Traceback (most recent call last): File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/cli.py", line 2044, in args_to_api config_settings=ConfigSettings( ^^^^^^^^^^^^^^^ File "", line 6, in __init__ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/settings/types.py", line 353, in __post_init__ self.overwrite_config = self._get_overwrite_config() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/settings/types.py", line 361, in _get_overwrite_config update_config(overwrite_config, load_configfile(f)) ^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/common/configfile.py", line 38, in load_configfile config = _load_configfile(configpath) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/common/configfile.py", line 12, in _load_configfile obj = open(configpath_or_obj, encoding="utf-8") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/code/phil_config.yml' Traceback (most recent call last): File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/cli.py", line 2044, in args_to_api config_settings=ConfigSettings( ^^^^^^^^^^^^^^^ File "", line 6, in __init__ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/settings/types.py", line 353, in __post_init__ self.overwrite_config = self._get_overwrite_config() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/settings/types.py", line 361, in _get_overwrite_config update_config(overwrite_config, load_configfile(f)) ^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/common/configfile.py", line 38, in load_configfile config = _load_configfile(configpath) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/common/configfile.py", line 12, in _load_configfile obj = open(configpath_or_obj, encoding="utf-8") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/code/37-phil_config.yml' TypeError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 68: 'NoneType' object is not subscriptable File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 68, in KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 72: 'path' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 72, in KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 100: 'n_pairs' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 100, in KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'use_llm' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... MissingInputException in rule annotate_seqs_pfam in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 58: Missing input files for rule annotate_seqs_pfam: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_hmmscan.tblout affected files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/data/Apulchra-genome.pep.fa Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... MissingInputException in rule generate_candidates in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 90: Missing input files for rule generate_candidates: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_candidates.tsv affected files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter.txt Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 10 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:17:42 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/pfam_gobp_most_specific.txt resources: tmpdir=/tmp host: raven [Sat Sep 27 05:18:14 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:18:14 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 05:18:59 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:18:59 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm threads: 10 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... IncompleteFilesException: The files below seem to be incomplete. If you are sure that certain files are not incomplete, mark them as complete with snakemake --cleanup-metadata To re-generate the files rerun your command with the --rerun-incomplete flag. Incomplete files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_hmmscan.tblout Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:20:33 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/go.obo resources: tmpdir=/tmp host: raven [Sat Sep 27 05:21:00 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:21:00 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 05:21:43 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:21:43 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Apulchra_PPI_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/output/philharmonic_output/Pfam-A.hmm.h3p threads: 10 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:39:47 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 05:40:28 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:40:28 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3p; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 05:41:11 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:41:11 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Apulchra_PPI_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Apulchra_PPI_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37-Apul-phil/Pfam-A.hmm.h3p threads: 48 resources: tmpdir=/tmp KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'OPENAI_API_KEY' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in File "", line 679, in __getitem__ Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:48:12 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/goslim_generic.obo resources: tmpdir=/tmp host: raven [Sat Sep 27 05:48:45 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:48:45 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 05:49:38 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 05:49:38 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p threads: 32 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:03:44 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 06:04:18 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:04:18 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'OPENAI_API_KEY' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in File "", line 679, in __getitem__ [Sat Sep 27 06:05:12 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:05:12 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m threads: 48 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:10:59 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt resources: tmpdir=/tmp host: raven RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 35: Command 'set -euo pipefail; curl ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/01_download_required_files.log 2>&1' returned non-zero exit status 56. [Sat Sep 27 06:11:01 2025] Error in rule download_required_files: jobid: 0 output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/01_download_required_files.log (check log file(s) for error details) Exiting because a job execution failed. Look above for error message WorkflowError: At least one job did not complete successfully. Traceback (most recent call last): File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/executors/local.py", line 232, in spawn_job subprocess.check_call(cmd, shell=True) File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'cd /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular && /opt/anaconda/anaconda3/envs/philharmonic_py311_env/bin/python -m snakemake --snakefile '/home/shared/philharmonic/philharmonic/philharmonic_snakefile' --target-jobs 'download_required_files:' --allowed-rules download_required_files --cores 48 --attempt 1 --force-use-threads --force --target-files-omit-workdir-adjustment --keep-storage-local-copies --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers mtime input code software-env params --conda-frontend 'conda' --shared-fs-usage persistence software-deployment sources input-output source-cache storage-local-copies --wrapper-prefix 'https://github.com/snakemake/snakemake-wrappers/raw/' --latency-wait 5 --scheduler 'greedy' --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path '/opt/anaconda/anaconda3/envs/philharmonic_py311_env/bin' --configfiles /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/code/38.02-phil-config.yml --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= --quiet progress rules --mode 'subprocess' --local-groupid 'local'' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, **self.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/executors/local.py", line 247, in cached_or_run run_func(*args) File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/executors/local.py", line 234, in spawn_job raise SpawnedJobError() snakemake.exceptions.SpawnedJobError [Sat Sep 27 06:11:01 2025] Error in rule download_required_files: jobid: 3 output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/01_download_required_files.log (check log file(s) for error details) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T061059.395083.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:12:18 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/goslim_generic.obo resources: tmpdir=/tmp host: raven [Sat Sep 27 06:12:53 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:12:53 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 06:13:49 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 06:13:49 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p threads: 32 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:26:26 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 07:26:49 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:26:49 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 07:27:43 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:27:43 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38-Apul-phil/Pfam-A.hmm.h3i threads: 32 resources: tmpdir=/tmp RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 76: KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'OPENAI_API_KEY' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in File "", line 679, in __getitem__ KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'OPENAI_API_KEY' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in File "", line 679, in __getitem__ Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... LockException: Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... LockException: Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:35:35 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo resources: tmpdir=/tmp host: raven [Sat Sep 27 07:36:04 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:36:04 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 07:36:59 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:36:59 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p threads: 32 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:49:53 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo resources: tmpdir=/tmp host: raven [Sat Sep 27 07:50:22 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:50:22 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 07:51:16 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 07:51:16 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i threads: 32 resources: tmpdir=/tmp KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'OPENAI_API_KEY' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in File "", line 679, in __getitem__ Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:19:26 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 35: Command 'set -euo pipefail; curl ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log 2>&1' returned non-zero exit status 56. [Sat Sep 27 08:19:28 2025] Error in rule download_required_files: jobid: 0 output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log (check log file(s) for error details) Exiting because a job execution failed. Look above for error message WorkflowError: At least one job did not complete successfully. Traceback (most recent call last): File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/executors/local.py", line 232, in spawn_job subprocess.check_call(cmd, shell=True) File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'cd /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular && /opt/anaconda/anaconda3/envs/philharmonic_py311_env/bin/python -m snakemake --snakefile '/home/shared/philharmonic/philharmonic/philharmonic_snakefile' --target-jobs 'download_required_files:' --allowed-rules download_required_files --cores 48 --attempt 1 --force-use-threads --force --target-files-omit-workdir-adjustment --keep-storage-local-copies --max-inventory-time 0 --nocolor --notemp --no-hooks --nolock --ignore-incomplete --rerun-triggers code input software-env mtime params --conda-frontend 'conda' --shared-fs-usage source-cache software-deployment input-output storage-local-copies sources persistence --wrapper-prefix 'https://github.com/snakemake/snakemake-wrappers/raw/' --latency-wait 5 --scheduler 'greedy' --local-storage-prefix base64//LnNuYWtlbWFrZS9zdG9yYWdl --scheduler-solver-path '/opt/anaconda/anaconda3/envs/philharmonic_py311_env/bin' --configfiles /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/code/38-phil-config.yml --default-resources base64//dG1wZGlyPXN5c3RlbV90bXBkaXI= --quiet progress rules --mode 'subprocess' --local-groupid 'local'' returned non-zero exit status 1. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/concurrent/futures/thread.py", line 58, in run result = self.fn(*self.args, **self.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/executors/local.py", line 247, in cached_or_run run_func(*args) File "/opt/anaconda/anaconda3/envs/philharmonic_py311_env/lib/python3.11/site-packages/snakemake/executors/local.py", line 234, in spawn_job raise SpawnedJobError() snakemake.exceptions.SpawnedJobError [Sat Sep 27 08:19:28 2025] Error in rule download_required_files: jobid: 3 output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log (check log file(s) for error details) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T081926.020514.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:20:25 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt resources: tmpdir=/tmp host: raven [Sat Sep 27 08:20:52 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:20:52 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 08:21:47 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:21:47 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f threads: 32 resources: tmpdir=/tmp RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 76: Command 'set -euo pipefail; hmmscan --cpu 32 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.out --tblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout --domtblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.domtblout --acc --noali --notextw --cut_ga /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/03_annotate_seqs_pfam.log 2>&1' returned non-zero exit status 241. [Sat Sep 27 08:30:48 2025] Error in rule annotate_seqs_pfam: jobid: 5 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/03_annotate_seqs_pfam.log (check log file(s) for error details) shell: hmmscan --cpu 32 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.out --tblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout --domtblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.domtblout --acc --noali --notextw --cut_ga /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/03_annotate_seqs_pfam.log 2>&1 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Removing output files of failed job annotate_seqs_pfam since they might be corrupted: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T061218.593668.snakemake.log WorkflowError: At least one job did not complete successfully. RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 76: Command 'set -euo pipefail; hmmscan --cpu 48 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.out --tblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout --domtblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.domtblout --acc --noali --notextw --cut_ga /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/03_annotate_seqs_pfam.log 2>&1' returned non-zero exit status 241. [Sat Sep 27 08:30:50 2025] Error in rule annotate_seqs_pfam: jobid: 5 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/03_annotate_seqs_pfam.log (check log file(s) for error details) shell: hmmscan --cpu 48 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.out --tblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout --domtblout /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.domtblout --acc --noali --notextw --cut_ga /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/03_annotate_seqs_pfam.log 2>&1 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Removing output files of failed job annotate_seqs_pfam since they might be corrupted: RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 76: KeyError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 217: 'OPENAI_API_KEY' File "/home/shared/philharmonic/philharmonic/philharmonic_snakefile", line 217, in File "", line 679, in __getitem__ Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:36:35 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 08:37:12 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:37:12 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 08:38:00 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:38:00 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p threads: 32 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count ----------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 download_required_files 1 generate_candidates 1 predict_network 1 prepare_hmmdb 1 reconnect_recipe 1 summarize_clusters 1 total 13 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:40:55 2025] localrule download_required_files: output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/01_download_required_files.log jobid: 3 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/goslim_generic.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 08:41:26 2025] Finished job 3. 1 of 13 steps (8%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:41:26 2025] localrule prepare_hmmdb: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/02_prepare_hmmdb.log jobid: 6 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.gz resources: tmpdir=/tmp host: raven [Sat Sep 27 08:42:14 2025] Finished job 6. 2 of 13 steps (15%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 08:42:14 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p threads: 32 resources: tmpdir=/tmp [Sat Sep 27 12:37:43 2025] Finished job 5. 3 of 13 steps (23%) done Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3m. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3p. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3i. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/Pfam-A.hmm.h3f. Select jobs to execute... Execute 1 jobs... [Sat Sep 27 12:37:43 2025] localrule annotate_seqs_go: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/04_annotate_seqs_go.log jobid: 4 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_hmmscan.tblout, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/pfam_gobp_most_specific.txt resources: tmpdir=/tmp [Sat Sep 27 12:38:42 2025] Finished job 4. 4 of 13 steps (31%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 12:38:42 2025] localrule generate_candidates: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, assets/go_filter.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/05_generate_candidates.log jobid: 2 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_candidates.tsv; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo resources: tmpdir=/tmp RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 105: Command 'set -euo pipefail; philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo --go_filter assets/go_filter.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/05_generate_candidates.log 2>&1' returned non-zero exit status 1. [Sat Sep 27 12:38:50 2025] Error in rule generate_candidates: jobid: 2 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo, assets/go_filter.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/05_generate_candidates.log (check log file(s) for error details) shell: philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/philharmonic_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/go.obo --go_filter assets/go_filter.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.01-Apul-phil/logs/05_generate_candidates.log 2>&1 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T084055.168891.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 generate_candidates 1 predict_network 1 reconnect_recipe 1 summarize_clusters 1 total 11 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 13:58:29 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout threads: 32 resources: tmpdir=/tmp Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 annotate_seqs_go 1 annotate_seqs_pfam 1 cluster_graph 1 cluster_network 1 compute_distances 1 generate_candidates 1 predict_network 1 reconnect_recipe 1 summarize_clusters 1 total 11 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 14:17:47 2025] localrule annotate_seqs_pfam: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/03_annotate_seqs_pfam.log jobid: 5 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout threads: 48 resources: tmpdir=/tmp [Sat Sep 27 17:52:16 2025] Finished job 5. 1 of 11 steps (9%) done Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3f. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3i. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3p. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/Pfam-A.hmm.h3m. Select jobs to execute... Execute 1 jobs... [Sat Sep 27 17:52:16 2025] localrule annotate_seqs_go: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/pfam_gobp_most_specific.txt output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/04_annotate_seqs_go.log jobid: 4 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_hmmscan.tblout resources: tmpdir=/tmp [Sat Sep 27 17:53:16 2025] Finished job 4. 2 of 11 steps (18%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 17:53:16 2025] localrule generate_candidates: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log jobid: 2 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv resources: tmpdir=/tmp RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 105: Command 'set -euo pipefail; philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo --go_filter /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log 2>&1' returned non-zero exit status 1. [Sat Sep 27 17:53:23 2025] Error in rule generate_candidates: jobid: 2 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log (check log file(s) for error details) shell: philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo --go_filter /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log 2>&1 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T135828.658013.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 cluster_graph 1 cluster_network 1 compute_distances 1 generate_candidates 1 predict_network 1 reconnect_recipe 1 summarize_clusters 1 total 9 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 18:03:04 2025] localrule generate_candidates: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log jobid: 2 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv resources: tmpdir=/tmp RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 105: Command 'set -euo pipefail; philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo --go_filter /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log 2>&1' returned non-zero exit status 1. [Sat Sep 27 18:03:11 2025] Error in rule generate_candidates: jobid: 2 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log (check log file(s) for error details) shell: philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/go.obo --go_filter /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/05_generate_candidates.log 2>&1 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T180303.501764.snakemake.log WorkflowError: At least one job did not complete successfully. [Sat Sep 27 18:10:44 2025] Finished job 5. 1 of 11 steps (9%) done Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3i. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3m. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3p. Removing temporary output /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Pfam-A.hmm.h3f. Select jobs to execute... Execute 1 jobs... [Sat Sep 27 18:10:44 2025] localrule annotate_seqs_go: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/pfam_gobp_most_specific.txt output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/04_annotate_seqs_go.log jobid: 4 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_hmmscan.tblout resources: tmpdir=/tmp [Sat Sep 27 18:11:35 2025] Finished job 4. 2 of 11 steps (18%) done Select jobs to execute... Execute 1 jobs... [Sat Sep 27 18:11:35 2025] localrule generate_candidates: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/05_generate_candidates.log jobid: 2 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_candidates.tsv; Input files updated by another job: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv resources: tmpdir=/tmp RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 105: Command 'set -euo pipefail; philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/go.obo --go_filter /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/05_generate_candidates.log 2>&1' returned non-zero exit status 1. [Sat Sep 27 18:11:42 2025] Error in rule generate_candidates: jobid: 2 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/go.obo, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_kept_proteins.txt, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_candidates.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/05_generate_candidates.log (check log file(s) for error details) shell: philharmonic generate-candidates --paircount -1 -o /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_candidates.tsv --seq_out /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_kept_proteins.txt --go_map /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/Apulchra_PPI_GO_map.csv --go_database /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/go.obo --go_filter /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/assets/go_filter_02.txt --sequences /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --seed 42 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/37.02-Apul-phil/logs/05_generate_candidates.log 2>&1 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T141746.347857.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 cluster_graph 1 cluster_network 1 compute_distances 1 predict_network 1 reconnect_recipe 1 summarize_clusters 1 total 8 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 18:18:34 2025] localrule predict_network: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log jobid: 1 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv resources: tmpdir=/tmp, nvidia_gpu=1 0%| | 0/16384 [00:00 /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log' returned non-zero exit status 1. [Sat Sep 27 18:19:28 2025] Error in rule predict_network: jobid: 1 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log (check log file(s) for error details) shell: dscript predict --pairs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seqs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --model samsl/dscript_human_v1 --outfile /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network --device 0 --thresh 0.5 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T181833.377241.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 cluster_graph 1 cluster_network 1 compute_distances 1 predict_network 1 reconnect_recipe 1 summarize_clusters 1 total 8 Select jobs to execute... Execute 1 jobs... [Sat Sep 27 18:25:49 2025] localrule predict_network: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log jobid: 1 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv; Params have changed since last execution: Union of exclusive params before and now across all output: before: 0 now: -1 resources: tmpdir=/tmp, nvidia_gpu=1 0%| | 0/16384 [00:00 /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log' returned non-zero exit status 1. [Sat Sep 27 18:26:42 2025] Error in rule predict_network: jobid: 1 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log (check log file(s) for error details) shell: dscript predict --pairs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seqs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --model samsl/dscript_human_v1 --outfile /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network --device -1 --thresh 0.5 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-27T182548.482837.snakemake.log WorkflowError: At least one job did not complete successfully. Assuming unrestricted shared filesystem usage. host: raven Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 48 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- PHILHARMONIC 1 add_cluster_functions 1 cluster_graph 1 cluster_network 1 compute_distances 1 predict_network 1 reconnect_recipe 1 summarize_clusters 1 total 8 Select jobs to execute... Execute 1 jobs... [Sun Sep 28 06:48:29 2025] localrule predict_network: input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log jobid: 1 reason: Missing output files: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv; Params have changed since last execution: Union of exclusive params before and now across all output: before: -1 now: 'cpu' resources: tmpdir=/tmp, nvidia_gpu=1 usage: dscript predict [-h] [--proteins PROTEINS] [--pairs PAIRS] [--model MODEL] --embeddings EMBEDDINGS [--foldseek_fasta FOLDSEEK_FASTA] [-o OUTFILE] [-d DEVICE] [--store_cmaps] [--thresh THRESH] [--load_proc LOAD_PROC] [--blocks BLOCKS] [--sparse_loading] dscript predict: error: the following arguments are required: --embeddings RuleException: CalledProcessError in file /home/shared/philharmonic/philharmonic/philharmonic_snakefile, line 125: Command 'set -euo pipefail; dscript predict --pairs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seqs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --model samsl/dscript_human_v1 --outfile /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network --device cpu --thresh 0.5 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log' returned non-zero exit status 2. [Sun Sep 28 06:48:36 2025] Error in rule predict_network: jobid: 1 input: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa, /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv output: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network.positive.tsv log: /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log (check log file(s) for error details) shell: dscript predict --pairs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_candidates.tsv --seqs /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/data/Apulchra-genome.pep.fa --model samsl/dscript_human_v1 --outfile /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/philharmonic_network --device cpu --thresh 0.5 > /home/shared/16TB_HDD_01/sr320/github/timeseries_molecular/D-Apul/output/38.02-Apul-phil/logs/06_predict_network.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2025-09-28T064828.281022.snakemake.log WorkflowError: At least one job did not complete successfully.