Watcher running with nmdc-dev configuration finds jobs but no data objects for the jobs

Results showing successful pickup and processing of a MAGs job:
(nmdc-automation-py3.11) (nersc-python) nmdcda@perlmutter:login29:~/nmdc_automation/dev> ./run_dev.sh
2024-11-18 14:14:07,463 INFO: Config file: /global/homes/n/nmdcda/nmdc_automation/dev/site_configuration_nersc.toml
2024-11-18 14:14:07,464 INFO: Using state file from config: /global/cfs/cdirs/m3408/var/dev/agent.state
2024-11-18 14:14:07,464 INFO: Reading state from /global/cfs/cdirs/m3408/var/dev/agent.state
2024-11-18 14:14:07,490 INFO: Restored 351 jobs from state
2024-11-18 14:14:07,490 INFO: Restoring 351 jobs from state.
2024-11-18 14:14:08,741 INFO: Entering polling loop
2024-11-18 14:14:08,742 INFO: Reading state from /global/cfs/cdirs/m3408/var/dev/agent.state
2024-11-18 14:14:08,753 INFO: Restored 0 jobs from state
2024-11-18 14:14:09,555 INFO: Found 0 unclaimed jobs.
2024-11-18 14:14:09,629 INFO: Found 1 successful jobs.
2024-11-18 14:14:09,629 INFO: Found 1 failed jobs.
2024-11-18 14:14:09,629 INFO: Process successful job:  nmdc:sys0m369xp60
2024-11-18 14:14:09,630 INFO: Getting job runner metadata for job 9492a397-eb30-472b-9d3b-b44b676f4652
2024-11-18 14:14:10,001 INFO: Processing output nmdc_mags.final_checkm
2024-11-18 14:14:10,001 INFO: Output file path: /pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_checkm_qa.out
2024-11-18 14:14:10,155 INFO: Processing output nmdc_mags.final_hqmq_bins_zip
2024-11-18 14:14:10,155 INFO: Output file path: /pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_hqmq_bin.zip
2024-11-18 14:14:10,226 INFO: Processing output nmdc_mags.final_gtdbtk_bac_summary
2024-11-18 14:14:10,226 INFO: Output file path: /pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_gtdbtk.bac122.summary.tsv
2024-11-18 14:14:10,229 INFO: Processing output nmdc_mags.final_gtdbtk_ar_summary
2024-11-18 14:14:10,229 INFO: Output file path: /pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_gtdbtk.ar122.summary.tsv
2024-11-18 14:14:10,232 INFO: Processing output nmdc_mags.mags_version
2024-11-18 14:14:10,232 INFO: Output file path: /pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_bin.info
2024-11-18 14:14:10,234 INFO: Found 5 data objects for job nmdc:sys0m369xp60
2024-11-18 14:14:11,466 INFO: Created workflow execution record for job nmdc:sys0m369xp60
2024-11-18 14:14:14,315 INFO: Database object validated for job nmdc:sys0m369xp60
2024-11-18 14:14:16,420 INFO: Posted objects response: {'message': 'jobs accepted'}
2024-11-18 14:14:17,942 INFO: Updated operation nmdc:sys0m369xp60 response {'id': 'nmdc:sys0m369xp60', 'done': True, 'expire_time': '2024-10-16T19:33:30.785000', 'result': None, 'metadata': {'model': 'nmdc_runtime.api.models.job.JobOperationMetadata', 'job': {'workflow': {'name': None, 'description': None, 'capability_ids': None, 'id': 'MAGs: v1.3.10', 'created_at': None}, 'name': None, 'description': None, 'id': 'nmdc:66cf64b6-7462-11ef-8b84-deaa01ab0f49', 'created_at': None, 'config': {'git_repo': 'https://github.com/microbiomedata/metaMAGs', 'release': 'v1.3.10', 'wdl': 'mbin_nmdc.wdl', 'activity_id': 'nmdc:wfmag-11-g7msr323.1', 'activity_set': 'mags_activity_set', 'was_informed_by': 'nmdc:omprc-11-9cdxha98', 'trigger_activity': 'nmdc:wfmgan-11-jv8kx789.1', 'iteration': 1, 'input_prefix': 'nmdc_mags', 'inputs': {'proj': 'nmdc:wfmag-11-g7msr323.1', 'contig_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contigs.fna', 'sam_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgas-11-0qvjnc54.1/nmdc_wfmgas-11-0qvjnc54.1_pairedMapped_sorted.bam', 'gff_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_functional_annotation.gff', 'proteins_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_proteins.faa', 'cog_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_cog.gff', 'ec_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ec.tsv', 'ko_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ko.tsv', 'pfam_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_pfam.gff', 'tigrfam_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_tigrfam.gff', 'crispr_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_crt.crisprs', 'product_names_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_product_names.tsv', 'gene_phylogeny_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_gene_phylogeny.tsv', 'lineage_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_scaffold_lineage.tsv', 'map_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contig_names_mapping.tsv'}, 'input_data_objects': [{'id': 'nmdc:dobj-11-1x850k20', 'name': 'nmdc_wfmgan-11-jv8kx789.1_contigs.fna', 'description': 'Assembly contigs (remapped) for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contigs.fna', 'md5_checksum': '6debed079383eeca2045ce23b0576607', 'file_size_bytes': 2084209623, 'data_object_type': 'Assembly Contigs'}, {'id': 'nmdc:dobj-11-fkj2kt47', 'name': 'nmdc_wfmgas-11-0qvjnc54.1_pairedMapped_sorted.bam', 'description': 'Metagenome Alignment BAM file for nmdc:omprc-11-9cdxha98', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgas-11-0qvjnc54.1/nmdc_wfmgas-11-0qvjnc54.1_pairedMapped_sorted.bam', 'md5_checksum': '88ec004bd037a3820060427098798666', 'file_size_bytes': 15704979428, 'data_object_type': 'Assembly Coverage BAM'}, {'id': 'nmdc:dobj-11-f9rnav80', 'name': 'nmdc_wfmgan-11-jv8kx789.1_functional_annotation.gff', 'description': 'Functional Annotation for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_functional_annotation.gff', 'md5_checksum': '349cae9b4fe62bb910f08a183e57b475', 'file_size_bytes': 1320869282, 'data_object_type': 'Functional Annotation GFF'}, {'id': 'nmdc:dobj-11-btqzf393', 'name': 'nmdc_wfmgan-11-jv8kx789.1_proteins.faa', 'description': 'FASTA Amino Acid File for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_proteins.faa', 'md5_checksum': '292eae73923605dae2ef9f5d582e4603', 'file_size_bytes': 1075716574, 'data_object_type': 'Annotation Amino Acid FASTA'}, {'id': 'nmdc:dobj-11-hdty3m42', 'name': 'nmdc_wfmgan-11-jv8kx789.1_cog.gff', 'description': 'COGs for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_cog.gff', 'md5_checksum': 'c4d1121c1ceb1229afb7190d23553003', 'file_size_bytes': 712459544, 'data_object_type': 'Clusters of Orthologous Groups (COG) Annotation GFF'}, {'id': 'nmdc:dobj-11-0gk70187', 'name': 'nmdc_wfmgan-11-jv8kx789.1_ec.tsv', 'description': 'EC Annotations for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ec.tsv', 'md5_checksum': '84cf22f39532e1bd001bea8425735a82', 'file_size_bytes': 116429630, 'data_object_type': 'Annotation Enzyme Commission'}, {'id': 'nmdc:dobj-11-3mtmhf26', 'name': 'nmdc_wfmgan-11-jv8kx789.1_ko.tsv', 'description': 'KEGG Orthology for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ko.tsv', 'md5_checksum': '17d699df17c97fc28796a198cf40a328', 'file_size_bytes': 169182276, 'data_object_type': 'Annotation KEGG Orthology'}, {'id': 'nmdc:dobj-11-7kfhf682', 'name': 'nmdc_wfmgan-11-jv8kx789.1_pfam.gff', 'description': 'Pfam Annotation for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_pfam.gff', 'md5_checksum': '23c33758dc138e1af0f39fa1f3ca07db', 'file_size_bytes': 602929841, 'data_object_type': 'Pfam Annotation GFF'}, {'id': 'nmdc:dobj-11-9hjg8y84', 'name': 'nmdc_wfmgan-11-jv8kx789.1_tigrfam.gff', 'description': 'TIGRFam for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_tigrfam.gff', 'md5_checksum': 'bbfded219e0b359602725c9efb4f0c54', 'file_size_bytes': 61788991, 'data_object_type': 'TIGRFam Annotation GFF'}, {'id': 'nmdc:dobj-11-2x0wy902', 'name': 'nmdc_wfmgan-11-jv8kx789.1_crt.crisprs', 'description': 'Crispr Terms for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_crt.crisprs', 'md5_checksum': '9d2255a63e39552328c4da20ccf2bb3f', 'file_size_bytes': 142989, 'data_object_type': 'Crispr Terms'}, {'id': 'nmdc:dobj-11-r0bx4g71', 'name': 'nmdc_wfmgan-11-jv8kx789.1_product_names.tsv', 'description': 'Product names for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_product_names.tsv', 'md5_checksum': '6f1325b2f8dee9b2a75598fb9645c43d', 'file_size_bytes': 401118634, 'data_object_type': 'Product Names'}, {'id': 'nmdc:dobj-11-7mj15p44', 'name': 'nmdc_wfmgan-11-jv8kx789.1_gene_phylogeny.tsv', 'description': 'Gene Phylogeny for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_gene_phylogeny.tsv', 'md5_checksum': '037aee803f1b81ac5ac1bccb9a18527d', 'file_size_bytes': 748420652, 'data_object_type': 'Gene Phylogeny tsv'}, {'id': 'nmdc:dobj-11-r2zqpy26', 'name': 'nmdc_wfmgan-11-jv8kx789.1_scaffold_lineage.tsv', 'description': 'Scaffold Lineage tsv for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_scaffold_lineage.tsv', 'md5_checksum': 'efdce9771cdda8bd8548e44ef6d1d3a3', 'file_size_bytes': 503898615, 'data_object_type': 'Scaffold Lineage tsv'}, {'id': 'nmdc:dobj-11-4k2bt072', 'name': 'nmdc_wfmgan-11-jv8kx789.1_contig_names_mapping.tsv', 'description': 'Contig mappings file for nmdc:wfmgan-11-jv8kx789.1', 'url': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contig_names_mapping.tsv', 'md5_checksum': '1056a6ef48ce9124de0828ee85246e65', 'file_size_bytes': 250129248, 'data_object_type': 'Contig Mapping File'}], 'activity': {'name': 'Metagenome Assembled Genomes Analysis Activity for {id}', 'type': 'nmdc:MagsAnalysisActivity', 'binned_contig_num': '{outputs.final_stats_json.binned_contig_num}', 'input_contig_num': '{outputs.final_stats_json.input_contig_num}', 'low_depth_contig_num': '{outputs.final_stats_json.low_depth_contig_num}', 'mags_list': '{outputs.final_stats_json.mags_list}', 'too_short_contig_num': '{outputs.final_stats_json.too_short_contig_num}', 'unbinned_contig_num': '{outputs.final_stats_json.unbinned_contig_num}'}, 'outputs': [{'output': 'final_checkm', 'data_object_type': 'CheckM Statistics', 'description': 'CheckM for {id}', 'name': 'CheckM statistics report', 'id': 'nmdc:dobj-11-xvjz5h55'}, {'output': 'final_hqmq_bins_zip', 'data_object_type': 'Metagenome Bins', 'description': 'Metagenome Bins for {id}', 'name': 'Metagenome bin tarfiles archive', 'id': 'nmdc:dobj-11-85q1v678'}, {'output': 'final_gtdbtk_bac_summary', 'data_object_type': 'GTDBTK Bacterial Summary', 'description': 'Bacterial Summary for {id}', 'name': 'GTDBTK bacterial summary', 'id': 'nmdc:dobj-11-j5p58211'}, {'output': 'final_gtdbtk_ar_summary', 'data_object_type': 'GTDBTK Archaeal Summary', 'description': 'Archaeal Summary for {id}', 'name': 'GTDBTK archaeal summary', 'suffix': '_gtdbtk.ar122.summary.tsv', 'id': 'nmdc:dobj-11-ec2fqk35'}, {'output': 'mags_version', 'data_object_type': 'Metagenome Bins Info File', 'description': 'Metagenome Bins Info File for {id}', 'name': 'Metagenome Bins Info File', 'id': 'nmdc:dobj-11-kg68h909'}]}, 'claims': []}, 'site_id': 'NERSC', 'extra': {'workflowName': 'nmdc_mags', 'workflowProcessingEvents': [{'cromwellId': 'cromid-43e4542', 'description': 'PickedUp', 'timestamp': '2024-09-16T19:33:50.770Z', 'cromwellVersion': '77'}, {'cromwellId': 'cromid-43e4542', 'description': 'Finished', 'timestamp': '2024-09-16T21:52:02.530Z', 'cromwellVersion': '77'}], 'actualWorkflowLanguageVersion': '1.0', 'submittedFiles': {'workflow': 'version 1.0\nworkflow nmdc_mags {\n    input {\n        String proj\n        String contig_file\n        String sam_file\n        String gff_file\n        String proteins_file\n        String cog_file\n        String ec_file\n        String ko_file\n        String pfam_file\n        String tigrfam_file\n        String crispr_file\n        String product_names_file\n        String gene_phylogeny_file\n        String lineage_file\n        String? map_file\n        String? scratch_dir\n        Int cpu=32\n        Int threads=64\n        Int pthreads=1\n        String gtdbtk_db="/refdata/GTDBTK_DB/gtdbtk_release207_v2"\n        String checkm_db="/refdata/checkM_DB/checkm_data_2015_01_16"\n        String eukcc2_db="/refdata/EUKCC2_DB/eukcc2_db_ver_1.2"\n        String package_container = "microbiomedata/nmdc_mbin_vis:0.7.0"\n        String container = "microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639"\n    }\n    call stage {\n        input:\n            container=container,\n            contig_file=contig_file,\n            sam_file=sam_file,\n            gff_file=gff_file,\n            proteins_file=proteins_file,\n            cog_file=cog_file,\n            ec_file=ec_file,\n            ko_file=ko_file,\n            pfam_file=pfam_file,\n            tigrfam_file=tigrfam_file,\n            crispr_file=crispr_file,\n            product_names_file=product_names_file,\n            gene_phylogeny_file=gene_phylogeny_file,\n            lineage_file=lineage_file,\n            map_file=map_file\n    }\n\n    call check_id_map {\n        input:\n            container=container,\n            contig_file=stage.contig,\n            proteins_file=stage.proteins\n    }\n\n    call mbin_nmdc {\n        input:  \n                name=proj,\n                fna = check_id_map.contig,\n                aln = stage.sam,\n                gff = stage.gff,\n                lineage=stage.lineage_tsv,\n                threads =  threads,\n                pthreads = pthreads,\n                gtdbtk_env = gtdbtk_db,\n                checkm_env = checkm_db,\n                eukcc2_env = eukcc2_db,\n                map_file = stage.map_tsv,\n                mbin_container = container\n    }\n    call package {\n         input:  proj = proj,\n                 bins=flatten([mbin_nmdc.hqmq_bin_fasta_files,mbin_nmdc.lq_bin_fasta_files]),\n                 json_stats=mbin_nmdc.stats_json,\n                 gff_file=stage.gff,\n                 proteins_file=stage.proteins,\n                 cog_file=stage.cog,\n                 ec_file=stage.ec,\n                 ko_file=stage.ko,\n                 pfam_file=stage.pfam,\n                 tigrfam_file=stage.tigrfam,\n                 crispr_file=stage.crispr,\n                 gene_phylogeny_file=stage.gene_phylogeny,\n                 product_names_file=stage.product_names,\n                 container=package_container\n    }\n\n    call finish_mags {\n        input:  container="microbiomedata/workflowmeta:1.1.1",\n        \tproj=proj,\n        \tbacsum= mbin_nmdc.bacsum,\n        \tarcsum = mbin_nmdc.arcsum,\n        \tshort = mbin_nmdc.short,\n        \tlow = mbin_nmdc.low,\n        \tunbinned = mbin_nmdc.unbinned,\n        \tcheckm = mbin_nmdc.checkm,\n        \tmbin_sdb = mbin_nmdc.mbin_sdb,\n        \tmbin_version = mbin_nmdc.mbin_version,\n        \tstats_json = package.stats_json,\n        \tstats_tsv = mbin_nmdc.stats_tsv,\n        \thqmq_bin_tarfiles = package.hqmq_bin_tarfiles,\n        \tlq_bin_tarfiles = package.lq_bin_tarfiles,\n        \tbarplot = package.barplot,\n        \theatmap = package.heatmap,\n        \tkronaplot = package.kronaplot,\n        \teukcc_file=mbin_nmdc.eukcc_csv,\n        \tko_matrix = package.ko_matrix\n    }\n\n    output {\n        File final_hqmq_bins_zip = finish_mags.final_hqmq_bins_zip\n        File final_lq_bins_zip = finish_mags.final_lq_bins_zip\n        File final_gtdbtk_bac_summary = finish_mags.final_gtdbtk_bac_summary\n        File final_gtdbtk_ar_summary = finish_mags.final_gtdbtk_ar_summary\n        File short = finish_mags.final_short\n        File low = finish_mags.final_lowDepth_fa\n        File final_unbinned_fa  = finish_mags.final_unbinned_fa\n        File final_checkm = finish_mags.final_checkm\n        File mags_version = finish_mags.final_version\n        File final_stats_json = finish_mags.final_stats_json\n        File barplot = finish_mags.final_barplot\n        File heatmap = finish_mags.final_heatmap\n        File kronaplot = finish_mags.final_kronaplot\n    }\n\n\n}\n\ntask mbin_nmdc {\n    input{\n        File fna\n        File aln\n        File gff\n        File lineage\n        String name\n        File? map_file\n        Int? threads\n        Int? pthreads\n        String gtdbtk_env\n        String checkm_env\n        String? eukcc2_env\n        String mbin_container\n    }\n\n    command<<<\n        set -euo pipefail\n        export GTDBTK_DATA_PATH=~{gtdbtk_env}\n        export CHECKM_DATA_PATH=~{checkm_env}\n        mbin.py ~{"--threads " + threads} ~{"--pthreads " + pthreads} ~{"--map " + map_file} ~{"--eukccdb " + eukcc2_env} --fna ~{fna} --gff ~{gff} --aln ~{aln} --lintsv ~{lineage}\n        mbin_stats.py $PWD\n        mbin_versions.py > mbin_nmdc_versions.log\n        touch MAGs_stats.tsv\n    \n        if [ -f  gtdbtk-output/gtdbtk.bac120.summary.tsv ]; then\n            echo "bacterial summary exists."\n        else\n            mkdir -p gtdbtk-output\n            echo "No Bacterial Results for ~{name}" > gtdbtk-output/gtdbtk.bac120.summary.tsv\n        fi\n\n        if [ -f  gtdbtk-output/gtdbtk.ar122.summary.tsv ]; then\n            echo "archaeal summary exists."\n        else\n            mkdir -p gtdbtk-output\n            echo "No Archaeal Results for ~{name}" > gtdbtk-output/gtdbtk.ar122.summary.tsv\n        fi\n\n        if [ -f checkm-qa.out ]; then\n            echo "checkm summary exists."\n        else\n            mkdir -p gtdbtk-output\n            echo "No Checkm Results for ~{name}" > checkm-qa.out\n        fi\n\n        if [ -f mbin.sdb ]; then\n            echo "mbin.sdb exists."\n        else\n            mkdir -p gtdbtk-output\n            echo "Mbin Sdb Could not be created for ~{name}" && touch mbin.sdb\n        fi\n\n        if [ -f eukcc_output/eukcc.csv.final ]; then\n            echo "eukcc.csv.final exists."\n        else\n            mkdir -p eukcc_output\n            echo "No EUKCC2 result for ~{name}" > eukcc_output/eukcc.csv.final\n        fi\n    >>>\n\n    runtime{\n        docker : mbin_container\n        memory : "120 G"\n        time : "2:00:00"\n        cpu : threads\n    }\n\n    output{\n        File short = "bins.tooShort.fa"\n        File low = "bins.lowDepth.fa"\n        File unbinned = "bins.unbinned.fa"\n        File checkm = "checkm-qa.out"\n        File stats_json = "MAGs_stats.json"\n        File stats_tsv = "MAGs_stats.tsv"\n        File mbin_sdb = "mbin.sdb"\n        File mbin_version = "mbin_nmdc_versions.log"\n        File bacsum = "gtdbtk-output/gtdbtk.bac120.summary.tsv"\n        File arcsum = "gtdbtk-output/gtdbtk.ar122.summary.tsv"\n        File eukcc_csv = "eukcc_output/eukcc.csv.final"\n        Array[File] hqmq_bin_fasta_files = glob("hqmq-metabat-bins/*fa")\n        Array[File] lq_bin_fasta_files = glob("filtered-metabat-bins/*fa")\n    }    \n}\n\n\ntask stage {\n    input{\n        String container\n        String contig_file\n        String sam_file\n        String gff_file\n        String proteins_file\n        String cog_file\n        String ec_file\n        String ko_file\n        String pfam_file\n        String tigrfam_file\n        String crispr_file\n        String product_names_file\n        String gene_phylogeny_file\n        String lineage_file\n        String? map_file\n        String contigs_out="contigs.fasta"\n        String bam_out="pairedMapped_sorted.bam"\n        String gff_out="functional_annotation.gff"\n        String proteins_out="proteins.faa"\n        String cog_out="cog.gff"\n        String ec_out="ec.tsv"\n        String ko_out="ko.tsv"\n        String pfam_out="pfam.gff"\n        String tigrfam_out="tigrfam.gff"\n        String crispr_out="crispr.tsv"\n        String products_out="products.tsv"\n        String gene_phylogeny_out="gene_phylogeny.tsv"\n        String lineage_out="lineage.tsv"\n        String map_out="map_file.tsv"\n    }\n   command<<<\n\n       set -euo pipefail\n\n        function stage() {\n            in=$1\n            out=$2\n            if [ $( echo $in |egrep -c "https*:") -gt 0 ] ; then\n                wget $in -O $out\n            else\n                ln $in $out || cp $in $out\n            fi\n        }\n\n        stage ~{contig_file} ~{contigs_out} &\n        stage ~{sam_file} ~{bam_out} &\n        stage ~{gff_file} ~{gff_out} &\n        stage ~{proteins_file} ~{proteins_out} &\n        stage ~{cog_file} ~{cog_out} &\n        stage ~{ec_file} ~{ec_out} &\n        stage ~{ko_file} ~{ko_out} &\n        stage ~{pfam_file} ~{pfam_out} &\n        stage ~{tigrfam_file} ~{tigrfam_out} &\n        stage ~{crispr_file} ~{crispr_out} &\n        stage ~{product_names_file} ~{products_out} &\n        stage ~{gene_phylogeny_file} ~{gene_phylogeny_out} &\n        stage ~{lineage_file} ~{lineage_out}\n        ~{"stage " + map_file + " " + map_out}\n        wait\n\n        date --iso-8601=seconds > start.txt\n\n    >>>\n\n   output{\n        File contig = contigs_out\n        File sam = bam_out\n        File gff = gff_out\n        File proteins = proteins_out\n        File cog = cog_out\n        File ec = ec_out\n        File ko = ko_out\n        File pfam = pfam_out\n        File tigrfam = tigrfam_out\n        File crispr = crispr_out\n        File product_names = products_out\n        File gene_phylogeny = gene_phylogeny_out\n        File lineage_tsv = lineage_out\n        File? map_tsv = map_out\n        String start = read_string("start.txt")\n   }\n   runtime {\n     memory: "1 GiB"\n     cpu:  2\n     maxRetries: 1\n     docker: container\n   }\n}\n\ntask check_id_map{\n    input{\n        String container\n        File contig_file\n        File proteins_file\n        String contig_file_name=basename(contig_file)\n    }\n    command<<<\n    set -euo pipefail \n\n    python <<CODE\n    import sys\n    contigIDs={}\n    with open("~{contig_file}","r") as c_file:\n        for line in c_file:\n            if line.startswith(">"):\n                seq_id = line[1:].rstrip().split()[0] # nmdc:wfmgan-12-gbysvd76.1_0000001\n                contigIDs[seq_id]=1\n    with open("~{proteins_file}","r") as p_file:\n        for line in p_file:\n            if line.startswith(">"):\n                seq_id = line[1:].rstrip().split()[0]  # nmdc:wfmgan-12-gbysvd76.1_0000001_1_225\n                contig_id = "_".join(seq_id.split("_")[0:-2]) # nmdc:wfmgan-12-gbysvd76.1_0000001\n                if contig_id not in contigIDs:\n                    print(f"{contig_id} is not in ~{contig_file_name}.", file=sys.stderr)\n                    sys.exit(1)\n    CODE\n    >>>\n\n    output{\n        File contig = contig_file\n    }\n    runtime {\n        memory: "1 GiB"\n        cpu:  1\n        docker: container\n   }\n}\n\ntask package{\n    input{\n        String proj\n        String prefix=sub(proj, ":", "_")\n        Array[File] bins\n        File json_stats\n        File gff_file\n        File proteins_file\n        File cog_file\n        File ec_file\n        File ko_file\n        File pfam_file\n        File tigrfam_file\n        File crispr_file\n        File gene_phylogeny_file\n        File product_names_file\n        String container \n    }\n     command<<<\n         set -euo pipefail\n         create_tarfiles.py ~{prefix} \\\n                     ~{json_stats} ~{gff_file} ~{proteins_file} ~{cog_file} \\\n                     ~{ec_file} ~{ko_file} ~{pfam_file} ~{tigrfam_file} \\\n                     ~{crispr_file} ~{gene_phylogeny_file} \\\n                     ~{product_names_file} \\\n                     ~{sep=" " bins}\n\n        if [ -f ~{prefix}_heatmap.pdf ]; then\n            if [ -f ~{prefix}_barplot.pdf ]; then\n                echo "KO analysis plot exists."\n            else\n                echo "There are no modules above 80% completeness. No barplot will be generated." && touch ~{prefix}_barplot.pdf\n            fi\n        else\n            echo "No KO analysis result for ~{proj}" && touch ~{prefix}_heatmap.pdf\n            echo "No KO analysis result for ~{proj}" && touch ~{prefix}_barplot.pdf\n            echo "No KO analysis result for ~{proj}" > ~{prefix}_ko_krona.html\n            echo "No KO analysis result for ~{proj}" > ~{prefix}_module_completeness.tab\n        fi\n     >>>\n     output {\n         Array[File] hqmq_bin_tarfiles = flatten([glob("*_HQ.tar.gz"), glob("*_MQ.tar.gz")])\n         Array[File] lq_bin_tarfiles = glob("*_LQ.tar.gz") \n         File barplot = prefix + "_barplot.pdf"\n         File heatmap = prefix + "_heatmap.pdf"\n         File kronaplot = prefix + "_ko_krona.html"\n         File ko_matrix = prefix + "_module_completeness.tab"\n         File stats_json = prefix + "_stats.json"\n     }\n     runtime {\n         docker: container\n         memory: "1 GiB"\n         cpu:  1\n     }\n}\n\ntask finish_mags {\n    input{\n        String container\n        File mbin_sdb\n        File mbin_version\n        String proj\n        String prefix=sub(proj, ":", "_")\n        File bacsum\n        File arcsum\n        File? short\n        File? low\n        File? unbinned\n        File? checkm\n        Array[File] hqmq_bin_tarfiles\n        Array[File] lq_bin_tarfiles\n        File stats_json\n        File stats_tsv\n        Int n_hqmq=length(hqmq_bin_tarfiles)\n        Int n_lq=length(lq_bin_tarfiles)\n        File barplot\n        File heatmap\n        File kronaplot\n        File ko_matrix\n        File eukcc_file\n    }\n    command<<<\n        set -euo pipefail\n        end=`date --iso-8601=seconds`\n\n        ln ~{low} ~{prefix}_bins.lowDepth.fa\n        ln ~{short} ~{prefix}_bins.tooShort.fa\n        ln ~{unbinned} ~{prefix}_bins.unbinned.fa\n        ln ~{checkm} ~{prefix}_checkm_qa.out\n        ln ~{mbin_version} ~{prefix}_bin.info\n        ln ~{bacsum} ~{prefix}_gtdbtk.bac122.summary.tsv\n        ln ~{arcsum} ~{prefix}_gtdbtk.ar122.summary.tsv\n        ln ~{barplot} ~{prefix}_barplot.pdf\n        ln ~{heatmap} ~{prefix}_heatmap.pdf\n        ln ~{kronaplot} ~{prefix}_kronaplot.html\n        ln ~{ko_matrix} ~{prefix}_ko_matrix.txt\n        ln ~{eukcc_file} ~{prefix}_eukcc.csv\n\n        # cp all tarfiles, zip them under prefix, if empty touch no_mags.txt\n        mkdir -p hqmq\n        if [ ~{n_hqmq} -gt 0 ] ; then\n            (cd hqmq && cp ~{sep=" " hqmq_bin_tarfiles} .)\n            (cd hqmq && cp ~{mbin_sdb} .)\n            (cd hqmq && zip -j ../~{prefix}_hqmq_bin.zip *tar.gz mbin.sdb ../*pdf ../*kronaplot.html ../*ko_matrix.txt)\n        else\n            (cd hqmq && touch no_hqmq_mags.txt)\n            (cd hqmq && cp ~{mbin_sdb} .)\n            (cd hqmq && zip -j ../~{prefix}_hqmq_bin.zip *.txt mbin.sdb)\n        fi\n\n        mkdir -p lq\n        if [ ~{n_lq} -gt 0 ] ; then\n            (cd lq && cp ~{sep=" " lq_bin_tarfiles} .)\n            (cd lq && cp ~{mbin_sdb} .)\n            (cd lq && zip -j ../~{prefix}_lq_bin.zip *tar.gz mbin.sdb ../~{prefix}_eukcc.csv ../*pdf ../*kronaplot.html ../*ko_matrix.txt)\n        else\n            (cd lq && touch no_lq_mags.txt)\n            (cd lq && cp ~{mbin_sdb} .)\n            (cd lq && zip -j ../~{prefix}_lq_bin.zip *.txt mbin.sdb ../~{prefix}_eukcc.csv )\n        fi\n\n        # Fix up attribute name\n        cat ~{stats_json} | \\\n           sed \'s/: null/: "null"/g\' | \\\n           sed \'s/lowDepth_/low_depth_/\' > ~{prefix}_mags_stats.json\n\n    >>>\n\n    output {\n        File final_checkm = "~{prefix}_checkm_qa.out"\n        File final_hqmq_bins_zip = "~{prefix}_hqmq_bin.zip"\n        File final_lq_bins_zip = "~{prefix}_lq_bin.zip"\n        File final_stats_json = "~{prefix}_mags_stats.json"\n        File final_gtdbtk_bac_summary = "~{prefix}_gtdbtk.bac122.summary.tsv"\n        File final_gtdbtk_ar_summary = "~{prefix}_gtdbtk.ar122.summary.tsv"\n        File final_lowDepth_fa = "~{prefix}_bins.lowDepth.fa"\n        File final_unbinned_fa = "~{prefix}_bins.unbinned.fa"\n        File final_short = "~{prefix}_bins.tooShort.fa"\n        File final_version = "~{prefix}_bin.info"\n        File final_kronaplot = "~{prefix}_kronaplot.html"\n        File final_heatmap = "~{prefix}_heatmap.pdf"\n        File final_barplot = "~{prefix}_barplot.pdf"\n    }\n\n    runtime {\n        memory: "10 GiB"\n        cpu:  4\n        maxRetries: 1\n        docker: container\n    }\n}\n', 'root': '', 'options': '{\n\n}', 'inputs': '{"nmdc_mags.cog_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_cog.gff","nmdc_mags.contig_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contigs.fna","nmdc_mags.crispr_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_crt.crisprs","nmdc_mags.ec_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ec.tsv","nmdc_mags.gene_phylogeny_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_gene_phylogeny.tsv","nmdc_mags.gff_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_functional_annotation.gff","nmdc_mags.ko_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ko.tsv","nmdc_mags.lineage_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_scaffold_lineage.tsv","nmdc_mags.map_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contig_names_mapping.tsv","nmdc_mags.pfam_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_pfam.gff","nmdc_mags.product_names_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_product_names.tsv","nmdc_mags.proj":"nmdc:wfmag-11-g7msr323.1","nmdc_mags.proteins_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_proteins.faa","nmdc_mags.sam_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgas-11-0qvjnc54.1/nmdc_wfmgas-11-0qvjnc54.1_pairedMapped_sorted.bam","nmdc_mags.tigrfam_file":"https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_tigrfam.gff"}', 'workflowUrl': '', 'labels': '{"release": "v1.3.10", "wdl": "mbin_nmdc.wdl", "git_repo": "https://github.com/microbiomedata/metaMAGs", "pipeline_version": "v1.3.10", "pipeline": "mbin_nmdc.wdl", "activity_id": "nmdc:wfmag-11-g7msr323.1", "opid": "nmdc:sys0m369xp60", "submitter": "nmdcda"}'}, 'calls': {'nmdc_mags.mbin_nmdc': [{'executionStatus': 'Done', 'stdout': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/stdout', 'backendStatus': 'Done', 'compressedDockerSize': 1191863655, 'commandLine': 'set -euo pipefail\nexport GTDBTK_DATA_PATH=/refdata/GTDBTK_DB/gtdbtk_release207_v2\nexport CHECKM_DATA_PATH=/refdata/checkM_DB/checkm_data_2015_01_16\nmbin.py --threads 64 --pthreads 1 --map /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/inputs/1577597465/map_file.tsv --eukccdb /refdata/EUKCC2_DB/eukcc2_db_ver_1.2 --fna /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/inputs/1577597465/contigs.fasta --gff /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/inputs/1577597465/functional_annotation.gff --aln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/inputs/1577597465/pairedMapped_sorted.bam --lintsv /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/inputs/1577597465/lineage.tsv\nmbin_stats.py $PWD\nmbin_versions.py > mbin_nmdc_versions.log\ntouch MAGs_stats.tsv\n\nif [ -f  gtdbtk-output/gtdbtk.bac120.summary.tsv ]; then\n    echo "bacterial summary exists."\nelse\n    mkdir -p gtdbtk-output\n    echo "No Bacterial Results for nmdc:wfmag-11-g7msr323.1" > gtdbtk-output/gtdbtk.bac120.summary.tsv\nfi\n\nif [ -f  gtdbtk-output/gtdbtk.ar122.summary.tsv ]; then\n    echo "archaeal summary exists."\nelse\n    mkdir -p gtdbtk-output\n    echo "No Archaeal Results for nmdc:wfmag-11-g7msr323.1" > gtdbtk-output/gtdbtk.ar122.summary.tsv\nfi\n\nif [ -f checkm-qa.out ]; then\n    echo "checkm summary exists."\nelse\n    mkdir -p gtdbtk-output\n    echo "No Checkm Results for nmdc:wfmag-11-g7msr323.1" > checkm-qa.out\nfi\n\nif [ -f mbin.sdb ]; then\n    echo "mbin.sdb exists."\nelse\n    mkdir -p gtdbtk-output\n    echo "Mbin Sdb Could not be created for nmdc:wfmag-11-g7msr323.1" && touch mbin.sdb\nfi\n\nif [ -f eukcc_output/eukcc.csv.final ]; then\n    echo "eukcc.csv.final exists."\nelse\n    mkdir -p eukcc_output\n    echo "No EUKCC2 result for nmdc:wfmag-11-g7msr323.1" > eukcc_output/eukcc.csv.final\nfi', 'shardIndex': -1, 'outputs': {'stats_json': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/MAGs_stats.json', 'eukcc_csv': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/eukcc_output/eukcc.csv.final', 'arcsum': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/gtdbtk-output/gtdbtk.ar122.summary.tsv', 'short': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/bins.tooShort.fa', 'stats_tsv': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/MAGs_stats.tsv', 'hqmq_bin_fasta_files': ['/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.10.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.16.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.18.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.20.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.25.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.26.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.3.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.34.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-02e2568c38f882b2a238a02d6634abe0/bins.6.fa'], 'low': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/bins.lowDepth.fa', 'lq_bin_fasta_files': ['/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.1.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.11.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.12.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.13.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.14.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.15.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.17.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.19.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.2.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.21.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.22.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.23.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.24.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.27.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.28.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.29.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.30.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.31.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.32.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.33.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.35.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.36.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.37.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.38.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.39.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.4.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.40.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.41.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.42.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.43.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.44.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.5.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.7.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.8.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.9.fa'], 'checkm': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/checkm-qa.out', 'unbinned': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/bins.unbinned.fa', 'mbin_version': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/mbin_nmdc_versions.log', 'mbin_sdb': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/mbin.sdb', 'bacsum': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/gtdbtk-output/gtdbtk.bac120.summary.tsv'}, 'runtimeAttributes': {'runtime_minutes': '120', 'priority': '0', 'disk': '0.244140625 GB', 'failOnStderr': 'false', 'continueOnReturnCode': '0', 'docker': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'maxRetries': '0', 'cpu': '64', 'memory': '120 GB'}, 'callCaching': {'allowResultReuse': True, 'hit': False, 'result': 'Cache Miss', 'hashes': {'output count': 'C51CE410C124A10E0DB5E4B97FC2AF39', 'runtime attribute': {'docker': '4DB5CCE48B9916E012489D88408A5D44', 'continueOnReturnCode': 'CFCD208495D565EF66E7DFF9F98764DA', 'failOnStderr': '68934A3E9455FA72420237EB05902327'}, 'output expression': {'File arcsum': '787FE996F609C8C519F3CAF8A1B6CC4C', 'File stats_tsv': '93F275502607D245963D78AA311B330F', 'Array(File) hqmq_bin_fasta_files': '9FEEFEF01742A6D55705986B498E72D6', 'File stats_json': 'BB64C91BA00FBFA822525C0CA83F7551', 'File bacsum': '0716BEAF9194B529A691ABA8169DF4A7', 'File mbin_version': '30DBADB0745B9CFBE83733A77E7B9ED2', 'File unbinned': 'C40A14993B2B418745AE85C7D38560A0', 'File mbin_sdb': 'C1F64B80E92F88AAAFD0F32281C86583', 'File checkm': '8014C70611B1425FB83B75AC0A646927', 'File eukcc_csv': '34B03AA4F494AF7218F14090EE042A0E', 'Array(File) lq_bin_fasta_files': '9A9271C31FA80817D2D58CE66E57A99C', 'File low': 'DD7E48A19D33A1E113823D26F8B1DA5D', 'File short': '7E351A09B6E8E88DCE39A4E9D6577D62'}, 'input count': 'C20AD4D76FE97759AA27A0C99BFF6710', 'backend name': '24B80D5AA1F64928B14AC8407909E586', 'command template': '2A96A444948330081748EF2DB21CD43C', 'input': {'File gff': '349cae9b4fe62bb910f08a183e57b475', 'String gtdbtk_env': 'CB23C84675C6493CC5F510B167E1EC23', 'String checkm_env': '12F5EA073DE844C333782082E5FFDEB9', 'File aln': '88ec004bd037a3820060427098798666', 'String mbin_container': 'BC62D4AAD87B08BA3DA19667EF278DCB', 'String name': 'C03E9C11B0107E590E6B4EC0F0E00BF7', 'Int pthreads': 'C4CA4238A0B923820DCC509A6F75849B', 'File fna': '6debed079383eeca2045ce23b0576607', 'File map_file': '1056a6ef48ce9124de0828ee85246e65', 'String eukcc2_env': '7EF9D719D5795EC372BD096B3A0766AE', 'Int threads': 'EA5D2F1C4608232E07D3AA3D998E5135', 'File lineage': 'efdce9771cdda8bd8548e44ef6d1d3a3'}}, 'effectiveCallCachingMode': 'ReadAndWriteCache'}, 'inputs': {'map_file': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/map_file.tsv', 'name': 'nmdc:wfmag-11-g7msr323.1', 'lineage': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/lineage.tsv', 'gff': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/functional_annotation.gff', 'fna': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/contigs.fasta', 'aln': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/pairedMapped_sorted.bam', 'mbin_container': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'eukcc2_env': '/refdata/EUKCC2_DB/eukcc2_db_ver_1.2', 'gtdbtk_env': '/refdata/GTDBTK_DB/gtdbtk_release207_v2', 'threads': 64, 'pthreads': 1, 'checkm_env': '/refdata/checkM_DB/checkm_data_2015_01_16'}, 'returnCode': 0, 'jobId': '275959', 'backend': 'HtCondor', 'end': '2024-09-16T21:49:15.761Z', 'dockerImageUsed': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'stderr': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/stderr', 'callRoot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc', 'attempt': 1, 'executionEvents': [{'startTime': '2024-09-16T20:43:32.883Z', 'description': 'RunningJob', 'endTime': '2024-09-16T21:49:14.651Z'}, {'startTime': '2024-09-16T20:43:31.919Z', 'description': 'RequestingExecutionToken', 'endTime': '2024-09-16T20:43:32.868Z'}, {'startTime': '2024-09-16T20:43:31.919Z', 'description': 'Pending', 'endTime': '2024-09-16T20:43:31.919Z'}, {'startTime': '2024-09-16T20:43:32.868Z', 'description': 'WaitingForValueStore', 'endTime': '2024-09-16T20:43:32.868Z'}, {'startTime': '2024-09-16T20:43:32.875Z', 'description': 'CallCacheReading', 'endTime': '2024-09-16T20:43:32.883Z'}, {'startTime': '2024-09-16T21:49:14.651Z', 'description': 'UpdatingCallCache', 'endTime': '2024-09-16T21:49:14.791Z'}, {'startTime': '2024-09-16T21:49:14.791Z', 'description': 'UpdatingJobStore', 'endTime': '2024-09-16T21:49:15.761Z'}, {'startTime': '2024-09-16T20:43:32.868Z', 'description': 'PreparingJob', 'endTime': '2024-09-16T20:43:32.875Z'}], 'start': '2024-09-16T20:43:31.919Z'}], 'nmdc_mags.finish_mags': [{'executionStatus': 'Done', 'stdout': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/stdout', 'backendStatus': 'Done', 'compressedDockerSize': 516978455, 'commandLine': 'set -euo pipefail\nend=`date --iso-8601=seconds`\n\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/bins.lowDepth.fa nmdc_wfmag-11-g7msr323.1_bins.lowDepth.fa\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/bins.tooShort.fa nmdc_wfmag-11-g7msr323.1_bins.tooShort.fa\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/bins.unbinned.fa nmdc_wfmag-11-g7msr323.1_bins.unbinned.fa\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/checkm-qa.out nmdc_wfmag-11-g7msr323.1_checkm_qa.out\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/mbin_nmdc_versions.log nmdc_wfmag-11-g7msr323.1_bin.info\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1473246459/gtdbtk.bac120.summary.tsv nmdc_wfmag-11-g7msr323.1_gtdbtk.bac122.summary.tsv\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1473246459/gtdbtk.ar122.summary.tsv nmdc_wfmag-11-g7msr323.1_gtdbtk.ar122.summary.tsv\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-287587103/nmdc_wfmag-11-g7msr323.1_barplot.pdf nmdc_wfmag-11-g7msr323.1_barplot.pdf\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-287587103/nmdc_wfmag-11-g7msr323.1_heatmap.pdf nmdc_wfmag-11-g7msr323.1_heatmap.pdf\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-287587103/nmdc_wfmag-11-g7msr323.1_ko_krona.html nmdc_wfmag-11-g7msr323.1_kronaplot.html\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-287587103/nmdc_wfmag-11-g7msr323.1_module_completeness.tab nmdc_wfmag-11-g7msr323.1_ko_matrix.txt\nln /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/900263638/eukcc.csv.final nmdc_wfmag-11-g7msr323.1_eukcc.csv\n\n# cp all tarfiles, zip them under prefix, if empty touch no_mags.txt\nmkdir -p hqmq\nif [ 9 -gt 0 ] ; then\n    (cd hqmq && cp /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.10_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.16_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.18_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.20_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.25_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.26_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.34_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.3_MQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-934850527/nmdc_wfmag-11-g7msr323.1_bins.6_MQ.tar.gz .)\n    (cd hqmq && cp /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/mbin.sdb .)\n    (cd hqmq && zip -j ../nmdc_wfmag-11-g7msr323.1_hqmq_bin.zip *tar.gz mbin.sdb ../*pdf ../*kronaplot.html ../*ko_matrix.txt)\nelse\n    (cd hqmq && touch no_hqmq_mags.txt)\n    (cd hqmq && cp /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/mbin.sdb .)\n    (cd hqmq && zip -j ../nmdc_wfmag-11-g7msr323.1_hqmq_bin.zip *.txt mbin.sdb)\nfi\n\nmkdir -p lq\nif [ 35 -gt 0 ] ; then\n    (cd lq && cp /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.11_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.12_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.13_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.14_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.15_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.17_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.19_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.1_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.21_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.22_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.23_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.24_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.27_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.28_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.29_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.2_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.30_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.31_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.32_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.33_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.35_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.36_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.37_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.38_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.39_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.40_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.41_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.42_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.43_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.44_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.4_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.5_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.7_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.8_LQ.tar.gz /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/98669466/nmdc_wfmag-11-g7msr323.1_bins.9_LQ.tar.gz .)\n    (cd lq && cp /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/mbin.sdb .)\n    (cd lq && zip -j ../nmdc_wfmag-11-g7msr323.1_lq_bin.zip *tar.gz mbin.sdb ../nmdc_wfmag-11-g7msr323.1_eukcc.csv ../*pdf ../*kronaplot.html ../*ko_matrix.txt)\nelse\n    (cd lq && touch no_lq_mags.txt)\n    (cd lq && cp /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/1484654078/mbin.sdb .)\n    (cd lq && zip -j ../nmdc_wfmag-11-g7msr323.1_lq_bin.zip *.txt mbin.sdb ../nmdc_wfmag-11-g7msr323.1_eukcc.csv )\nfi\n\n# Fix up attribute name\ncat /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/inputs/-287587103/nmdc_wfmag-11-g7msr323.1_stats.json | \\\n   sed \'s/: null/: "null"/g\' | \\\n   sed \'s/lowDepth_/low_depth_/\' > nmdc_wfmag-11-g7msr323.1_mags_stats.json', 'shardIndex': -1, 'outputs': {'final_kronaplot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_kronaplot.html', 'final_heatmap': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_heatmap.pdf', 'final_stats_json': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_mags_stats.json', 'final_barplot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_barplot.pdf', 'final_checkm': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_checkm_qa.out', 'final_lq_bins_zip': 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'/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.38_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.39_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.40_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.41_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.42_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.43_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.44_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.4_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.5_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.7_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.8_LQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6831c5627738b7bab7ea0c95f8ba7cd3/nmdc_wfmag-11-g7msr323.1_bins.9_LQ.tar.gz'], '__n_hqmq': 9, 'eukcc_file': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/eukcc_output/eukcc.csv.final', '__n_lq': 35}, 'returnCode': 0, 'jobId': '275961', 'backend': 'HtCondor', 'end': '2024-09-16T21:52:00.757Z', 'dockerImageUsed': 'microbiomedata/workflowmeta@sha256:f0ca787887e43851bbda55bef4c7b68513ffd7940e1f24f586c1d6fe220624a8', 'stderr': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/stderr', 'callRoot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags', 'attempt': 1, 'executionEvents': [{'startTime': '2024-09-16T21:51:43.419Z', 'description': 'CallCacheReading', 'endTime': '2024-09-16T21:51:43.426Z'}, {'startTime': '2024-09-16T21:51:41.088Z', 'description': 'Pending', 'endTime': '2024-09-16T21:51:41.088Z'}, {'startTime': '2024-09-16T21:51:59.771Z', 'description': 'UpdatingJobStore', 'endTime': '2024-09-16T21:52:00.757Z'}, {'startTime': '2024-09-16T21:51:42.858Z', 'description': 'PreparingJob', 'endTime': '2024-09-16T21:51:43.419Z'}, {'startTime': '2024-09-16T21:51:43.426Z', 'description': 'RunningJob', 'endTime': '2024-09-16T21:51:58.535Z'}, {'startTime': '2024-09-16T21:51:58.535Z', 'description': 'UpdatingCallCache', 'endTime': '2024-09-16T21:51:59.771Z'}, {'startTime': '2024-09-16T21:51:42.858Z', 'description': 'WaitingForValueStore', 'endTime': '2024-09-16T21:51:42.858Z'}, {'startTime': '2024-09-16T21:51:41.088Z', 'description': 'RequestingExecutionToken', 'endTime': '2024-09-16T21:51:42.858Z'}], 'start': '2024-09-16T21:51:41.088Z'}], 'nmdc_mags.stage': [{'executionStatus': 'Done', 'stdout': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/stdout', 'backendStatus': 'Done', 'compressedDockerSize': 1191863655, 'commandLine': 'set -euo pipefail\n\n function stage() {\n     in=$1\n     out=$2\n     if [ $( echo $in |egrep -c "https*:") -gt 0 ] ; then\n         wget $in -O $out\n     else\n         ln $in $out || cp $in $out\n     fi\n }\n\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contigs.fna contigs.fasta &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgas-11-0qvjnc54.1/nmdc_wfmgas-11-0qvjnc54.1_pairedMapped_sorted.bam pairedMapped_sorted.bam &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_functional_annotation.gff functional_annotation.gff &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_proteins.faa proteins.faa &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_cog.gff cog.gff &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ec.tsv ec.tsv &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ko.tsv ko.tsv &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_pfam.gff pfam.gff &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_tigrfam.gff tigrfam.gff &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_crt.crisprs crispr.tsv &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_product_names.tsv products.tsv &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_gene_phylogeny.tsv gene_phylogeny.tsv &\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_scaffold_lineage.tsv lineage.tsv\n stage https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contig_names_mapping.tsv map_file.tsv\n wait\n\n date --iso-8601=seconds > start.txt', 'shardIndex': -1, 'outputs': {'cog': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/cog.gff', 'map_tsv': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/map_file.tsv', 'ec': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/ec.tsv', 'gene_phylogeny': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/gene_phylogeny.tsv', 'tigrfam': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/tigrfam.gff', 'gff': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/functional_annotation.gff', 'sam': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/pairedMapped_sorted.bam', 'proteins': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/proteins.faa', 'pfam': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/pfam.gff', 'ko': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/ko.tsv', 'contig': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/contigs.fasta', 'crispr': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/crispr.tsv', 'start': '2024-09-16T20:41:22+00:00', 'lineage_tsv': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/lineage.tsv', 'product_names': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/products.tsv'}, 'runtimeAttributes': {'runtime_minutes': '120', 'priority': '0', 'disk': '0.244140625 GB', 'failOnStderr': 'false', 'continueOnReturnCode': '0', 'docker': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'maxRetries': '1', 'cpu': '2', 'memory': '1 GB'}, 'callCaching': {'allowResultReuse': True, 'hit': False, 'result': 'Cache Miss', 'hashes': {'output count': '9BF31C7FF062936A96D3C8BD1F8F2FF3', 'runtime attribute': {'docker': '4DB5CCE48B9916E012489D88408A5D44', 'continueOnReturnCode': 'CFCD208495D565EF66E7DFF9F98764DA', 'failOnStderr': '68934A3E9455FA72420237EB05902327'}, 'output expression': {'File gff': '9DFA93171F64FF1EC049FAB63EE49559', 'Optional(File) map_tsv': 'C29FBF836DB250C6ED8906A84A03C351', 'File contig': '3979BBE6655FA4081324B866BCAD857F', 'File lineage_tsv': 'A5A1CC5DF795C170AC18E13FD529CDF9', 'File tigrfam': '7FEC3F9DF0AEEABDB32E539B6E31A786', 'File ko': '4A1EFE6E081D889485FF177EAFFA0341', 'File gene_phylogeny': '790C86C705B10928B88B0667276B292A', 'String start': '9180F439602EB455553A080D43DB2473', 'File cog': '675ED671AEF02AA51BC7A63FDAF9E368', 'File sam': '64310B84EF19067D9EDFCC11659FFC63', 'File crispr': '85C44715FB71D543B88246F2941B998D', 'File proteins': '90970BF28EAD79A8D39F26B2CB5E0B39', 'File product_names': 'AED4995618D0A3D260A56CB1B3C1CB8C', 'File pfam': 'F2868E7A1DD49DB7754F2698C1BB0BEB', 'File ec': 'CA35D2BE8F98C7472AEE0B2494ECFF2B'}, 'input count': '6EA9AB1BAA0EFB9E19094440C317E21B', 'backend name': '24B80D5AA1F64928B14AC8407909E586', 'command template': '7E6C1783BECB18AD19DA61778AD2255C', 'input': {'String sam_file': '063D169CC138D1144D399E31ED3C59E4', 'String crispr_out': '5C9183A85E33EB06FA1E91866D860AF7', 'String contig_file': 'C5141AC37DE20EC05984417A5D318DBF', 'String tigrfam_out': '7C3B7598C68086C56536F1484BF6B4E7', 'String proteins_file': 'A2704436BD3F98204EC33BF919E71A98', 'String container': 'BC62D4AAD87B08BA3DA19667EF278DCB', 'String gene_phylogeny_file': '0DFB8B5CBE8F3551A501DDB773FE7C76', 'String ec_out': '9B2989B8720CFF2E291E152C83908B58', 'String cog_out': '57E7D9F6C6027CB5F88CF52197A0E09A', 'String contigs_out': 'B3B220254A872C9A27EEEA164CEA7180', 'String ec_file': 'CE23FF1571E1CB0E6FD7C74F837B72EF', 'String pfam_file': '7F72F8E6099B362896D56039134A0752', 'String ko_file': '46F721054373C2B1494E755F69F9CD50', 'String map_file': '06FB1F4B8C8038E2CDFB1D2F01C64473', 'String products_out': '121113CFD93DA6D5AB12948E5AEC22B3', 'String proteins_out': '78FF964764B16900FF2D3F5A7B34FB7B', 'String gff_file': '3048BF5CEAEC5F4EB1039FFCF239DFF9', 'String tigrfam_file': '1BD75FFD6CF5D4AE731F45FE1C79735E', 'String lineage_out': 'AA53DB68E93BC4D66EA98BBFF733FA07', 'String ko_out': 'C0DF3CDC23F8B885E8F2D1C783D961EB', 'String map_out': '7BDA07D6B2E6F9A1CCA29C373E3F769E', 'String lineage_file': '661022B8FF1D4C1414CF21811AFB9186', 'String gene_phylogeny_out': '77F6C9BA0C2A6969FEC44C172C557157', 'String gff_out': '1480321F9248DF00AB8D641DB3A80283', 'String pfam_out': 'E1434D4AE774C068C3993C5DA573CCC1', 'String product_names_file': '0891B74C498F7F251263A6B8669D5BCD', 'String bam_out': '297A5965C834F32050A732873F038C12', 'String crispr_file': 'F900BD4413CB04416A3D9A3F106B9DA9', 'String cog_file': 'FC4A8854717517CD62D5F7EED98E3B78'}}, 'effectiveCallCachingMode': 'ReadAndWriteCache'}, 'inputs': {'map_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contig_names_mapping.tsv', 'crispr_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_crt.crisprs', 'proteins_out': 'proteins.faa', 'pfam_out': 'pfam.gff', 'lineage_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_scaffold_lineage.tsv', 'cog_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_cog.gff', 'cog_out': 'cog.gff', 'crispr_out': 'crispr.tsv', 'container': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'proteins_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_proteins.faa', 'gene_phylogeny_out': 'gene_phylogeny.tsv', 'product_names_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_product_names.tsv', 'contigs_out': 'contigs.fasta', 'tigrfam_out': 'tigrfam.gff', 'gene_phylogeny_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_gene_phylogeny.tsv', 'map_out': 'map_file.tsv', 'lineage_out': 'lineage.tsv', 'ko_out': 'ko.tsv', 'ko_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ko.tsv', 'ec_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_ec.tsv', 'gff_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_functional_annotation.gff', 'pfam_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_pfam.gff', 'gff_out': 'functional_annotation.gff', 'bam_out': 'pairedMapped_sorted.bam', 'products_out': 'products.tsv', 'ec_out': 'ec.tsv', 'tigrfam_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_tigrfam.gff', 'sam_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgas-11-0qvjnc54.1/nmdc_wfmgas-11-0qvjnc54.1_pairedMapped_sorted.bam', 'contig_file': 'https://data.microbiomedata.org/data/nmdc:omprc-11-9cdxha98/nmdc:wfmgan-11-jv8kx789.1/nmdc_wfmgan-11-jv8kx789.1_contigs.fna'}, 'returnCode': 0, 'jobId': '275957', 'backend': 'HtCondor', 'end': '2024-09-16T20:43:00.781Z', 'dockerImageUsed': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'stderr': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/stderr', 'callRoot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage', 'attempt': 1, 'executionEvents': [{'startTime': '2024-09-16T19:34:02.867Z', 'description': 'WaitingForValueStore', 'endTime': '2024-09-16T19:34:02.873Z'}, {'startTime': '2024-09-16T20:42:59.823Z', 'description': 'UpdatingJobStore', 'endTime': '2024-09-16T20:43:00.781Z'}, {'startTime': '2024-09-16T19:34:04.203Z', 'description': 'RunningJob', 'endTime': '2024-09-16T20:42:57.930Z'}, {'startTime': '2024-09-16T19:33:54.024Z', 'description': 'RequestingExecutionToken', 'endTime': '2024-09-16T19:34:02.867Z'}, {'startTime': '2024-09-16T20:42:57.930Z', 'description': 'UpdatingCallCache', 'endTime': '2024-09-16T20:42:59.823Z'}, {'startTime': '2024-09-16T19:33:54.013Z', 'description': 'Pending', 'endTime': '2024-09-16T19:33:54.024Z'}, {'startTime': '2024-09-16T19:34:04.139Z', 'description': 'CallCacheReading', 'endTime': '2024-09-16T19:34:04.203Z'}, {'startTime': '2024-09-16T19:34:02.873Z', 'description': 'PreparingJob', 'endTime': '2024-09-16T19:34:04.139Z'}], 'start': '2024-09-16T19:33:54.000Z'}], 'nmdc_mags.package': [{'executionStatus': 'Done', 'stdout': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/stdout', 'backendStatus': 'Done', 'compressedDockerSize': 502671902, 'commandLine': ' set -euo pipefail\n create_tarfiles.py nmdc_wfmag-11-g7msr323.1 \\\n             /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1484654078/MAGs_stats.json /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/functional_annotation.gff /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/proteins.faa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/cog.gff \\\n             /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/ec.tsv /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/ko.tsv /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/pfam.gff /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/tigrfam.gff \\\n             /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/crispr.tsv /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/gene_phylogeny.tsv \\\n             /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1577597465/products.tsv \\\n             /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.10.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.16.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.18.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.20.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.25.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.26.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.3.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.34.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/-1912378940/bins.6.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.1.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.11.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.12.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.13.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.14.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.15.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.17.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.19.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.2.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.21.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.22.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.23.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.24.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.27.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.28.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.29.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.30.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.31.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.32.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.33.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.35.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.36.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.37.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.38.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.39.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.4.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.40.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.41.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.42.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.43.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.44.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.5.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.7.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.8.fa /cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/inputs/1282319600/bins.9.fa\n\nif [ -f nmdc_wfmag-11-g7msr323.1_heatmap.pdf ]; then\n    if [ -f nmdc_wfmag-11-g7msr323.1_barplot.pdf ]; then\n        echo "KO analysis plot exists."\n    else\n        echo "There are no modules above 80% completeness. No barplot will be generated." && touch nmdc_wfmag-11-g7msr323.1_barplot.pdf\n    fi\nelse\n    echo "No KO analysis result for nmdc:wfmag-11-g7msr323.1" && touch nmdc_wfmag-11-g7msr323.1_heatmap.pdf\n    echo "No KO analysis result for nmdc:wfmag-11-g7msr323.1" && touch nmdc_wfmag-11-g7msr323.1_barplot.pdf\n    echo "No KO analysis result for nmdc:wfmag-11-g7msr323.1" > nmdc_wfmag-11-g7msr323.1_ko_krona.html\n    echo "No KO analysis result for nmdc:wfmag-11-g7msr323.1" > nmdc_wfmag-11-g7msr323.1_module_completeness.tab\nfi', 'shardIndex': -1, 'outputs': {'stats_json': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/nmdc_wfmag-11-g7msr323.1_stats.json', 'barplot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/nmdc_wfmag-11-g7msr323.1_barplot.pdf', 'ko_matrix': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/nmdc_wfmag-11-g7msr323.1_module_completeness.tab', 'heatmap': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/nmdc_wfmag-11-g7msr323.1_heatmap.pdf', 'hqmq_bin_tarfiles': ['/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.10_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.16_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.18_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.20_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.25_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.26_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.34_MQ.tar.gz', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/glob-6fd876838902671f0b26b85826255b77/nmdc_wfmag-11-g7msr323.1_bins.3_MQ.tar.gz', 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'/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.14.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.15.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.17.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.19.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.2.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.21.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.22.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.23.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.24.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.27.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.28.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.29.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.30.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.31.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.32.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.33.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.35.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.36.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.37.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.38.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.39.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.4.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.40.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.41.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.42.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.43.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.44.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.5.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.7.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.8.fa', '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-mbin_nmdc/execution/glob-cfa371426bf53219d565e0cd37e297b4/bins.9.fa'], 'tigrfam_file': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/tigrfam.gff'}, 'returnCode': 0, 'jobId': '275960', 'backend': 'HtCondor', 'end': '2024-09-16T21:51:39.759Z', 'dockerImageUsed': 'microbiomedata/nmdc_mbin_vis@sha256:69aae8905fab7105eb0a82c547959c4b9ec7dcc1d5d574e6e32d60f9fadcc284', 'stderr': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package/execution/stderr', 'callRoot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-package', 'attempt': 1, 'executionEvents': [{'startTime': '2024-09-16T21:49:23.480Z', 'description': 'RunningJob', 'endTime': '2024-09-16T21:51:36.296Z'}, {'startTime': '2024-09-16T21:51:36.296Z', 'description': 'UpdatingCallCache', 'endTime': '2024-09-16T21:51:38.770Z'}, {'startTime': '2024-09-16T21:49:22.858Z', 'description': 'PreparingJob', 'endTime': '2024-09-16T21:49:23.472Z'}, {'startTime': '2024-09-16T21:51:38.770Z', 'description': 'UpdatingJobStore', 'endTime': '2024-09-16T21:51:39.759Z'}, {'startTime': '2024-09-16T21:49:22.858Z', 'description': 'WaitingForValueStore', 'endTime': '2024-09-16T21:49:22.858Z'}, {'startTime': '2024-09-16T21:49:17.269Z', 'description': 'Pending', 'endTime': '2024-09-16T21:49:17.269Z'}, {'startTime': '2024-09-16T21:49:17.269Z', 'description': 'RequestingExecutionToken', 'endTime': '2024-09-16T21:49:22.858Z'}, {'startTime': '2024-09-16T21:49:23.472Z', 'description': 'CallCacheReading', 'endTime': '2024-09-16T21:49:23.480Z'}], 'start': '2024-09-16T21:49:17.268Z'}], 'nmdc_mags.check_id_map': [{'executionStatus': 'Done', 'stdout': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-check_id_map/execution/stdout', 'backendStatus': 'Done', 'compressedDockerSize': 1191863655, 'commandLine': 'set -euo pipefail \n\npython <<CODE\nimport sys\ncontigIDs={}\nwith open("/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-check_id_map/inputs/1577597465/contigs.fasta","r") as c_file:\n    for line in c_file:\n        if line.startswith(">"):\n            seq_id = line[1:].rstrip().split()[0] # nmdc:wfmgan-12-gbysvd76.1_0000001\n            contigIDs[seq_id]=1\nwith open("/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-check_id_map/inputs/1577597465/proteins.faa","r") as p_file:\n    for line in p_file:\n        if line.startswith(">"):\n            seq_id = line[1:].rstrip().split()[0]  # nmdc:wfmgan-12-gbysvd76.1_0000001_1_225\n            contig_id = "_".join(seq_id.split("_")[0:-2]) # nmdc:wfmgan-12-gbysvd76.1_0000001\n            if contig_id not in contigIDs:\n                print(f"{contig_id} is not in contigs.fasta.", file=sys.stderr)\n                sys.exit(1)\nCODE', 'shardIndex': -1, 'outputs': {'contig': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/contigs.fasta'}, 'runtimeAttributes': {'runtime_minutes': '120', 'priority': '0', 'disk': '0.244140625 GB', 'failOnStderr': 'false', 'continueOnReturnCode': '0', 'docker': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'maxRetries': '0', 'cpu': '1', 'memory': '1 GB'}, 'callCaching': {'allowResultReuse': True, 'hit': False, 'result': 'Cache Miss', 'hashes': {'output count': 'C4CA4238A0B923820DCC509A6F75849B', 'runtime attribute': {'docker': '4DB5CCE48B9916E012489D88408A5D44', 'continueOnReturnCode': 'CFCD208495D565EF66E7DFF9F98764DA', 'failOnStderr': '68934A3E9455FA72420237EB05902327'}, 'output expression': {'File contig': '9172A50B2726E3AFC54E69F5457FA165'}, 'input count': 'A87FF679A2F3E71D9181A67B7542122C', 'backend name': '24B80D5AA1F64928B14AC8407909E586', 'command template': '56BF79472C3FB22C51FC90FE7563BFCA', 'input': {'File contig_file': '6debed079383eeca2045ce23b0576607', 'String __contig_file_name': 'B3B220254A872C9A27EEEA164CEA7180', 'String container': 'BC62D4AAD87B08BA3DA19667EF278DCB', 'File proteins_file': '292eae73923605dae2ef9f5d582e4603'}}, 'effectiveCallCachingMode': 'ReadAndWriteCache'}, 'inputs': {'contig_file_name': None, '__contig_file_name': 'contigs.fasta', 'container': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'proteins_file': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/proteins.faa', 'contig_file': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-stage/execution/contigs.fasta'}, 'returnCode': 0, 'jobId': '275958', 'backend': 'HtCondor', 'end': '2024-09-16T20:43:30.762Z', 'dockerImageUsed': 'microbiomedata/nmdc_mbin@sha256:f3b154718474d2e21b53dbf4c1c35a1d3190eba3fe6b8f3fda105fcde22d9639', 'stderr': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-check_id_map/execution/stderr', 'callRoot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-check_id_map', 'attempt': 1, 'executionEvents': [{'startTime': '2024-09-16T20:43:02.339Z', 'description': 'Pending', 'endTime': '2024-09-16T20:43:02.340Z'}, {'startTime': '2024-09-16T20:43:02.872Z', 'description': 'CallCacheReading', 'endTime': '2024-09-16T20:43:02.878Z'}, {'startTime': '2024-09-16T20:43:02.878Z', 'description': 'RunningJob', 'endTime': '2024-09-16T20:43:27.992Z'}, {'startTime': '2024-09-16T20:43:29.773Z', 'description': 'UpdatingJobStore', 'endTime': '2024-09-16T20:43:30.762Z'}, {'startTime': '2024-09-16T20:43:02.340Z', 'description': 'RequestingExecutionToken', 'endTime': '2024-09-16T20:43:02.858Z'}, {'startTime': '2024-09-16T20:43:02.858Z', 'description': 'PreparingJob', 'endTime': '2024-09-16T20:43:02.872Z'}, {'startTime': '2024-09-16T20:43:02.858Z', 'description': 'WaitingForValueStore', 'endTime': '2024-09-16T20:43:02.858Z'}, {'startTime': '2024-09-16T20:43:27.992Z', 'description': 'UpdatingCallCache', 'endTime': '2024-09-16T20:43:29.773Z'}], 'start': '2024-09-16T20:43:02.339Z'}]}, 'outputs': {'nmdc_mags.kronaplot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_kronaplot.html', 'nmdc_mags.short': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_bins.tooShort.fa', 'nmdc_mags.final_unbinned_fa': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_bins.unbinned.fa', 'nmdc_mags.heatmap': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_heatmap.pdf', 'nmdc_mags.final_gtdbtk_ar_summary': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_gtdbtk.ar122.summary.tsv', 'nmdc_mags.final_hqmq_bins_zip': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_hqmq_bin.zip', 'nmdc_mags.final_checkm': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_checkm_qa.out', 'nmdc_mags.mags_version': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_bin.info', 'nmdc_mags.final_lq_bins_zip': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_lq_bin.zip', 'nmdc_mags.barplot': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_barplot.pdf', 'nmdc_mags.final_gtdbtk_bac_summary': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_gtdbtk.bac122.summary.tsv', 'nmdc_mags.low': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_bins.lowDepth.fa', 'nmdc_mags.final_stats_json': '/pscratch/sd/n/nmdcda/cromwell-executions/nmdc_mags/9492a397-eb30-472b-9d3b-b44b676f4652/call-finish_mags/execution/nmdc_wfmag-11-g7msr323.1_mags_stats.json'}, 'workflowRoot': 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'2024-09-16T19:33:50.808Z'}}}
microbiomedata / nmdc_automation

Watcher running with nmdc-dev configuration finds jobs but no data objects for the jobs #282
