## Rule(s): get_drugbank_vocabulary (53155.log) ``` SNAKEMAKE ========= Date: 2026-07-14 02:24:30 Workflow ID: e9e925e7-7c16-46cd-af66-df61025eed56 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-8 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 1 --force-use-threads --wait-for-files /projects/babel/runs/gaurav/babel-1.18/.snakemake/tmp.ql03kfde --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers code software-env params input mtime --conda-frontend conda --shared-fs-usage source-cache software-deployment-cache software-deployment persistence input-output sources storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --executor slurm-jobstep --jobs 1 --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:24:30+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:24:30+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:24:30+0000]: Using shell: /usr/bin/bash Provided remote nodes: 1 INFO snakemake.logging [2026-07-14T06:24:30+0000]: Provided remote nodes: 1 Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:30+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:30+0000]: Execute 1 jobs... [Tue Jul 14 02:24:30 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:30+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:30+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:24:34 Workflow ID: 911e14f4-755b-4a5c-ac42-1ae6c55e543d Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-8 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 1 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers input code params software-env mtime --conda-frontend conda --shared-fs-usage source-cache sources storage-local-copies input-output persistence software-deployment-cache software-deployment --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:24:34+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:24:34+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:24:34+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:24:34+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:24:34+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:34+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:34+0000]: Execute 1 jobs... [Tue Jul 14 02:24:34 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:34+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:34+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:34+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:34 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:34+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:34+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:34+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:34+0000]: Execute 1 jobs... [Tue Jul 14 02:24:34 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:34+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:34+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:35+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:35 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:35+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:35+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:35+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:35+0000]: Execute 1 jobs... [Tue Jul 14 02:24:35 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:35+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:35+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:35+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:35 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:35+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:35+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:35+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:35+0000]: Execute 1 jobs... [Tue Jul 14 02:24:35 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:35+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:35+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:35+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:35 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:35+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:24:35+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:24:35+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:24:35 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:35+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:24:35+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:24:35+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-8: task 0: Exited with exit code 1 [Tue Jul 14 02:24:36 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:36+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:36+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:36+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:36+0000]: Execute 1 jobs... [Tue Jul 14 02:24:36 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:36+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:36+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:24:40 Workflow ID: c07e7ddf-faee-4453-91fb-a240d1daaa12 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-8 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 2 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers input code params software-env mtime --conda-frontend conda --shared-fs-usage source-cache sources storage-local-copies input-output persistence software-deployment-cache software-deployment --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:24:40+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:24:40+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:24:40+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Execute 1 jobs... [Tue Jul 14 02:24:40 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:40+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:40 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:40+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:40+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Execute 1 jobs... [Tue Jul 14 02:24:40 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:40+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:40 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:40+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:40+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:40+0000]: Execute 1 jobs... [Tue Jul 14 02:24:40 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:40+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:40+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:40 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:40+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:24:40+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:24:40+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:24:40 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:40+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:24:40+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:24:40+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-8: task 0: Exited with exit code 1 [Tue Jul 14 02:24:41 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:41+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:41+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:41+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:41+0000]: Execute 1 jobs... [Tue Jul 14 02:24:41 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:41+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:41+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:24:45 Workflow ID: 11077811-b7a8-4e0f-84fc-989a0a606c46 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-8 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 3 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers input code params software-env mtime --conda-frontend conda --shared-fs-usage source-cache sources storage-local-copies input-output persistence software-deployment-cache software-deployment --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:24:45+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:24:45+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:24:45+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:24:45+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:24:45+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:45+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:45+0000]: Execute 1 jobs... [Tue Jul 14 02:24:45 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:45+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:45+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:45+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:45 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:45+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:45+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:45+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:45+0000]: Execute 1 jobs... [Tue Jul 14 02:24:45 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:45+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:45+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:45+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:45 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:45+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:24:45+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:24:45+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:24:45 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:45+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:24:45+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:24:45+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-8: task 0: Exited with exit code 1 [Tue Jul 14 02:24:47 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:47+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:24:47+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:47+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:47+0000]: Execute 1 jobs... [Tue Jul 14 02:24:47 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:47+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:47+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:24:50 Workflow ID: 5a7604b7-d1eb-4651-95aa-ad358acbea5f Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-8 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 4 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers input code params software-env mtime --conda-frontend conda --shared-fs-usage source-cache sources storage-local-copies input-output persistence software-deployment-cache software-deployment --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:24:50+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:24:50+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:24:50+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:24:50+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:24:50+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:24:50+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:24:50+0000]: Execute 1 jobs... [Tue Jul 14 02:24:50 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:24:50+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:24:50+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:24:50+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:24:50 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:50+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:24:50+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:24:50+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:24:50 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:50+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:24:50+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:24:50+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-8: task 0: Exited with exit code 1 [Tue Jul 14 02:24:51 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:51+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:24:51+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:24:51+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:24:51 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:24:51+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:24:51+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:24:51+0000]: WorkflowError: At least one job did not complete successfully. ``` ## Rule(s): get_drugbank_vocabulary (53159.log) ``` SNAKEMAKE ========= Date: 2026-07-14 02:25:40 Workflow ID: 0ef4494d-fcb1-457b-931b-794b01f18b9e Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 2 --force-use-threads --wait-for-files /projects/babel/runs/gaurav/babel-1.18/.snakemake/tmp.ql03kfde --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers code software-env params input mtime --conda-frontend conda --shared-fs-usage source-cache software-deployment-cache software-deployment persistence input-output sources storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --executor slurm-jobstep --jobs 1 --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:25:40+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:25:40+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:25:40+0000]: Using shell: /usr/bin/bash Provided remote nodes: 1 INFO snakemake.logging [2026-07-14T06:25:40+0000]: Provided remote nodes: 1 Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:40+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:40+0000]: Execute 1 jobs... [Tue Jul 14 02:25:40 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:40+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:40+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:25:43 Workflow ID: 1193b7c0-3b5c-4ff4-a50b-b75a14429a5c Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 2 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime params software-env code input --conda-frontend conda --shared-fs-usage sources software-deployment persistence software-deployment-cache source-cache input-output storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:25:43+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:25:43+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:25:43+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Execute 1 jobs... [Tue Jul 14 02:25:43 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:25:43+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:25:43 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:43+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:25:43+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Execute 1 jobs... [Tue Jul 14 02:25:43 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:25:43+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:25:43 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:43+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:25:43+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:43+0000]: Execute 1 jobs... [Tue Jul 14 02:25:43 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:43+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:25:44+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:25:44 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:44+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:25:44+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:25:44+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:25:44 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:44+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:25:44+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:25:44+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-1: task 0: Exited with exit code 1 [Tue Jul 14 02:25:45 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:45+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:25:45+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:45+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:45+0000]: Execute 1 jobs... [Tue Jul 14 02:25:45 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:45+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:45+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:25:48 Workflow ID: 3495ecf8-9eb2-4406-adf9-2aef049cbc13 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 3 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime params software-env code input --conda-frontend conda --shared-fs-usage sources software-deployment persistence software-deployment-cache source-cache input-output storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:25:48+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:25:48+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:25:48+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:25:48+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:25:48+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:48+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:48+0000]: Execute 1 jobs... [Tue Jul 14 02:25:48 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:48+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:48+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:25:48+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:25:48 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:48+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:25:48+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:48+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:48+0000]: Execute 1 jobs... [Tue Jul 14 02:25:48 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:48+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:48+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:25:48+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:25:48 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:48+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:25:48+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:25:48+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:25:48 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:48+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:25:48+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:25:48+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-1: task 0: Exited with exit code 1 [Tue Jul 14 02:25:49 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:49+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:25:49+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:49+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:49+0000]: Execute 1 jobs... [Tue Jul 14 02:25:49 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:49+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:49+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:25:53 Workflow ID: fa3c1dbb-e03c-4742-b47b-e790bc217cb6 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 4 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime params software-env code input --conda-frontend conda --shared-fs-usage sources software-deployment persistence software-deployment-cache source-cache input-output storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:25:53+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:25:53+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:25:53+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:25:53+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:25:53+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:25:53+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:25:53+0000]: Execute 1 jobs... [Tue Jul 14 02:25:53 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:25:53+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:25:53+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:25:53+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:25:53 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:53+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:25:53+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:25:53+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:25:53 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:53+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:25:53+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:25:53+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-1: task 0: Exited with exit code 1 [Tue Jul 14 02:25:54 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:54+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:25:54+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:25:54+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:25:54 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:25:54+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:25:54+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:25:54+0000]: WorkflowError: At least one job did not complete successfully. ``` ## Rule(s): get_drugbank_vocabulary (53161.log) ``` SNAKEMAKE ========= Date: 2026-07-14 02:26:19 Workflow ID: 802bee25-d80c-4c61-8806-586baf656319 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 3 --force-use-threads --wait-for-files /projects/babel/runs/gaurav/babel-1.18/.snakemake/tmp.ql03kfde --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers code software-env params input mtime --conda-frontend conda --shared-fs-usage source-cache software-deployment-cache software-deployment persistence input-output sources storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --executor slurm-jobstep --jobs 1 --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:26:19+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:26:19+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:26:19+0000]: Using shell: /usr/bin/bash Provided remote nodes: 1 INFO snakemake.logging [2026-07-14T06:26:19+0000]: Provided remote nodes: 1 Select jobs to execute... INFO snakemake.logging [2026-07-14T06:26:19+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:26:19+0000]: Execute 1 jobs... [Tue Jul 14 02:26:19 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:26:19+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:26:19+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:26:22 Workflow ID: 9e76c6ad-cf38-443d-a04d-009388ff89f0 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 3 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime params input software-env code --conda-frontend conda --shared-fs-usage storage-local-copies persistence input-output sources source-cache software-deployment software-deployment-cache --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:26:22+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:26:22+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:26:22+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:26:22+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:26:22+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:26:22+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:26:22+0000]: Execute 1 jobs... [Tue Jul 14 02:26:22 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:26:22+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:26:22+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:26:23+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:26:23 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:23+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:26:23+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:26:23+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:26:23+0000]: Execute 1 jobs... [Tue Jul 14 02:26:23 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:26:23+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:26:23+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:26:23+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:26:23 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:23+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:26:23+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:26:23+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:26:23 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:23+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:26:23+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:26:23+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-1: task 0: Exited with exit code 1 [Tue Jul 14 02:26:24 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:24+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Trying to restart job 0. INFO snakemake.logging [2026-07-14T06:26:24+0000]: Trying to restart job 0. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:26:24+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:26:24+0000]: Execute 1 jobs... [Tue Jul 14 02:26:24 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:26:24+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:26:24+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:26:27 Workflow ID: 23359e8a-c7ce-4836-8f3e-633fe18d9f3c Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 4 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime params input software-env code --conda-frontend conda --shared-fs-usage storage-local-copies persistence input-output sources source-cache software-deployment software-deployment-cache --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:26:27+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:26:27+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:26:27+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:26:27+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:26:27+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:26:27+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:26:27+0000]: Execute 1 jobs... [Tue Jul 14 02:26:27 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, mem_mb=16000, mem=16 GB, mem_mib=15259, disk_mb=50000, disk=50 GB, disk_mib=47684, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:26:27+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:26:27+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:26:28+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:26:28 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:28+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:26:28+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:26:28+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:26:28 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:28+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:26:28+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:26:28+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-1: task 0: Exited with exit code 1 [Tue Jul 14 02:26:29 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:29+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:26:29+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:26:29+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:26:29 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:26:29+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:26:29+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:26:29+0000]: WorkflowError: At least one job did not complete successfully. ``` ## Rule(s): get_drugbank_vocabulary (53162.log) ``` SNAKEMAKE ========= Date: 2026-07-14 02:27:10 Workflow ID: 99c99420-4458-4c16-82d2-f9c7df9d7eb2 Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 4 --force-use-threads --wait-for-files /projects/babel/runs/gaurav/babel-1.18/.snakemake/tmp.ql03kfde --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers code software-env params input mtime --conda-frontend conda --shared-fs-usage source-cache software-deployment-cache software-deployment persistence input-output sources storage-local-copies --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --executor slurm-jobstep --jobs 1 --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:27:10+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:27:10+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:27:10+0000]: Using shell: /usr/bin/bash Provided remote nodes: 1 INFO snakemake.logging [2026-07-14T06:27:10+0000]: Provided remote nodes: 1 Select jobs to execute... INFO snakemake.logging [2026-07-14T06:27:10+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:27:10+0000]: Execute 1 jobs... [Tue Jul 14 02:27:10 2026] rule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:27:10+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:27:10+0000]: Shell command: None SNAKEMAKE ========= Date: 2026-07-14 02:27:13 Workflow ID: 6a5d08a1-f880-4973-9b8d-9006d736f23b Platform: Linux-5.14.0-427.70.1.el9_4.x86_64-x86_64-with-glibc2.34 Host: compute-13-1 User: gaurav Snakemake version: 9.23.1 Python version: 3.13.9 (main, Oct 14 2025, 21:29:44) [Clang 20.1.4 ] Command: /projects/babel/runs/gaurav/babel-1.18/.venv/lib/python3.13/site-packages/snakemake/__main__.py --snakefile /projects/babel/runs/gaurav/babel-1.18/Snakefile --target-jobs get_drugbank_vocabulary: --allowed-rules get_drugbank_vocabulary --cores all --attempt 4 --force-use-threads --force --target-files-omit-workdir-adjustment --max-inventory-time 0 --retries 0 --nocolor --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime input params code software-env --conda-frontend conda --shared-fs-usage persistence storage-local-copies source-cache software-deployment-cache sources software-deployment input-output --latency-wait 60 --scheduler ilp --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path /projects/babel/runs/gaurav/babel-1.18/.venv/bin --runtime-source-cache-path /home/gaurav/.cache/snakemake/snakemake/source-cache/snakemake-runtime-cache/tmp4tbkvqhk --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= base64//bWVtX21iPTE2MDAw base64//cnVudGltZT0xMjA= base64//Y3B1c19wZXJfdGFzaz0x --mode remote Snakefile: /projects/babel/runs/gaurav/babel-1.18/Snakefile Base directory: /projects/babel/runs/gaurav/babel-1.18 Run directory: /projects/babel/runs/gaurav/babel-1.18 Working directory: /projects/babel/runs/gaurav/babel-1.18 Config file(s): ['config.yaml', 'config.yaml'] Config MD5: eda72a598cf6f8676e7be6b40ac56b9d INFO snakemake.logging [2026-07-14T06:27:13+0000]: Workflow has started! Building DAG of jobs... INFO snakemake.logging [2026-07-14T06:27:13+0000]: Building DAG of jobs... Using shell: /usr/bin/bash INFO snakemake.logging [2026-07-14T06:27:13+0000]: Using shell: /usr/bin/bash Provided cores: 64 INFO snakemake.logging [2026-07-14T06:27:13+0000]: Provided cores: 64 Rules claiming more threads will be scaled down. INFO snakemake.logging [2026-07-14T06:27:13+0000]: Rules claiming more threads will be scaled down. Select jobs to execute... INFO snakemake.logging [2026-07-14T06:27:13+0000]: Select jobs to execute... Execute 1 jobs... INFO snakemake.logging [2026-07-14T06:27:13+0000]: Execute 1 jobs... [Tue Jul 14 02:27:13 2026] localrule get_drugbank_vocabulary: output: babel_downloads/DRUGBANK/drugbank vocabulary.csv jobid: 0 benchmark: babel_outputs/benchmarks/get_drugbank_vocabulary.tsv reason: Forced execution resources: tmpdir=/projects/babel/runs/gaurav/babel-1.18/babel_downloads/tmp, disk_mb=50000, disk=50 GB, disk_mib=47684, mem_mb=16000, mem=16 GB, mem_mib=15259, runtime=120, cpus_per_task=1 INFO snakemake.logging [2026-07-14T06:27:13+0000]: Rule: get_drugbank_vocabulary, Jobid: 0 INFO snakemake.logging [2026-07-14T06:27:13+0000]: Shell command: None RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents ERROR snakemake.logging [2026-07-14T06:27:13+0000]: RuleException: BadZipFile in file "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848: File is not a zip file File "/projects/babel/runs/gaurav/babel-1.18/src/snakefiles/datacollect.snakefile", line 848, in __rule_get_drugbank_vocabulary File "/projects/babel/runs/gaurav/babel-1.18/src/datahandlers/drugbank.py", line 28, in download_drugbank_vocabulary File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1385, in __init__ File "/home/gaurav/.local/share/uv/python/cpython-3.13.9-linux-x86_64-gnu/lib/python3.13/zipfile/__init__.py", line 1452, in _RealGetContents [Tue Jul 14 02:27:13 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:27:13+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:27:13+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:27:13+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:27:13 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:27:13+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:27:13+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:27:13+0000]: WorkflowError: At least one job did not complete successfully. srun: error: compute-13-1: task 0: Exited with exit code 1 [Tue Jul 14 02:27:14 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:27:14+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Shutting down, this might take some time. INFO snakemake.logging [2026-07-14T06:27:14+0000]: Shutting down, this might take some time. Exiting because a job execution failed. Look below for error messages ERROR snakemake.logging [2026-07-14T06:27:14+0000]: Exiting because a job execution failed. Look below for error messages [Tue Jul 14 02:27:14 2026] Error in rule get_drugbank_vocabulary: message: None jobid: 0 output: babel_downloads/DRUGBANK/drugbank vocabulary.csv ERROR snakemake.logging [2026-07-14T06:27:14+0000]: Error in rule get_drugbank_vocabulary, jobid: 0 Storing output in storage. INFO snakemake.logging [2026-07-14T06:27:14+0000]: Storing output in storage. WorkflowError: At least one job did not complete successfully. ERROR snakemake.logging [2026-07-14T06:27:14+0000]: WorkflowError: At least one job did not complete successfully. ```