84 has version 0.12.3, which satisfies requirement kneaddata==0.12.3 from https://files.pythonhosted.org/packages/30/84/725452fdb0003bb6aa31c61a57308b3bd374de1f21a04e1cbc0679a561fa/kneaddata-0.12.3.tar.gz 2025-05-30T19:18:50,498 Removed kneaddata==0.12.3 from https://files.pythonhosted.org/packages/30/84/725452fdb0003bb6aa31c61a57308b3bd374de1f21a04e1cbc0679a561fa/kneaddata-0.12.3.tar.gz from build tracker '/tmp/pip-build-tracker-db4ftzve' 2025-05-30T19:18:50,502 Created temporary directory: /tmp/pip-unpack-lk63qv72 2025-05-30T19:18:50,503 Created temporary directory: /tmp/pip-unpack-0wrump2b 2025-05-30T19:18:50,504 Building wheels for collected packages: kneaddata 2025-05-30T19:18:50,508 Created temporary directory: /tmp/pip-wheel-xxxyh_wx 2025-05-30T19:18:50,509 DEPRECATION: Building 'kneaddata' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'kneaddata'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-05-30T19:18:50,511 Building wheel for kneaddata (setup.py): started 2025-05-30T19:18:50,512 Destination directory: /tmp/pip-wheel-xxxyh_wx 2025-05-30T19:18:50,513 Running command python setup.py bdist_wheel 2025-05-30T19:18:51,589 running bdist_wheel 2025-05-30T19:18:51,730 running build 2025-05-30T19:18:51,731 running build_py 2025-05-30T19:18:51,762 creating build/lib/kneaddata 2025-05-30T19:18:51,764 copying kneaddata/__init__.py -> build/lib/kneaddata 2025-05-30T19:18:51,765 copying kneaddata/bowtie2_discordant_pairs.py -> build/lib/kneaddata 2025-05-30T19:18:51,768 copying kneaddata/generate_db.py -> build/lib/kneaddata 2025-05-30T19:18:51,770 copying kneaddata/utilities.py -> build/lib/kneaddata 2025-05-30T19:18:51,773 copying kneaddata/read_count_table_concat_pairs.py -> build/lib/kneaddata 2025-05-30T19:18:51,776 copying kneaddata/knead_data.py -> build/lib/kneaddata 2025-05-30T19:18:51,779 copying kneaddata/trf_parallel.py -> build/lib/kneaddata 2025-05-30T19:18:51,781 copying kneaddata/download_db.py -> build/lib/kneaddata 2025-05-30T19:18:51,783 copying kneaddata/config.py -> build/lib/kneaddata 2025-05-30T19:18:51,785 copying kneaddata/run.py -> build/lib/kneaddata 2025-05-30T19:18:51,788 copying kneaddata/read_count_table.py -> build/lib/kneaddata 2025-05-30T19:18:51,791 creating build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,792 copying kneaddata/db_preprocessing/__init__.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,794 copying kneaddata/db_preprocessing/downsample.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,796 copying kneaddata/db_preprocessing/Modify_RNA_to_DNA.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,798 copying kneaddata/db_preprocessing/fastq_to_fasta.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,800 copying kneaddata/db_preprocessing/reservoir.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,802 copying kneaddata/db_preprocessing/mergesams.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,804 copying kneaddata/db_preprocessing/filter_bugs.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,806 copying kneaddata/db_preprocessing/prefix_human_transcriptome.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,808 copying kneaddata/db_preprocessing/filter_silva.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,810 copying kneaddata/db_preprocessing/convert_rna.py -> build/lib/kneaddata/db_preprocessing 2025-05-30T19:18:51,813 creating build/lib/kneaddata/tests 2025-05-30T19:18:51,814 copying kneaddata/tests/__init__.py -> build/lib/kneaddata/tests 2025-05-30T19:18:51,816 copying kneaddata/tests/cfg.py -> build/lib/kneaddata/tests 2025-05-30T19:18:51,818 copying kneaddata/tests/kneaddata_test.py -> build/lib/kneaddata/tests 2025-05-30T19:18:51,820 copying kneaddata/tests/functional_tests.py -> build/lib/kneaddata/tests 2025-05-30T19:18:51,823 copying kneaddata/tests/basic_tests.py -> build/lib/kneaddata/tests 2025-05-30T19:18:51,825 copying kneaddata/tests/utils.py -> build/lib/kneaddata/tests 2025-05-30T19:18:51,833 creating build/lib/kneaddata/tests/data 2025-05-30T19:18:51,834 copying kneaddata/tests/data/demo.sam -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,847 copying kneaddata/tests/data/merge3.fastq -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,849 copying kneaddata/tests/data/demo.fastq -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,861 copying kneaddata/tests/data/merge1.fastq -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,863 copying kneaddata/tests/data/demo_matches_sam_and_bam.fastq -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,879 copying kneaddata/tests/data/demo2.fastq -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,892 copying kneaddata/tests/data/demo.bam -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,896 copying kneaddata/tests/data/merge2.fastq -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,898 copying kneaddata/tests/data/demo.fastq.gz -> build/lib/kneaddata/tests/data 2025-05-30T19:18:51,902 creating build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:51,903 copying kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.1.bt2 -> build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:51,977 copying kneaddata/tests/data/demo_bowtie2_db/demo_db.3.bt2 -> build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:51,980 copying kneaddata/tests/data/demo_bowtie2_db/demo_db.4.bt2 -> build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:51,982 copying kneaddata/tests/data/demo_bowtie2_db/demo_db.2.bt2 -> build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:51,984 copying kneaddata/tests/data/demo_bowtie2_db/demo_db.1.bt2 -> build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,168 copying kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.2.bt2 -> build/lib/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,170 creating build/lib/kneaddata/adapters 2025-05-30T19:18:52,171 copying kneaddata/adapters/TruSeq2-SE.fa -> build/lib/kneaddata/adapters 2025-05-30T19:18:52,173 copying kneaddata/adapters/TruSeq3-SE.fa -> build/lib/kneaddata/adapters 2025-05-30T19:18:52,175 copying kneaddata/adapters/NexteraPE-PE.fa -> build/lib/kneaddata/adapters 2025-05-30T19:18:52,177 copying kneaddata/adapters/TruSeq3-PE.fa -> build/lib/kneaddata/adapters 2025-05-30T19:18:52,179 copying kneaddata/adapters/TruSeq2-PE.fa -> build/lib/kneaddata/adapters 2025-05-30T19:18:52,183 /tmp/pip-wheel-owxyj8ci/kneaddata_6e0fa76b592a4463922e0f07e7619d84/setup.py:341: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-05-30T19:18:52,184 !! 2025-05-30T19:18:52,185 ******************************************************************************** 2025-05-30T19:18:52,185 Please avoid running ``setup.py`` directly. 2025-05-30T19:18:52,186 Instead, use pypa/build, pypa/installer or other 2025-05-30T19:18:52,187 standards-based tools. 2025-05-30T19:18:52,188 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-05-30T19:18:52,189 or your builds will no longer be supported. 2025-05-30T19:18:52,190 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-05-30T19:18:52,191 ******************************************************************************** 2025-05-30T19:18:52,192 !! 2025-05-30T19:18:52,193 _install.initialize_options(self) 2025-05-30T19:18:52,216 installing to build/bdist.linux-armv7l/wheel 2025-05-30T19:18:52,216 running install 2025-05-30T19:18:52,240 running install_lib 2025-05-30T19:18:52,266 creating build/bdist.linux-armv7l/wheel 2025-05-30T19:18:52,268 creating build/bdist.linux-armv7l/wheel/kneaddata 2025-05-30T19:18:52,270 copying build/lib/kneaddata/__init__.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,271 copying build/lib/kneaddata/bowtie2_discordant_pairs.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,274 copying build/lib/kneaddata/generate_db.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,276 copying build/lib/kneaddata/utilities.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,280 creating build/bdist.linux-armv7l/wheel/kneaddata/db_preprocessing 2025-05-30T19:18:52,281 copying build/lib/kneaddata/db_preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,283 copying build/lib/kneaddata/db_preprocessing/downsample.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,285 copying build/lib/kneaddata/db_preprocessing/Modify_RNA_to_DNA.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,288 copying build/lib/kneaddata/db_preprocessing/fastq_to_fasta.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,290 copying build/lib/kneaddata/db_preprocessing/reservoir.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,292 copying build/lib/kneaddata/db_preprocessing/mergesams.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,295 copying build/lib/kneaddata/db_preprocessing/filter_bugs.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,297 copying build/lib/kneaddata/db_preprocessing/prefix_human_transcriptome.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,300 copying build/lib/kneaddata/db_preprocessing/filter_silva.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,302 copying build/lib/kneaddata/db_preprocessing/convert_rna.py -> build/bdist.linux-armv7l/wheel/./kneaddata/db_preprocessing 2025-05-30T19:18:52,305 copying build/lib/kneaddata/read_count_table_concat_pairs.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,308 copying build/lib/kneaddata/knead_data.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,312 creating build/bdist.linux-armv7l/wheel/kneaddata/adapters 2025-05-30T19:18:52,313 copying build/lib/kneaddata/adapters/TruSeq2-SE.fa -> build/bdist.linux-armv7l/wheel/./kneaddata/adapters 2025-05-30T19:18:52,316 copying build/lib/kneaddata/adapters/TruSeq3-SE.fa -> build/bdist.linux-armv7l/wheel/./kneaddata/adapters 2025-05-30T19:18:52,318 copying build/lib/kneaddata/adapters/NexteraPE-PE.fa -> build/bdist.linux-armv7l/wheel/./kneaddata/adapters 2025-05-30T19:18:52,321 copying build/lib/kneaddata/adapters/TruSeq3-PE.fa -> build/bdist.linux-armv7l/wheel/./kneaddata/adapters 2025-05-30T19:18:52,323 copying build/lib/kneaddata/adapters/TruSeq2-PE.fa -> build/bdist.linux-armv7l/wheel/./kneaddata/adapters 2025-05-30T19:18:52,326 creating build/bdist.linux-armv7l/wheel/kneaddata/tests 2025-05-30T19:18:52,327 copying build/lib/kneaddata/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./kneaddata/tests 2025-05-30T19:18:52,329 copying build/lib/kneaddata/tests/cfg.py -> build/bdist.linux-armv7l/wheel/./kneaddata/tests 2025-05-30T19:18:52,332 copying build/lib/kneaddata/tests/kneaddata_test.py -> build/bdist.linux-armv7l/wheel/./kneaddata/tests 2025-05-30T19:18:52,334 copying build/lib/kneaddata/tests/functional_tests.py -> build/bdist.linux-armv7l/wheel/./kneaddata/tests 2025-05-30T19:18:52,338 creating build/bdist.linux-armv7l/wheel/kneaddata/tests/data 2025-05-30T19:18:52,340 copying build/lib/kneaddata/tests/data/demo.sam -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,351 copying build/lib/kneaddata/tests/data/merge3.fastq -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,354 copying build/lib/kneaddata/tests/data/demo.fastq -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,368 copying build/lib/kneaddata/tests/data/merge1.fastq -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,370 copying build/lib/kneaddata/tests/data/demo_matches_sam_and_bam.fastq -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,383 copying build/lib/kneaddata/tests/data/demo2.fastq -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,392 copying build/lib/kneaddata/tests/data/demo.bam -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,396 copying build/lib/kneaddata/tests/data/merge2.fastq -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,399 creating build/bdist.linux-armv7l/wheel/kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,400 copying build/lib/kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,477 copying build/lib/kneaddata/tests/data/demo_bowtie2_db/demo_db.3.bt2 -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,479 copying build/lib/kneaddata/tests/data/demo_bowtie2_db/demo_db.4.bt2 -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,481 copying build/lib/kneaddata/tests/data/demo_bowtie2_db/demo_db.2.bt2 -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,482 copying build/lib/kneaddata/tests/data/demo_bowtie2_db/demo_db.1.bt2 -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,554 copying build/lib/kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data/demo_bowtie2_db 2025-05-30T19:18:52,556 copying build/lib/kneaddata/tests/data/demo.fastq.gz -> build/bdist.linux-armv7l/wheel/./kneaddata/tests/data 2025-05-30T19:18:52,559 copying build/lib/kneaddata/tests/basic_tests.py -> build/bdist.linux-armv7l/wheel/./kneaddata/tests 2025-05-30T19:18:52,561 copying build/lib/kneaddata/tests/utils.py -> build/bdist.linux-armv7l/wheel/./kneaddata/tests 2025-05-30T19:18:52,563 copying build/lib/kneaddata/trf_parallel.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,565 copying build/lib/kneaddata/download_db.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,567 copying build/lib/kneaddata/config.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,570 copying build/lib/kneaddata/run.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,572 copying build/lib/kneaddata/read_count_table.py -> build/bdist.linux-armv7l/wheel/./kneaddata 2025-05-30T19:18:52,574 running install_egg_info 2025-05-30T19:18:52,608 running egg_info 2025-05-30T19:18:52,635 writing kneaddata.egg-info/PKG-INFO 2025-05-30T19:18:52,638 writing dependency_links to kneaddata.egg-info/dependency_links.txt 2025-05-30T19:18:52,640 writing entry points to kneaddata.egg-info/entry_points.txt 2025-05-30T19:18:52,642 writing top-level names to kneaddata.egg-info/top_level.txt 2025-05-30T19:18:52,679 reading manifest file 'kneaddata.egg-info/SOURCES.txt' 2025-05-30T19:18:52,684 reading manifest template 'MANIFEST.in' 2025-05-30T19:18:52,687 adding license file 'LICENSE' 2025-05-30T19:18:52,691 writing manifest file 'kneaddata.egg-info/SOURCES.txt' 2025-05-30T19:18:52,693 Copying kneaddata.egg-info to build/bdist.linux-armv7l/wheel/./kneaddata-0.12.3-py3.11.egg-info 2025-05-30T19:18:52,703 running install_scripts 2025-05-30T19:18:52,707 Installing Trimmomatic. 2025-05-30T19:18:52,708 Downloading http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip 2025-05-30T19:18:53,831 Downloading file of size: 0.12 MB 2025-05-30T19:18:53,841 0.01 MB 6.59 % 23.59 MB/sec 0 min 0 sec 2025-05-30T19:18:53,842 0.02 MB 13.19 % 1.62 MB/sec 0 min 0 sec 2025-05-30T19:18:53,842 0.02 MB 19.78 % 2.35 MB/sec 0 min 0 sec 2025-05-30T19:18:53,843 0.03 MB 26.38 % 3.04 MB/sec 0 min 0 sec 2025-05-30T19:18:53,852 0.04 MB 32.97 % 3.71 MB/sec 0 min 0 sec 2025-05-30T19:18:53,853 0.05 MB 39.57 % 2.21 MB/sec 0 min 0 sec 2025-05-30T19:18:53,854 0.05 MB 46.16 % 2.54 MB/sec 0 min 0 sec 2025-05-30T19:18:53,855 0.06 MB 52.75 % 2.87 MB/sec 0 min 0 sec 2025-05-30T19:18:53,864 0.07 MB 59.35 % 3.19 MB/sec 0 min 0 sec 2025-05-30T19:18:53,865 0.08 MB 65.94 % 2.37 MB/sec 0 min 0 sec 2025-05-30T19:18:53,866 0.09 MB 72.54 % 2.59 MB/sec 0 min 0 sec 2025-05-30T19:18:53,867 0.09 MB 79.13 % 2.80 MB/sec 0 min 0 sec 2025-05-30T19:18:53,868 0.10 MB 85.73 % 3.02 MB/sec 0 min 0 sec 2025-05-30T19:18:53,869 0.11 MB 92.32 % 3.22 MB/sec 0 min 0 sec 2025-05-30T19:18:53,871 0.12 MB 98.91 % 3.43 MB/sec 0 min 0 sec 2025-05-30T19:18:53,895 0.12 MB 105.51 % 3.63 MB/sec 0 min -0 sec 2025-05-30T19:18:53,896 Warning: Unable to install Trimmomatic. Please install Trimmomatic. 2025-05-30T19:18:53,899 Installing bowtie2. 2025-05-30T19:18:53,900 Downloading http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip 2025-05-30T19:18:54,249 Warning: Unable to download http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip 2025-05-30T19:18:54,252 Warning: Unable to extract bowtie2. 2025-05-30T19:18:54,253 Warning: Bowtie2 files not found. 2025-05-30T19:18:54,255 Warning: Unable to install bowtie2. Please install bowtie2. 2025-05-30T19:18:54,255 Downloading https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64 2025-05-30T19:18:54,798 Warning: Unable to download https://github.com/Benson-Genomics-Lab/TRF/releases/download/v4.09.1/trf409.linux64 2025-05-30T19:18:54,799 ERROR: Unable to install TRF 2025-05-30T19:18:54,817 creating build/bdist.linux-armv7l/wheel/kneaddata-0.12.3.dist-info/WHEEL 2025-05-30T19:18:54,820 creating '/tmp/pip-wheel-xxxyh_wx/kneaddata-0.12.3-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-05-30T19:18:54,822 adding 'kneaddata/__init__.py' 2025-05-30T19:18:54,824 adding 'kneaddata/bowtie2_discordant_pairs.py' 2025-05-30T19:18:54,826 adding 'kneaddata/config.py' 2025-05-30T19:18:54,828 adding 'kneaddata/download_db.py' 2025-05-30T19:18:54,829 adding 'kneaddata/generate_db.py' 2025-05-30T19:18:54,833 adding 'kneaddata/knead_data.py' 2025-05-30T19:18:54,835 adding 'kneaddata/read_count_table.py' 2025-05-30T19:18:54,836 adding 'kneaddata/read_count_table_concat_pairs.py' 2025-05-30T19:18:54,840 adding 'kneaddata/run.py' 2025-05-30T19:18:54,842 adding 'kneaddata/trf_parallel.py' 2025-05-30T19:18:54,848 adding 'kneaddata/utilities.py' 2025-05-30T19:18:54,850 adding 'kneaddata/adapters/NexteraPE-PE.fa' 2025-05-30T19:18:54,851 adding 'kneaddata/adapters/TruSeq2-PE.fa' 2025-05-30T19:18:54,853 adding 'kneaddata/adapters/TruSeq2-SE.fa' 2025-05-30T19:18:54,854 adding 'kneaddata/adapters/TruSeq3-PE.fa' 2025-05-30T19:18:54,855 adding 'kneaddata/adapters/TruSeq3-SE.fa' 2025-05-30T19:18:54,857 adding 'kneaddata/db_preprocessing/Modify_RNA_to_DNA.py' 2025-05-30T19:18:54,858 adding 'kneaddata/db_preprocessing/__init__.py' 2025-05-30T19:18:54,860 adding 'kneaddata/db_preprocessing/convert_rna.py' 2025-05-30T19:18:54,861 adding 'kneaddata/db_preprocessing/downsample.py' 2025-05-30T19:18:54,862 adding 'kneaddata/db_preprocessing/fastq_to_fasta.py' 2025-05-30T19:18:54,863 adding 'kneaddata/db_preprocessing/filter_bugs.py' 2025-05-30T19:18:54,865 adding 'kneaddata/db_preprocessing/filter_silva.py' 2025-05-30T19:18:54,866 adding 'kneaddata/db_preprocessing/mergesams.py' 2025-05-30T19:18:54,867 adding 'kneaddata/db_preprocessing/prefix_human_transcriptome.py' 2025-05-30T19:18:54,869 adding 'kneaddata/db_preprocessing/reservoir.py' 2025-05-30T19:18:54,870 adding 'kneaddata/tests/__init__.py' 2025-05-30T19:18:54,872 adding 'kneaddata/tests/basic_tests.py' 2025-05-30T19:18:54,873 adding 'kneaddata/tests/cfg.py' 2025-05-30T19:18:54,875 adding 'kneaddata/tests/functional_tests.py' 2025-05-30T19:18:54,877 adding 'kneaddata/tests/kneaddata_test.py' 2025-05-30T19:18:54,879 adding 'kneaddata/tests/utils.py' 2025-05-30T19:18:54,889 adding 'kneaddata/tests/data/demo.bam' 2025-05-30T19:18:55,005 adding 'kneaddata/tests/data/demo.fastq' 2025-05-30T19:18:55,016 adding 'kneaddata/tests/data/demo.fastq.gz' 2025-05-30T19:18:55,121 adding 'kneaddata/tests/data/demo.sam' 2025-05-30T19:18:55,232 adding 'kneaddata/tests/data/demo2.fastq' 2025-05-30T19:18:55,345 adding 'kneaddata/tests/data/demo_matches_sam_and_bam.fastq' 2025-05-30T19:18:55,349 adding 'kneaddata/tests/data/merge1.fastq' 2025-05-30T19:18:55,350 adding 'kneaddata/tests/data/merge2.fastq' 2025-05-30T19:18:55,351 adding 'kneaddata/tests/data/merge3.fastq' 2025-05-30T19:18:55,440 adding 'kneaddata/tests/data/demo_bowtie2_db/demo_db.1.bt2' 2025-05-30T19:18:55,467 adding 'kneaddata/tests/data/demo_bowtie2_db/demo_db.2.bt2' 2025-05-30T19:18:55,468 adding 'kneaddata/tests/data/demo_bowtie2_db/demo_db.3.bt2' 2025-05-30T19:18:55,469 adding 'kneaddata/tests/data/demo_bowtie2_db/demo_db.4.bt2' 2025-05-30T19:18:55,554 adding 'kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.1.bt2' 2025-05-30T19:18:55,581 adding 'kneaddata/tests/data/demo_bowtie2_db/demo_db.rev.2.bt2' 2025-05-30T19:18:55,584 adding 'kneaddata-0.12.3.dist-info/licenses/LICENSE' 2025-05-30T19:18:55,585 adding 'kneaddata-0.12.3.dist-info/METADATA' 2025-05-30T19:18:55,586 adding 'kneaddata-0.12.3.dist-info/WHEEL' 2025-05-30T19:18:55,587 adding 'kneaddata-0.12.3.dist-info/entry_points.txt' 2025-05-30T19:18:55,587 adding 'kneaddata-0.12.3.dist-info/top_level.txt' 2025-05-30T19:18:55,589 adding 'kneaddata-0.12.3.dist-info/RECORD' 2025-05-30T19:18:55,596 removing build/bdist.linux-armv7l/wheel 2025-05-30T19:18:55,728 Building wheel for kneaddata (setup.py): finished with status 'done' 2025-05-30T19:18:55,736 Created wheel for kneaddata: filename=kneaddata-0.12.3-py3-none-any.whl size=558775 sha256=a418cf5d312f1b243f19502b7cf258b746c89e6fe7c9f17daa132093c4687cd7 2025-05-30T19:18:55,737 Stored in directory: /tmp/pip-ephem-wheel-cache-he0n4yzn/wheels/8f/31/f4/c8d0357c248072a11e71038f40ace96c9e9923246d33dee379 2025-05-30T19:18:55,752 Successfully built kneaddata 2025-05-30T19:18:55,769 Removed build tracker: '/tmp/pip-build-tracker-db4ftzve'