05:47:12 INFO [ vustruct.py:137 ] Log file opened by /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py 05:47:12 INFO [ psb_config.py:77 ] Attempting to read config from ['../config/global.config', '../mothcw.config', './SampleCase.config'] 05:47:12 INFO [ psb_config.py:79 ] Successfully read config from ['../config/global.config'] 05:47:12 WARNING [ psb_config.py:94 ] No UserSpecific section was found in the read configuration files 05:47:12 INFO [ PDBMapGlobals.py:55 ] Setting PDBMapGlobal config from dictionary: {'alphafold_dir': '/dors/capra_lab/data/alphafold', 'chgrp_to': 'capra_lab', 'chimera_headless': '/dors/capra_lab/users/mothcw/chimera_headless/bin/chimera', 'cluster_type': 'Slurm', 'collaboration': 'VUStruct', 'container_or_rhenium_home': '/home/mothcw', 'cosmis_dir': '/dors/capra_lab/data/cosmis', 'create_new_db': 'False', 'dbhost': 'vgi01.accre.vanderbilt.edu', 'dbname': 'pdbmap_v14', 'dbpass 'dbuser': 'mothcw', 'ddg_config': '/dors/capra_lab/projects/ddg_repo/ddg_repo_singularity.config', 'downloaded_data': '/dors/capra_lab/data', 'dssp_exe': '/dors/capra_lab/projects/psb_collab/psb_pipeline/data/dssp/dssp_local.exe', 'ensembl_registry': '/dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf', 'gnomad_dir': '/dors/capra_lab/data/gnomad/2.1.1/liftover_grch38/vcf/exomes/exomes', 'gnomad_filename_template': 'gnomad.exomes.r2.1.1.sites.%s.liftover_grch38.vcf.bgz', 'idmapping': '/dors/capra_lab/data/uniprot/current/HUMAN_9606_idmapping_sprot.dat.gz', 'interpro_dir': '/dors/capra_lab/data/interpro/current', 'modbase2020_dir': '/dors/capra_lab/data/modbase/current/model', 'modbase2020_summary': '/dors/capra_lab/data/modbase/current/Homo_sapiens_2020.summary.txt', 'output_rootdir': '/dors/capra_lab/users/mothcw', 'pdb_dir': '/dors/capra_lab/data/pdb/', 'pfam': 'pfam/pdb_pfam_mapping.txt', 'rate4site_dir': '/dors/capra_lab/users/lib14/cosmis/data/rate4site_results', 'refseq_genomic_gff': '/dors/capra_lab/data/refseq/GRCh38_latest_genomic.gff.gz', 'sec2prim': '/dors/capra_lab/data/uniprot/current/uniprot_sec2prim_ac.txt', 'sifts': '/dors/capra_lab/data/sifts/current/xml', 'sprot': '/dors/capra_lab/data/uniprot/current/uniprot_sprot_human.dat', 'swiss_dir': '/dors/capra_lab/data/swissmodel/current/SWISS-MODEL_Repository/', 'swiss_summary': '/dors/capra_lab/data/swissmodel/current/SWISS-MODEL_Repository/INDEX.json', 'vep': '/dors/capra_lab/users/mothcw/ensembl/ensembl-vep/vep', 'vep_assembly': 'GRCh38', 'vep_cache_dir': '/dors/capra_lab/data/ensembl/vep_cache', 'vep_db_version': '105'} 05:47:12 INFO [ psb_launch.py:129 ] Command: /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py 05:47:12 INFO [ psb_launch.py:157 ] Command Line Arguments: {'caseconfig': './SampleCase.config', 'config': '../config/global.config', 'debug': False, 'nolaunch': False, 'projectORworkplan': 'SampleCase', 'relaunch': False, 'userconfig': '../mothcw.config', 'verbose': False} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersPathProx: {'account': 'capra_lab_csb', 'mem': '30GB', 'ntasks': '1', 'time': '2-0'} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersDDGMonomer: {'account': 'capra_lab_csb', 'mem': '20GB', 'ntasks': '1', 'time': '4-00:00:00'} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersDDGCartesian: {'account': 'capra_lab_csb', 'mem': '20GB', 'ntasks': '1', 'time': '4-00:00:00'} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersUDNSequence: {'account': 'capra_lab_csb', 'mem': '10GB', 'ntasks': '1', 'time': '12:00:00'} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersMusiteDeep: {'account': 'capra_lab_csb', 'mem': '15GB', 'ntasks': '1', 'time': '0-04:00:00'} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersDiGePred: {'account': 'capra_lab_csb', 'mem': '30GB', 'ntasks': '1', 'time': '0-1'} 05:47:12 INFO [ psb_launch.py:200 ] SlurmParametersDIEP: {'account': 'capra_lab_csb', 'mem': '12GB', 'ntasks': '1', 'time': '0-1'} 05:47:12 INFO [ psb_launch.py:963 ] launch_SampleCase.py will be created as an external launch utility 05:47:12 INFO [ psb_launch.py:887 ] 8 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/COA5_NM_001008215.2_P9L_workplan.csv 05:47:12 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/psb_launch.log 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:P9L' --chainAunp='Q86WW8' --alphafold=AF-Q86WW8-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/AF-Q86WW8-F1_A/PP_monomer_clinvar38 --uniquekey COA5_NM_001008215.2_P9L_AF-Q86WW8-F1_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:P9L' --chainAunp='Q86WW8' --alphafold=AF-Q86WW8-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/AF-Q86WW8-F1_A/PP_monomer_cosmicV94 --uniquekey COA5_NM_001008215.2_P9L_AF-Q86WW8-F1_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q86WW8-F1 --chain A --variant P9L 05:47:12 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q86WW8-F1 --chain A --variant P9L 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:P9L' --chainAunp='Q86WW8' --swiss=Q86WW8_10_59_8e73.59.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/Q86WW8_10_59_8e73.59.A_A/PP_monomer_clinvar38 --uniquekey COA5_NM_001008215.2_P9L_Q86WW8_10_59_8e73.59.A_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:P9L' --chainAunp='Q86WW8' --swiss=Q86WW8_10_59_8e73.59.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/Q86WW8_10_59_8e73.59.A_A/PP_monomer_cosmicV94 --uniquekey COA5_NM_001008215.2_P9L_Q86WW8_10_59_8e73.59.A_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q86WW8 --transcript_variant P9L --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/MusiteDeep --uniquekey COA5_NM_001008215.2_Q86WW8_MusiteDeep 05:47:12 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp Q86WW8 --transcript_variant P9L --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/ScanNet --uniquekey COA5_NM_001008215.2_Q86WW8_ScanNet 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/PathProx/COA5_NM_001008215.2_P9L_PathProx.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/PathProx/COA5_NM_001008215.2_P9L_PathProx.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/PathProx/COA5_NM_001008215.2_P9L_PathProx.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214767 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ddG_monomer/COA5_NM_001008215.2_P9L_ddG_monomer.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ddG_monomer/COA5_NM_001008215.2_P9L_ddG_monomer.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ddG_monomer/COA5_NM_001008215.2_P9L_ddG_monomer.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214768 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ddG_cartesian/COA5_NM_001008215.2_P9L_ddG_cartesian.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ddG_cartesian/COA5_NM_001008215.2_P9L_ddG_cartesian.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ddG_cartesian/COA5_NM_001008215.2_P9L_ddG_cartesian.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214769 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/MusiteDeep/COA5_NM_001008215.2_P9L_MusiteDeep.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/MusiteDeep/COA5_NM_001008215.2_P9L_MusiteDeep.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/MusiteDeep/COA5_NM_001008215.2_P9L_MusiteDeep.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214770 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ScanNet/COA5_NM_001008215.2_P9L_ScanNet.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ScanNet/COA5_NM_001008215.2_P9L_ScanNet.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/COA5_NM_001008215.2_P9L/slurm/ScanNet/COA5_NM_001008215.2_P9L_ScanNet.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214771 05:47:12 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for COA5 NM_001008215.2 P9L 05:47:12 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for COA5 NM_001008215.2 P9L 05:47:12 INFO [ psb_launch.py:887 ] 22 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/NAGA_NM_000262.2_D136N_workplan.csv 05:47:12 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/psb_launch.log 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:D136N' --chainBunp='P17050' --pdb=4do4 --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/4do4_B/PP_monomer_clinvar38 --uniquekey NAGA_NM_000262.2_D136N_4do4_B_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:D136N' --chainBunp='P17050' --pdb=4do4 --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/4do4_B/PP_monomer_cosmicV94 --uniquekey NAGA_NM_000262.2_D136N_4do4_B_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --pdb 4do4 --chain B --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --pdb 4do4 --chain B --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --biounit=4do6 --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/4do6_A/PP_complex_clinvar38 --uniquekey NAGA_NM_000262.2_D136N_4do6_A_PP_complex_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --biounit=4do6 --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/4do6_A/PP_complex_cosmicV94 --uniquekey NAGA_NM_000262.2_D136N_4do6_A_PP_complex_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --alphafold=AF-P17050-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/AF-P17050-F1_A/PP_monomer_clinvar38 --uniquekey NAGA_NM_000262.2_D136N_AF-P17050-F1_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --alphafold=AF-P17050-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/AF-P17050-F1_A/PP_monomer_cosmicV94 --uniquekey NAGA_NM_000262.2_D136N_AF-P17050-F1_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-P17050-F1 --chain A --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-P17050-F1 --chain A --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --modbase=ENSP00000379680.3_1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/ENSP00000379680.3_1_A/PP_monomer_clinvar38 --uniquekey NAGA_NM_000262.2_D136N_ENSP00000379680.3_1_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --modbase=ENSP00000379680.3_1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/ENSP00000379680.3_1_A/PP_monomer_cosmicV94 --uniquekey NAGA_NM_000262.2_D136N_ENSP00000379680.3_1_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000379680.3_1 --chain A --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000379680.3_1 --chain A --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --swiss=P17050_19_404_1ktb.1.B --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/P17050_19_404_1ktb.1.B_A/PP_complex_clinvar38 --uniquekey NAGA_NM_000262.2_D136N_P17050_19_404_1ktb.1.B_A_PP_complex_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --swiss=P17050_19_404_1ktb.1.B --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/P17050_19_404_1ktb.1.B_A/PP_complex_cosmicV94 --uniquekey NAGA_NM_000262.2_D136N_P17050_19_404_1ktb.1.B_A_PP_complex_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --swiss=P17050_19_404_1ktb.1.B --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/P17050_19_404_1ktb.1.B_A/PP_monomer_clinvar38 --uniquekey NAGA_NM_000262.2_D136N_P17050_19_404_1ktb.1.B_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:D136N' --chainAunp='P17050' --swiss=P17050_19_404_1ktb.1.B --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/P17050_19_404_1ktb.1.B_A/PP_monomer_cosmicV94 --uniquekey NAGA_NM_000262.2_D136N_P17050_19_404_1ktb.1.B_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --swiss P17050_19_404_1ktb.1.B --chain A --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --swiss P17050_19_404_1ktb.1.B --chain A --variant D136N 05:47:12 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp P17050 --transcript_variant D136N --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/MusiteDeep --uniquekey NAGA_NM_000262.2_P17050_MusiteDeep 05:47:12 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp P17050 --transcript_variant D136N --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/ScanNet --uniquekey NAGA_NM_000262.2_P17050_ScanNet 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/PathProx/NAGA_NM_000262.2_D136N_PathProx.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/PathProx/NAGA_NM_000262.2_D136N_PathProx.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/PathProx/NAGA_NM_000262.2_D136N_PathProx.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214772 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ddG_monomer/NAGA_NM_000262.2_D136N_ddG_monomer.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ddG_monomer/NAGA_NM_000262.2_D136N_ddG_monomer.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ddG_monomer/NAGA_NM_000262.2_D136N_ddG_monomer.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214773 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ddG_cartesian/NAGA_NM_000262.2_D136N_ddG_cartesian.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ddG_cartesian/NAGA_NM_000262.2_D136N_ddG_cartesian.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ddG_cartesian/NAGA_NM_000262.2_D136N_ddG_cartesian.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214774 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/MusiteDeep/NAGA_NM_000262.2_D136N_MusiteDeep.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/MusiteDeep/NAGA_NM_000262.2_D136N_MusiteDeep.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/MusiteDeep/NAGA_NM_000262.2_D136N_MusiteDeep.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214775 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ScanNet/NAGA_NM_000262.2_D136N_ScanNet.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ScanNet/NAGA_NM_000262.2_D136N_ScanNet.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/NAGA_NM_000262.2_D136N/slurm/ScanNet/NAGA_NM_000262.2_D136N_ScanNet.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214776 05:47:12 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for NAGA NM_000262.2 D136N 05:47:12 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for NAGA NM_000262.2 D136N 05:47:12 INFO [ psb_launch.py:887 ] 8 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/SMYD5_NM_006062.2_A57E_workplan.csv 05:47:12 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/psb_launch.log 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A57E' --chainAunp='Q6GMV2' --alphafold=AF-Q6GMV2-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/AF-Q6GMV2-F1_A/PP_monomer_clinvar38 --uniquekey SMYD5_NM_006062.2_A57E_AF-Q6GMV2-F1_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A57E' --chainAunp='Q6GMV2' --alphafold=AF-Q6GMV2-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/AF-Q6GMV2-F1_A/PP_monomer_cosmicV94 --uniquekey SMYD5_NM_006062.2_A57E_AF-Q6GMV2-F1_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q6GMV2-F1 --chain A --variant A57E 05:47:12 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q6GMV2-F1 --chain A --variant A57E 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A57E' --chainAunp='Q6GMV2' --modbase=ENSP00000374152.4_1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/ENSP00000374152.4_1_A/PP_monomer_clinvar38 --uniquekey SMYD5_NM_006062.2_A57E_ENSP00000374152.4_1_A_PP_monomer_clinvar38 05:47:12 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A57E' --chainAunp='Q6GMV2' --modbase=ENSP00000374152.4_1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/ENSP00000374152.4_1_A/PP_monomer_cosmicV94 --uniquekey SMYD5_NM_006062.2_A57E_ENSP00000374152.4_1_A_PP_monomer_cosmicV94 05:47:12 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q6GMV2 --transcript_variant A57E --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/MusiteDeep --uniquekey SMYD5_NM_006062.2_Q6GMV2_MusiteDeep 05:47:12 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp Q6GMV2 --transcript_variant A57E --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/ScanNet --uniquekey SMYD5_NM_006062.2_Q6GMV2_ScanNet 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/PathProx/SMYD5_NM_006062.2_A57E_PathProx.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/PathProx/SMYD5_NM_006062.2_A57E_PathProx.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/PathProx/SMYD5_NM_006062.2_A57E_PathProx.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214777 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ddG_monomer/SMYD5_NM_006062.2_A57E_ddG_monomer.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ddG_monomer/SMYD5_NM_006062.2_A57E_ddG_monomer.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ddG_monomer/SMYD5_NM_006062.2_A57E_ddG_monomer.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214778 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ddG_cartesian/SMYD5_NM_006062.2_A57E_ddG_cartesian.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ddG_cartesian/SMYD5_NM_006062.2_A57E_ddG_cartesian.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ddG_cartesian/SMYD5_NM_006062.2_A57E_ddG_cartesian.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214779 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/MusiteDeep/SMYD5_NM_006062.2_A57E_MusiteDeep.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/MusiteDeep/SMYD5_NM_006062.2_A57E_MusiteDeep.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/MusiteDeep/SMYD5_NM_006062.2_A57E_MusiteDeep.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214780 05:47:12 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ScanNet/SMYD5_NM_006062.2_A57E_ScanNet.slurm 05:47:12 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:12 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:12 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:12 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ScanNet/SMYD5_NM_006062.2_A57E_ScanNet.slurm 05:47:12 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMYD5_NM_006062.2_A57E/slurm/ScanNet/SMYD5_NM_006062.2_A57E_ScanNet.slurm'] 05:47:12 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214781 05:47:12 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for SMYD5 NM_006062.2 A57E 05:47:12 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for SMYD5 NM_006062.2 A57E 05:47:13 INFO [ psb_launch.py:887 ] 30 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/SMARCAL1_NM_001127207.1_A588T_workplan.csv 05:47:13 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/psb_launch.log 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --alphafold=AF-Q9NZC9-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/AF-Q9NZC9-F1_A/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_AF-Q9NZC9-F1_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --alphafold=AF-Q9NZC9-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/AF-Q9NZC9-F1_A/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_AF-Q9NZC9-F1_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q9NZC9-F1 --chain A --variant A588T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q9NZC9-F1 --chain A --variant A588T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --modbase=ENSP00000349823.4_2 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/ENSP00000349823.4_2_A/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_ENSP00000349823.4_2_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --modbase=ENSP00000349823.4_2 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/ENSP00000349823.4_2_A/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_ENSP00000349823.4_2_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --modbase=ENSP00000349823.4_3 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/ENSP00000349823.4_3_A/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_ENSP00000349823.4_3_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --modbase=ENSP00000349823.4_3 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/ENSP00000349823.4_3_A/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_ENSP00000349823.4_3_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --swiss=Q9NZC9_427_852_5jxr.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_852_5jxr.1.A_A/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_852_5jxr.1.A_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --swiss=Q9NZC9_427_852_5jxr.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_852_5jxr.1.A_A/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_852_5jxr.1.A_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='L:A588T' --chainLunp='Q9NZC9' --swiss=Q9NZC9_427_860_6gej.1.L --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_860_6gej.1.L_L/PP_complex_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_860_6gej.1.L_L_PP_complex_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='L:A588T' --chainLunp='Q9NZC9' --swiss=Q9NZC9_427_860_6gej.1.L --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_860_6gej.1.L_L/PP_complex_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_860_6gej.1.L_L_PP_complex_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='L:A588T' --chainLunp='Q9NZC9' --swiss=Q9NZC9_427_860_6gej.1.L --chain='L' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_860_6gej.1.L_L/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_860_6gej.1.L_L_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='L:A588T' --chainLunp='Q9NZC9' --swiss=Q9NZC9_427_860_6gej.1.L --chain='L' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_860_6gej.1.L_L/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_860_6gej.1.L_L_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --swiss Q9NZC9_427_860_6gej.1.L --chain L --variant A588T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --swiss Q9NZC9_427_860_6gej.1.L --chain L --variant A588T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='D:A588T' --chainDunp='Q9NZC9' --swiss=Q9NZC9_427_885_7z8s.1.D --chain='D' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_885_7z8s.1.D_D/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_885_7z8s.1.D_D_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='D:A588T' --chainDunp='Q9NZC9' --swiss=Q9NZC9_427_885_7z8s.1.D --chain='D' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_885_7z8s.1.D_D/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_885_7z8s.1.D_D_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --swiss=Q9NZC9_427_889_6g7e.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_889_6g7e.1.A_A/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_889_6g7e.1.A_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --swiss=Q9NZC9_427_889_6g7e.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_427_889_6g7e.1.A_A/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_427_889_6g7e.1.A_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='G:A588T' --chainGunp='Q9NZC9' --swiss=Q9NZC9_429_860_6fml.1.G --chain='G' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_429_860_6fml.1.G_G/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_429_860_6fml.1.G_G_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='G:A588T' --chainGunp='Q9NZC9' --swiss=Q9NZC9_429_860_6fml.1.G --chain='G' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_429_860_6fml.1.G_G/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_429_860_6fml.1.G_G_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --swiss=Q9NZC9_431_844_5hzr.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_431_844_5hzr.1.A_A/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_431_844_5hzr.1.A_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A588T' --chainAunp='Q9NZC9' --swiss=Q9NZC9_431_844_5hzr.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_431_844_5hzr.1.A_A/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_431_844_5hzr.1.A_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A588T' --chainBunp='Q9NZC9' --swiss=Q9NZC9_434_855_7epu.1.B --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_434_855_7epu.1.B_B/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_434_855_7epu.1.B_B_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A588T' --chainBunp='Q9NZC9' --swiss=Q9NZC9_434_855_7epu.1.B --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_434_855_7epu.1.B_B/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_434_855_7epu.1.B_B_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='G:A588T' --chainGunp='Q9NZC9' --swiss=Q9NZC9_436_859_7zi4.1.G --chain='G' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_436_859_7zi4.1.G_G/PP_monomer_clinvar38 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_436_859_7zi4.1.G_G_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='G:A588T' --chainGunp='Q9NZC9' --swiss=Q9NZC9_436_859_7zi4.1.G --chain='G' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/Q9NZC9_436_859_7zi4.1.G_G/PP_monomer_cosmicV94 --uniquekey SMARCAL1_NM_001127207.1_A588T_Q9NZC9_436_859_7zi4.1.G_G_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZC9 --transcript_variant A588T --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/MusiteDeep --uniquekey SMARCAL1_NM_001127207.1_Q9NZC9_MusiteDeep 05:47:13 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZC9 --transcript_variant A588T --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/ScanNet --uniquekey SMARCAL1_NM_001127207.1_Q9NZC9_ScanNet 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/PathProx/SMARCAL1_NM_001127207.1_A588T_PathProx.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/PathProx/SMARCAL1_NM_001127207.1_A588T_PathProx.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/PathProx/SMARCAL1_NM_001127207.1_A588T_PathProx.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214782 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ddG_monomer/SMARCAL1_NM_001127207.1_A588T_ddG_monomer.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ddG_monomer/SMARCAL1_NM_001127207.1_A588T_ddG_monomer.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ddG_monomer/SMARCAL1_NM_001127207.1_A588T_ddG_monomer.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214783 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ddG_cartesian/SMARCAL1_NM_001127207.1_A588T_ddG_cartesian.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ddG_cartesian/SMARCAL1_NM_001127207.1_A588T_ddG_cartesian.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ddG_cartesian/SMARCAL1_NM_001127207.1_A588T_ddG_cartesian.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214784 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/MusiteDeep/SMARCAL1_NM_001127207.1_A588T_MusiteDeep.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/MusiteDeep/SMARCAL1_NM_001127207.1_A588T_MusiteDeep.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/MusiteDeep/SMARCAL1_NM_001127207.1_A588T_MusiteDeep.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214785 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ScanNet/SMARCAL1_NM_001127207.1_A588T_ScanNet.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ScanNet/SMARCAL1_NM_001127207.1_A588T_ScanNet.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/SMARCAL1_NM_001127207.1_A588T/slurm/ScanNet/SMARCAL1_NM_001127207.1_A588T_ScanNet.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214786 05:47:13 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for SMARCAL1 NM_001127207.1 A588T 05:47:13 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for SMARCAL1 NM_001127207.1 A588T 05:47:13 INFO [ psb_launch.py:887 ] 6 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/ONECUT1_NM_004498.2_R269G_workplan.csv 05:47:13 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/psb_launch.log 05:47:13 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9UBC0 --transcript_variant R269G --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/MusiteDeep --uniquekey ONECUT1_NM_004498.2_Q9UBC0_MusiteDeep 05:47:13 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9UBC0 --transcript_variant R269G --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/ScanNet --uniquekey ONECUT1_NM_004498.2_Q9UBC0_ScanNet 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:R269G' --chainAunp='Q9UBC0' --alphafold=AF-Q9UBC0-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/AF-Q9UBC0-F1_A/PP_monomer_clinvar38 --uniquekey ONECUT1_NM_004498.2_R269G_AF-Q9UBC0-F1_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:R269G' --chainAunp='Q9UBC0' --alphafold=AF-Q9UBC0-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/AF-Q9UBC0-F1_A/PP_monomer_cosmicV94 --uniquekey ONECUT1_NM_004498.2_R269G_AF-Q9UBC0-F1_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q9UBC0-F1 --chain A --variant R269G 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q9UBC0-F1 --chain A --variant R269G 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/PathProx/ONECUT1_NM_004498.2_R269G_PathProx.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/PathProx/ONECUT1_NM_004498.2_R269G_PathProx.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/PathProx/ONECUT1_NM_004498.2_R269G_PathProx.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214787 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ddG_monomer/ONECUT1_NM_004498.2_R269G_ddG_monomer.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ddG_monomer/ONECUT1_NM_004498.2_R269G_ddG_monomer.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ddG_monomer/ONECUT1_NM_004498.2_R269G_ddG_monomer.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214788 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ddG_cartesian/ONECUT1_NM_004498.2_R269G_ddG_cartesian.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ddG_cartesian/ONECUT1_NM_004498.2_R269G_ddG_cartesian.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ddG_cartesian/ONECUT1_NM_004498.2_R269G_ddG_cartesian.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214789 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/MusiteDeep/ONECUT1_NM_004498.2_R269G_MusiteDeep.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/MusiteDeep/ONECUT1_NM_004498.2_R269G_MusiteDeep.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/MusiteDeep/ONECUT1_NM_004498.2_R269G_MusiteDeep.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214790 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ScanNet/ONECUT1_NM_004498.2_R269G_ScanNet.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ScanNet/ONECUT1_NM_004498.2_R269G_ScanNet.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ONECUT1_NM_004498.2_R269G/slurm/ScanNet/ONECUT1_NM_004498.2_R269G_ScanNet.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214791 05:47:13 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for ONECUT1 NM_004498.2 R269G 05:47:13 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for ONECUT1 NM_004498.2 R269G 05:47:13 INFO [ psb_launch.py:887 ] 28 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/ALAS2_NM_000032.4_A282T_workplan.csv 05:47:13 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/psb_launch.log 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --biounit=5qr1 --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/5qr1_A/PP_complex_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_5qr1_A_PP_complex_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --biounit=5qr1 --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/5qr1_A/PP_complex_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_5qr1_A_PP_complex_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A282T' --chainBunp='P22557-1' --pdb=5qr1 --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/5qr1_B/PP_monomer_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_5qr1_B_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A282T' --chainBunp='P22557-1' --pdb=5qr1 --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/5qr1_B/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_5qr1_B_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --pdb 5qr1 --chain B --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --pdb 5qr1 --chain B --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --alphafold=AF-P22557-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/AF-P22557-F1_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_AF-P22557-F1_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --alphafold=AF-P22557-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/AF-P22557-F1_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_AF-P22557-F1_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-P22557-F1 --chain A --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-P22557-F1 --chain A --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --modbase=GENSCAN00000017881_2 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/GENSCAN00000017881_2_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_GENSCAN00000017881_2_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --modbase=GENSCAN00000017881_2 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/GENSCAN00000017881_2_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_GENSCAN00000017881_2_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase GENSCAN00000017881_2 --chain A --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase GENSCAN00000017881_2 --chain A --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --modbase=GENSCAN00000017881_3 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/GENSCAN00000017881_3_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_GENSCAN00000017881_3_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --modbase=GENSCAN00000017881_3 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/GENSCAN00000017881_3_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_GENSCAN00000017881_3_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --modbase=GENSCAN00000017881_4 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/GENSCAN00000017881_4_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_GENSCAN00000017881_4_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A282T' --chainAunp='P22557-1' --modbase=GENSCAN00000017881_4 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/GENSCAN00000017881_4_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_GENSCAN00000017881_4_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase GENSCAN00000017881_4 --chain A --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase GENSCAN00000017881_4 --chain A --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A282T' --chainBunp='P22557-1' --swiss=P22557-1_143_578_6hrh.1.A --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/P22557-1_143_578_6hrh.1.A_B/PP_complex_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_P22557-1_143_578_6hrh.1.A_B_PP_complex_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A282T' --chainBunp='P22557-1' --swiss=P22557-1_143_578_6hrh.1.A --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/P22557-1_143_578_6hrh.1.A_B/PP_complex_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_P22557-1_143_578_6hrh.1.A_B_PP_complex_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A282T' --chainBunp='P22557-1' --swiss=P22557-1_143_578_6hrh.1.A --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/P22557-1_143_578_6hrh.1.A_B/PP_monomer_clinvar38 --uniquekey ALAS2_NM_000032.4_A282T_P22557-1_143_578_6hrh.1.A_B_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A282T' --chainBunp='P22557-1' --swiss=P22557-1_143_578_6hrh.1.A --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/P22557-1_143_578_6hrh.1.A_B/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_000032.4_A282T_P22557-1_143_578_6hrh.1.A_B_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --swiss P22557-1_143_578_6hrh.1.A --chain B --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --swiss P22557-1_143_578_6hrh.1.A --chain B --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp P22557-1 --transcript_variant A282T --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/MusiteDeep --uniquekey ALAS2_NM_000032.4_P22557-1_MusiteDeep 05:47:13 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp P22557-1 --transcript_variant A282T --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/ScanNet --uniquekey ALAS2_NM_000032.4_P22557-1_ScanNet 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/PathProx/ALAS2_NM_000032.4_A282T_PathProx.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/PathProx/ALAS2_NM_000032.4_A282T_PathProx.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/PathProx/ALAS2_NM_000032.4_A282T_PathProx.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214792 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ddG_monomer/ALAS2_NM_000032.4_A282T_ddG_monomer.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ddG_monomer/ALAS2_NM_000032.4_A282T_ddG_monomer.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ddG_monomer/ALAS2_NM_000032.4_A282T_ddG_monomer.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214793 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ddG_cartesian/ALAS2_NM_000032.4_A282T_ddG_cartesian.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ddG_cartesian/ALAS2_NM_000032.4_A282T_ddG_cartesian.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ddG_cartesian/ALAS2_NM_000032.4_A282T_ddG_cartesian.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214794 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/MusiteDeep/ALAS2_NM_000032.4_A282T_MusiteDeep.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/MusiteDeep/ALAS2_NM_000032.4_A282T_MusiteDeep.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/MusiteDeep/ALAS2_NM_000032.4_A282T_MusiteDeep.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214795 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ScanNet/ALAS2_NM_000032.4_A282T_ScanNet.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ScanNet/ALAS2_NM_000032.4_A282T_ScanNet.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_000032.4_A282T/slurm/ScanNet/ALAS2_NM_000032.4_A282T_ScanNet.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214796 05:47:13 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for ALAS2 NM_000032.4 A282T 05:47:13 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for ALAS2 NM_000032.4 A282T 05:47:13 INFO [ psb_launch.py:887 ] 23 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ALAS2_NM_001037967.3_A245T_workplan.csv 05:47:13 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/psb_launch.log 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --biounit=5qqr --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/5qqr_A/PP_complex_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_5qqr_A_PP_complex_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --biounit=5qqr --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/5qqr_A/PP_complex_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_5qqr_A_PP_complex_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A245T' --chainBunp='P22557-2' --pdb=5qqr --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/5qqr_B/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_5qqr_B_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A245T' --chainBunp='P22557-2' --pdb=5qqr --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/5qqr_B/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_5qqr_B_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --pdb 5qqr --chain B --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --pdb 5qqr --chain B --variant A282T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --modbase=ENSP00000337131.4_1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ENSP00000337131.4_1_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_ENSP00000337131.4_1_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --modbase=ENSP00000337131.4_1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ENSP00000337131.4_1_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_ENSP00000337131.4_1_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000337131.4_1 --chain A --variant A245T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000337131.4_1 --chain A --variant A245T 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --modbase=ENSP00000337131.4_2 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ENSP00000337131.4_2_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_ENSP00000337131.4_2_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --modbase=ENSP00000337131.4_2 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ENSP00000337131.4_2_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_ENSP00000337131.4_2_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --modbase=ENSP00000337131.4_3 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ENSP00000337131.4_3_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_ENSP00000337131.4_3_A_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A245T' --chainAunp='P22557-2' --modbase=ENSP00000337131.4_3 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/ENSP00000337131.4_3_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_ENSP00000337131.4_3_A_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000337131.4_3 --chain A --variant A245T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000337131.4_3 --chain A --variant A245T 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A245T' --chainBunp='P22557-2' --swiss=P22557-2_106_541_6hrh.1.A --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/P22557-2_106_541_6hrh.1.A_B/PP_complex_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_P22557-2_106_541_6hrh.1.A_B_PP_complex_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A245T' --chainBunp='P22557-2' --swiss=P22557-2_106_541_6hrh.1.A --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/P22557-2_106_541_6hrh.1.A_B/PP_complex_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_P22557-2_106_541_6hrh.1.A_B_PP_complex_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A245T' --chainBunp='P22557-2' --swiss=P22557-2_106_541_6hrh.1.A --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/P22557-2_106_541_6hrh.1.A_B/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037967.3_A245T_P22557-2_106_541_6hrh.1.A_B_PP_monomer_clinvar38 05:47:13 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A245T' --chainBunp='P22557-2' --swiss=P22557-2_106_541_6hrh.1.A --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/P22557-2_106_541_6hrh.1.A_B/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037967.3_A245T_P22557-2_106_541_6hrh.1.A_B_PP_monomer_cosmicV94 05:47:13 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --swiss P22557-2_106_541_6hrh.1.A --chain B --variant A245T 05:47:13 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --swiss P22557-2_106_541_6hrh.1.A --chain B --variant A245T 05:47:13 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp P22557-2 --transcript_variant A245T --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/MusiteDeep --uniquekey ALAS2_NM_001037967.3_P22557-2_MusiteDeep 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/PathProx/ALAS2_NM_001037967.3_A245T_PathProx.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/PathProx/ALAS2_NM_001037967.3_A245T_PathProx.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/PathProx/ALAS2_NM_001037967.3_A245T_PathProx.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214797 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/ddG_monomer/ALAS2_NM_001037967.3_A245T_ddG_monomer.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/ddG_monomer/ALAS2_NM_001037967.3_A245T_ddG_monomer.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/ddG_monomer/ALAS2_NM_001037967.3_A245T_ddG_monomer.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214798 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/ddG_cartesian/ALAS2_NM_001037967.3_A245T_ddG_cartesian.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/ddG_cartesian/ALAS2_NM_001037967.3_A245T_ddG_cartesian.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/ddG_cartesian/ALAS2_NM_001037967.3_A245T_ddG_cartesian.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214799 05:47:13 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/MusiteDeep/ALAS2_NM_001037967.3_A245T_MusiteDeep.slurm 05:47:13 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:13 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:13 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:13 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/MusiteDeep/ALAS2_NM_001037967.3_A245T_MusiteDeep.slurm 05:47:13 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037967.3_A245T/slurm/MusiteDeep/ALAS2_NM_001037967.3_A245T_MusiteDeep.slurm'] 05:47:13 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214800 05:47:13 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for ALAS2 NM_001037967.3 A245T 05:47:13 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for ALAS2 NM_001037967.3 A245T 05:47:13 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for ALAS2 NM_001037967.3 A245T 05:47:14 INFO [ psb_launch.py:887 ] 23 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ALAS2_NM_001037968.3_A269T_workplan.csv 05:47:14 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/psb_launch.log 05:47:14 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --biounit=5qqr --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/5qqr_A/PP_complex_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_5qqr_A_PP_complex_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --biounit=5qqr --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/5qqr_A/PP_complex_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_5qqr_A_PP_complex_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A269T' --chainBunp='P22557-4' --pdb=5qqr --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/5qqr_B/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_5qqr_B_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A269T' --chainBunp='P22557-4' --pdb=5qqr --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/5qqr_B/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_5qqr_B_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --pdb 5qqr --chain B --variant A282T 05:47:14 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --pdb 5qqr --chain B --variant A282T 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --modbase=ENSP00000379501.3_2 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ENSP00000379501.3_2_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_ENSP00000379501.3_2_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --modbase=ENSP00000379501.3_2 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ENSP00000379501.3_2_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_ENSP00000379501.3_2_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000379501.3_2 --chain A --variant A269T 05:47:14 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000379501.3_2 --chain A --variant A269T 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --modbase=ENSP00000379501.3_3 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ENSP00000379501.3_3_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_ENSP00000379501.3_3_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --modbase=ENSP00000379501.3_3 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ENSP00000379501.3_3_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_ENSP00000379501.3_3_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --modbase=ENSP00000379501.3_4 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ENSP00000379501.3_4_A/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_ENSP00000379501.3_4_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:A269T' --chainAunp='P22557-4' --modbase=ENSP00000379501.3_4 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/ENSP00000379501.3_4_A/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_ENSP00000379501.3_4_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000379501.3_4 --chain A --variant A269T 05:47:14 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --modbase ENSP00000379501.3_4 --chain A --variant A269T 05:47:14 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A269T' --chainBunp='P22557-4' --swiss=P22557-4_130_565_6hrh.1.A --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/P22557-4_130_565_6hrh.1.A_B/PP_complex_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_P22557-4_130_565_6hrh.1.A_B_PP_complex_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A269T' --chainBunp='P22557-4' --swiss=P22557-4_130_565_6hrh.1.A --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/P22557-4_130_565_6hrh.1.A_B/PP_complex_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_P22557-4_130_565_6hrh.1.A_B_PP_complex_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A269T' --chainBunp='P22557-4' --swiss=P22557-4_130_565_6hrh.1.A --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/P22557-4_130_565_6hrh.1.A_B/PP_monomer_clinvar38 --uniquekey ALAS2_NM_001037968.3_A269T_P22557-4_130_565_6hrh.1.A_B_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:A269T' --chainBunp='P22557-4' --swiss=P22557-4_130_565_6hrh.1.A --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/P22557-4_130_565_6hrh.1.A_B/PP_monomer_cosmicV94 --uniquekey ALAS2_NM_001037968.3_A269T_P22557-4_130_565_6hrh.1.A_B_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --swiss P22557-4_130_565_6hrh.1.A --chain B --variant A269T 05:47:14 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --swiss P22557-4_130_565_6hrh.1.A --chain B --variant A269T 05:47:14 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp P22557-4 --transcript_variant A269T --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/MusiteDeep --uniquekey ALAS2_NM_001037968.3_P22557-4_MusiteDeep 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/PathProx/ALAS2_NM_001037968.3_A269T_PathProx.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/PathProx/ALAS2_NM_001037968.3_A269T_PathProx.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/PathProx/ALAS2_NM_001037968.3_A269T_PathProx.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214801 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/ddG_monomer/ALAS2_NM_001037968.3_A269T_ddG_monomer.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/ddG_monomer/ALAS2_NM_001037968.3_A269T_ddG_monomer.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/ddG_monomer/ALAS2_NM_001037968.3_A269T_ddG_monomer.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214802 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/ddG_cartesian/ALAS2_NM_001037968.3_A269T_ddG_cartesian.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/ddG_cartesian/ALAS2_NM_001037968.3_A269T_ddG_cartesian.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/ddG_cartesian/ALAS2_NM_001037968.3_A269T_ddG_cartesian.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214803 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/MusiteDeep/ALAS2_NM_001037968.3_A269T_MusiteDeep.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/MusiteDeep/ALAS2_NM_001037968.3_A269T_MusiteDeep.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/ALAS2_NM_001037968.3_A269T/slurm/MusiteDeep/ALAS2_NM_001037968.3_A269T_MusiteDeep.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214804 05:47:14 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for ALAS2 NM_001037968.3 A269T 05:47:14 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for ALAS2 NM_001037968.3 A269T 05:47:14 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for ALAS2 NM_001037968.3 A269T 05:47:14 INFO [ psb_launch.py:887 ] 14 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/AP3D1_NM_003938.6_V699M_workplan.csv 05:47:14 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/psb_launch.log 05:47:14 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp O14617-1 --transcript_variant V699M --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/MusiteDeep --uniquekey AP3D1_NM_003938.6_O14617-1_MusiteDeep 05:47:14 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp O14617-1 --transcript_variant V699M --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/ScanNet --uniquekey AP3D1_NM_003938.6_O14617-1_ScanNet 05:47:14 INFO [ psb_launch.py:377 ] PP_complex_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --biounit=4afi --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/4afi_A/PP_complex_clinvar38 --uniquekey AP3D1_NM_003938.6_V699M_4afi_A_PP_complex_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_complex_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --biounit=4afi --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/4afi_A/PP_complex_cosmicV94 --uniquekey AP3D1_NM_003938.6_V699M_4afi_A_PP_complex_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --pdb=4afi --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/4afi_A/PP_monomer_clinvar38 --uniquekey AP3D1_NM_003938.6_V699M_4afi_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --pdb=4afi --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/4afi_A/PP_monomer_cosmicV94 --uniquekey AP3D1_NM_003938.6_V699M_4afi_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --pdb 4afi --chain A --variant V22M 05:47:14 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --pdb 4afi --chain A --variant V22M 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --alphafold=AF-O14617-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/AF-O14617-F1_A/PP_monomer_clinvar38 --uniquekey AP3D1_NM_003938.6_V699M_AF-O14617-F1_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --alphafold=AF-O14617-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/AF-O14617-F1_A/PP_monomer_cosmicV94 --uniquekey AP3D1_NM_003938.6_V699M_AF-O14617-F1_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-O14617-F1 --chain A --variant V699M 05:47:14 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-O14617-F1 --chain A --variant V699M 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --modbase=ENSP00000344055.4_3 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/ENSP00000344055.4_3_A/PP_monomer_clinvar38 --uniquekey AP3D1_NM_003938.6_V699M_ENSP00000344055.4_3_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-1' --modbase=ENSP00000344055.4_3 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/ENSP00000344055.4_3_A/PP_monomer_cosmicV94 --uniquekey AP3D1_NM_003938.6_V699M_ENSP00000344055.4_3_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/PathProx/AP3D1_NM_003938.6_V699M_PathProx.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/PathProx/AP3D1_NM_003938.6_V699M_PathProx.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/PathProx/AP3D1_NM_003938.6_V699M_PathProx.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214805 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ddG_monomer/AP3D1_NM_003938.6_V699M_ddG_monomer.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ddG_monomer/AP3D1_NM_003938.6_V699M_ddG_monomer.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ddG_monomer/AP3D1_NM_003938.6_V699M_ddG_monomer.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214806 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ddG_cartesian/AP3D1_NM_003938.6_V699M_ddG_cartesian.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ddG_cartesian/AP3D1_NM_003938.6_V699M_ddG_cartesian.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ddG_cartesian/AP3D1_NM_003938.6_V699M_ddG_cartesian.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214807 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/MusiteDeep/AP3D1_NM_003938.6_V699M_MusiteDeep.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/MusiteDeep/AP3D1_NM_003938.6_V699M_MusiteDeep.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/MusiteDeep/AP3D1_NM_003938.6_V699M_MusiteDeep.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214808 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ScanNet/AP3D1_NM_003938.6_V699M_ScanNet.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ScanNet/AP3D1_NM_003938.6_V699M_ScanNet.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_003938.6_V699M/slurm/ScanNet/AP3D1_NM_003938.6_V699M_ScanNet.slurm'] 05:47:14 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214809 05:47:14 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for AP3D1 NM_003938.6 V699M 05:47:14 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for AP3D1 NM_003938.6 V699M 05:47:14 INFO [ psb_launch.py:887 ] 3 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/AP3D1_NM_001261826.1_V699M_workplan.csv 05:47:14 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/psb_launch.log 05:47:14 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp O14617-5 --transcript_variant V699M --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/MusiteDeep --uniquekey AP3D1_NM_001261826.1_O14617-5_MusiteDeep 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-5' --modbase=ENSP00000495274.1_2 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/ENSP00000495274.1_2_A/PP_monomer_clinvar38 --uniquekey AP3D1_NM_001261826.1_V699M_ENSP00000495274.1_2_A_PP_monomer_clinvar38 05:47:14 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:V699M' --chainAunp='O14617-5' --modbase=ENSP00000495274.1_2 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/ENSP00000495274.1_2_A/PP_monomer_cosmicV94 --uniquekey AP3D1_NM_001261826.1_V699M_ENSP00000495274.1_2_A_PP_monomer_cosmicV94 05:47:14 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/slurm/PathProx/AP3D1_NM_001261826.1_V699M_PathProx.slurm 05:47:14 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:14 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:14 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:14 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/slurm/PathProx/AP3D1_NM_001261826.1_V699M_PathProx.slurm 05:47:14 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/slurm/PathProx/AP3D1_NM_001261826.1_V699M_PathProx.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214810 05:47:15 INFO [ psb_launch.py:798 ] No ddG_monomer jobs will be run for AP3D1 NM_001261826.1 V699M 05:47:15 INFO [ psb_launch.py:798 ] No ddG_cartesian jobs will be run for AP3D1 NM_001261826.1 V699M 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/slurm/MusiteDeep/AP3D1_NM_001261826.1_V699M_MusiteDeep.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/slurm/MusiteDeep/AP3D1_NM_001261826.1_V699M_MusiteDeep.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/AP3D1_NM_001261826.1_V699M/slurm/MusiteDeep/AP3D1_NM_001261826.1_V699M_MusiteDeep.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214811 05:47:15 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for AP3D1 NM_001261826.1 V699M 05:47:15 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for AP3D1 NM_001261826.1 V699M 05:47:15 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for AP3D1 NM_001261826.1 V699M 05:47:15 INFO [ psb_launch.py:887 ] 14 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/RTEL1_NM_016434.3_G546D_workplan.csv 05:47:15 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/psb_launch.log 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --alphafold=AF-Q9NZ71-F1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/AF-Q9NZ71-F1_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_016434.3_G546D_AF-Q9NZ71-F1_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --alphafold=AF-Q9NZ71-F1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/AF-Q9NZ71-F1_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_016434.3_G546D_AF-Q9NZ71-F1_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] ddG_cartesian: ddg_run_cartesian.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q9NZ71-F1 --chain A --variant G546D 05:47:15 INFO [ psb_launch.py:377 ] ddG_monomer: ddg_run.py --config ../config/global.config --userconfig ../mothcw.config --alphafold AF-Q9NZ71-F1 --chain A --variant G546D 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --modbase=ENSP00000359035.3_1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ENSP00000359035.3_1_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_016434.3_G546D_ENSP00000359035.3_1_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --modbase=ENSP00000359035.3_1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ENSP00000359035.3_1_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_016434.3_G546D_ENSP00000359035.3_1_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --modbase=ENSP00000359035.3_2 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ENSP00000359035.3_2_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_016434.3_G546D_ENSP00000359035.3_2_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --modbase=ENSP00000359035.3_2 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ENSP00000359035.3_2_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_016434.3_G546D_ENSP00000359035.3_2_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --modbase=ENSP00000359035.3_3 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ENSP00000359035.3_3_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_016434.3_G546D_ENSP00000359035.3_3_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --modbase=ENSP00000359035.3_3 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ENSP00000359035.3_3_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_016434.3_G546D_ENSP00000359035.3_3_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --swiss=Q9NZ71-1_3_756_7o75.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/Q9NZ71-1_3_756_7o75.1.A_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_016434.3_G546D_Q9NZ71-1_3_756_7o75.1.A_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-1' --swiss=Q9NZ71-1_3_756_7o75.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/Q9NZ71-1_3_756_7o75.1.A_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_016434.3_G546D_Q9NZ71-1_3_756_7o75.1.A_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZ71-1 --transcript_variant G546D --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/MusiteDeep --uniquekey RTEL1_NM_016434.3_Q9NZ71-1_MusiteDeep 05:47:15 INFO [ psb_launch.py:377 ] ScanNet: run_ScanNet.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZ71-1 --transcript_variant G546D --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/ScanNet --uniquekey RTEL1_NM_016434.3_Q9NZ71-1_ScanNet 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/PathProx/RTEL1_NM_016434.3_G546D_PathProx.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/PathProx/RTEL1_NM_016434.3_G546D_PathProx.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/PathProx/RTEL1_NM_016434.3_G546D_PathProx.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214812 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ddG_monomer/RTEL1_NM_016434.3_G546D_ddG_monomer.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ddG_monomer/RTEL1_NM_016434.3_G546D_ddG_monomer.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ddG_monomer/RTEL1_NM_016434.3_G546D_ddG_monomer.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214813 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ddG_cartesian/RTEL1_NM_016434.3_G546D_ddG_cartesian.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ddG_cartesian/RTEL1_NM_016434.3_G546D_ddG_cartesian.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ddG_cartesian/RTEL1_NM_016434.3_G546D_ddG_cartesian.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214814 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/MusiteDeep/RTEL1_NM_016434.3_G546D_MusiteDeep.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/MusiteDeep/RTEL1_NM_016434.3_G546D_MusiteDeep.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/MusiteDeep/RTEL1_NM_016434.3_G546D_MusiteDeep.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214815 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ScanNet/RTEL1_NM_016434.3_G546D_ScanNet.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ScanNet/RTEL1_NM_016434.3_G546D_ScanNet.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_016434.3_G546D/slurm/ScanNet/RTEL1_NM_016434.3_G546D_ScanNet.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214816 05:47:15 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for RTEL1 NM_016434.3 G546D 05:47:15 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for RTEL1 NM_016434.3 G546D 05:47:15 INFO [ psb_launch.py:887 ] 3 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/RTEL1_NM_001283009.1_G546D_workplan.csv 05:47:15 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/psb_launch.log 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:G546D' --chainBunp='Q9NZ71-6' --swiss=Q9NZ71-6_3_757_8ebs.1.B --chain='B' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/Q9NZ71-6_3_757_8ebs.1.B_B/PP_monomer_clinvar38 --uniquekey RTEL1_NM_001283009.1_G546D_Q9NZ71-6_3_757_8ebs.1.B_B_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='B:G546D' --chainBunp='Q9NZ71-6' --swiss=Q9NZ71-6_3_757_8ebs.1.B --chain='B' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/Q9NZ71-6_3_757_8ebs.1.B_B/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_001283009.1_G546D_Q9NZ71-6_3_757_8ebs.1.B_B_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZ71-6 --transcript_variant G546D --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/MusiteDeep --uniquekey RTEL1_NM_001283009.1_Q9NZ71-6_MusiteDeep 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/slurm/PathProx/RTEL1_NM_001283009.1_G546D_PathProx.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/slurm/PathProx/RTEL1_NM_001283009.1_G546D_PathProx.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/slurm/PathProx/RTEL1_NM_001283009.1_G546D_PathProx.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214817 05:47:15 INFO [ psb_launch.py:798 ] No ddG_monomer jobs will be run for RTEL1 NM_001283009.1 G546D 05:47:15 INFO [ psb_launch.py:798 ] No ddG_cartesian jobs will be run for RTEL1 NM_001283009.1 G546D 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/slurm/MusiteDeep/RTEL1_NM_001283009.1_G546D_MusiteDeep.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/slurm/MusiteDeep/RTEL1_NM_001283009.1_G546D_MusiteDeep.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283009.1_G546D/slurm/MusiteDeep/RTEL1_NM_001283009.1_G546D_MusiteDeep.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214818 05:47:15 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for RTEL1 NM_001283009.1 G546D 05:47:15 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for RTEL1 NM_001283009.1 G546D 05:47:15 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for RTEL1 NM_001283009.1 G546D 05:47:15 INFO [ psb_launch.py:887 ] 5 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/RTEL1_NM_032957.4_G570D_workplan.csv 05:47:15 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/psb_launch.log 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G570D' --chainAunp='Q9NZ71-7' --modbase=ENSP00000424307.2_1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/ENSP00000424307.2_1_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_032957.4_G570D_ENSP00000424307.2_1_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G570D' --chainAunp='Q9NZ71-7' --modbase=ENSP00000424307.2_1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/ENSP00000424307.2_1_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_032957.4_G570D_ENSP00000424307.2_1_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G570D' --chainAunp='Q9NZ71-7' --swiss=Q9NZ71-7_3_780_7o75.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/Q9NZ71-7_3_780_7o75.1.A_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_032957.4_G570D_Q9NZ71-7_3_780_7o75.1.A_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G570D' --chainAunp='Q9NZ71-7' --swiss=Q9NZ71-7_3_780_7o75.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/Q9NZ71-7_3_780_7o75.1.A_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_032957.4_G570D_Q9NZ71-7_3_780_7o75.1.A_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZ71-7 --transcript_variant G570D --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/MusiteDeep --uniquekey RTEL1_NM_032957.4_Q9NZ71-7_MusiteDeep 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/slurm/PathProx/RTEL1_NM_032957.4_G570D_PathProx.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/slurm/PathProx/RTEL1_NM_032957.4_G570D_PathProx.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/slurm/PathProx/RTEL1_NM_032957.4_G570D_PathProx.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214819 05:47:15 INFO [ psb_launch.py:798 ] No ddG_monomer jobs will be run for RTEL1 NM_032957.4 G570D 05:47:15 INFO [ psb_launch.py:798 ] No ddG_cartesian jobs will be run for RTEL1 NM_032957.4 G570D 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/slurm/MusiteDeep/RTEL1_NM_032957.4_G570D_MusiteDeep.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/slurm/MusiteDeep/RTEL1_NM_032957.4_G570D_MusiteDeep.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_032957.4_G570D/slurm/MusiteDeep/RTEL1_NM_032957.4_G570D_MusiteDeep.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214820 05:47:15 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for RTEL1 NM_032957.4 G570D 05:47:15 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for RTEL1 NM_032957.4 G570D 05:47:15 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for RTEL1 NM_032957.4 G570D 05:47:15 INFO [ psb_launch.py:887 ] 3 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/RTEL1_NA_G546D_workplan.csv 05:47:15 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/psb_launch.log 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-8' --swiss=Q9NZ71-8_3_755_7o75.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/Q9NZ71-8_3_755_7o75.1.A_A/PP_monomer_clinvar38 --uniquekey RTEL1_NA_G546D_Q9NZ71-8_3_755_7o75.1.A_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G546D' --chainAunp='Q9NZ71-8' --swiss=Q9NZ71-8_3_755_7o75.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/Q9NZ71-8_3_755_7o75.1.A_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NA_G546D_Q9NZ71-8_3_755_7o75.1.A_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZ71-8 --transcript_variant G546D --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/MusiteDeep --uniquekey RTEL1_NA_Q9NZ71-8_MusiteDeep 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/slurm/PathProx/RTEL1_NA_G546D_PathProx.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/slurm/PathProx/RTEL1_NA_G546D_PathProx.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/slurm/PathProx/RTEL1_NA_G546D_PathProx.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214821 05:47:15 INFO [ psb_launch.py:798 ] No ddG_monomer jobs will be run for RTEL1 NA G546D 05:47:15 INFO [ psb_launch.py:798 ] No ddG_cartesian jobs will be run for RTEL1 NA G546D 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/slurm/MusiteDeep/RTEL1_NA_G546D_MusiteDeep.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/slurm/MusiteDeep/RTEL1_NA_G546D_MusiteDeep.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NA_G546D/slurm/MusiteDeep/RTEL1_NA_G546D_MusiteDeep.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214822 05:47:15 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for RTEL1 NA G546D 05:47:15 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for RTEL1 NA G546D 05:47:15 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for RTEL1 NA G546D 05:47:15 INFO [ psb_launch.py:887 ] 5 rows read from work plan file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/RTEL1_NM_001283010.1_G323D_workplan.csv 05:47:15 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/psb_launch.log 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G323D' --chainAunp='Q9NZ71-9' --modbase=ENSP00000322287.5_1 --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/ENSP00000322287.5_1_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_001283010.1_G323D_ENSP00000322287.5_1_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G323D' --chainAunp='Q9NZ71-9' --modbase=ENSP00000322287.5_1 --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/ENSP00000322287.5_1_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_001283010.1_G323D_ENSP00000322287.5_1_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_clinvar38: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G323D' --chainAunp='Q9NZ71-9' --swiss=Q9NZ71-9_226_533_7o75.1.A --chain='A' --add_pathogenic38 --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/Q9NZ71-9_226_533_7o75.1.A_A/PP_monomer_clinvar38 --uniquekey RTEL1_NM_001283010.1_G323D_Q9NZ71-9_226_533_7o75.1.A_A_PP_monomer_clinvar38 05:47:15 INFO [ psb_launch.py:377 ] PP_monomer_cosmicV94: pathprox3.py -c ../config/global.config -u ../mothcw.config --variants='A:G323D' --chainAunp='Q9NZ71-9' --swiss=Q9NZ71-9_226_533_7o75.1.A --chain='A' --add_cosmic --add_gnomad38 --radius=D --permutations=99999 --overwrite --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/Q9NZ71-9_226_533_7o75.1.A_A/PP_monomer_cosmicV94 --uniquekey RTEL1_NM_001283010.1_G323D_Q9NZ71-9_226_533_7o75.1.A_A_PP_monomer_cosmicV94 05:47:15 INFO [ psb_launch.py:377 ] MusiteDeep: run_MusiteDeep.py --config ../config/global.config --userconfig ../mothcw.config --unp Q9NZ71-9 --transcript_variant G323D --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/MusiteDeep --uniquekey RTEL1_NM_001283010.1_Q9NZ71-9_MusiteDeep 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/slurm/PathProx/RTEL1_NM_001283010.1_G323D_PathProx.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/slurm/PathProx/RTEL1_NM_001283010.1_G323D_PathProx.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/slurm/PathProx/RTEL1_NM_001283010.1_G323D_PathProx.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214823 05:47:15 INFO [ psb_launch.py:798 ] No ddG_monomer jobs will be run for RTEL1 NM_001283010.1 G323D 05:47:15 INFO [ psb_launch.py:798 ] No ddG_cartesian jobs will be run for RTEL1 NM_001283010.1 G323D 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/slurm/MusiteDeep/RTEL1_NM_001283010.1_G323D_MusiteDeep.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/slurm/MusiteDeep/RTEL1_NM_001283010.1_G323D_MusiteDeep.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/slurm/MusiteDeep/RTEL1_NM_001283010.1_G323D_MusiteDeep.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214824 05:47:15 INFO [ psb_launch.py:798 ] No ScanNet jobs will be run for RTEL1 NM_001283010.1 G323D 05:47:15 INFO [ psb_launch.py:798 ] No SequenceAnnotation jobs will be run for RTEL1 NM_001283010.1 G323D 05:47:15 INFO [ psb_launch.py:798 ] No DIEP jobs will be run for RTEL1 NM_001283010.1 G323D 05:47:15 INFO [ psb_launch.py:887 ] 2 rows read from work plan file casewide/casewide_workplan.csv 05:47:15 INFO [ psb_launch.py:923 ] additionally logging to file /dors/capra_lab/users/mothcw/VUStruct/SampleCase/RTEL1_NM_001283010.1_G323D/psb_launch.log 05:47:15 INFO [ psb_launch.py:377 ] DIEP: run_DIEP.py --genesfile=SampleCase_genes_inheritance_zygosity.csv --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/DIEP --uniquekey DIEP 05:47:15 INFO [ psb_launch.py:377 ] DiGePred: /dors/meilerlab/data/mukhes1/digepred/scripts/run_digepred_july2022.py -n SampleCase -e /dors/capra_lab/users/mothcw/VUStruct/SampleCase/SampleCase.xlsx --outdir /dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/DiGePred --uniquekey DiGePred 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/slurm/DiGePred/casewide_DiGePred.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/slurm/DiGePred/casewide_DiGePred.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/slurm/DiGePred/casewide_DiGePred.slurm'] 05:47:15 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214825 05:47:15 INFO [ psb_launch.py:814 ] Creating: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/slurm/DIEP/casewide_DIEP.slurm 05:47:15 INFO [ psb_launch.py:462 ] Setting PATH to match launch-time /dors/capra_lab/users/mothcw/psbadmin/bin/psb_launch.py environment 05:47:15 INFO [ psb_launch.py:463 ] PATH=/home/mothcw/anaconda3/bin:/home/mothcw/anaconda3/condabin:/dors/capra_lab/users/mothcw/localperl/bin:/home/mothcw/anaconda3/bin:/dors/capra_lab/users/mothcw/psbadmin/bin:/dors/capra_lab/users/mothcw/psbadmin/pdbmap:/dors/capra_lab/users/mothcw/psbadmin/pathprox:/accre/usr/sbin:/accre/usr/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/mothcw/bin:$PATH 05:47:15 INFO [ psb_launch.py:468 ] Setting ENSEMBL_REGISTRY from .config: /dors/capra_lab/users/mothcw/VUStruct/config/ensembl_registry_GRCh38.conf 05:47:15 INFO [ psb_launch.py:620 ] Slurm file created: /dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/slurm/DIEP/casewide_DIEP.slurm 05:47:15 INFO [ slurm.py:89 ] ['sbatch', '/dors/capra_lab/users/mothcw/VUStruct/SampleCase/casewide/slurm/DIEP/casewide_DIEP.slurm'] 05:47:16 INFO [ slurm.py:119 ] sbatch successfully launched: Submitted batch job 59214826