Using Windows 11, newest version of Docker Desktop, newest version of PGAP (build7061) I run this command in Command Prompt:

./pgap.py -r -o E_coli_result5 -g $HOME/.pgap/test_genomes/MG37/E_coli_seq1.fasta -s 'Eschericahi coli' --ignore-all-errors

Docker container starts up and runs for a while and then ends with "WARNING Final process status is permanentFail" I'm not sure where I might be going wrong.

PGAP version 2023-10-03.build7061 is up to date. Output will be placed in: /home/namho4577/PGAP/E_coli_result5 WARNING: memory (GiB) is less than the recommended value of 8 WARNING: memory per CPU core (GiB) is less than the recommended value of 2 PGAP failed, docker exited with rc = 1 Printing log starting from failed job:

[2024-05-01 11:30:00] DEBUG [step pgapx_yaml_ctl] job input { "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/ignore_all_errors": true, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input": { "location": "file:///tmp/6b_9y3_s/submol.json", "basename": "submol.json", "nameroot": "submol", "nameext": ".json", "class": "File", "checksum": "sha1$556fc658cd60a5504f673333a51469998eb149d5", "size": 404, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta": { "class": "File", "location": "file:///pgap/user_input/E_coli_seq1.fasta", "size": 67004, "basename": "E_coli_seq1.fasta", "nameroot": "E_coli_seq1", "nameext": ".fasta" }, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet": null, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1112997888, "nameroot": "taxonomy", "nameext": ".sqlite3" } } [2024-05-01 11:30:00] DEBUG [step pgapx_yaml_ctl] evaluated job input to { "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/ignore_all_errors": true, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input": { "location": "file:///tmp/6b_9y3_s/submol.json", "basename": "submol.json", "nameroot": "submol", "nameext": ".json", "class": "File", "checksum": "sha1$556fc658cd60a5504f673333a51469998eb149d5", "size": 404, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input_fasta": { "class": "File", "location": "file:///pgap/user_input/E_coli_seq1.fasta", "size": 67004, "basename": "E_coli_seq1.fasta", "nameroot": "E_coli_seq1", "nameext": ".fasta" }, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/no_internet": null, "file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/taxon_db": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1112997888, "nameroot": "taxonomy", "nameext": ".sqlite3" } } [2024-05-01 11:30:00] INFO [step pgapx_yaml_ctl] start [2024-05-01 11:30:00] DEBUG [job pgapx_yaml_ctl] initializing from file:///pgap/pgap/progs/pgapx_yaml_ctl.cwl as part of step pgapx_yaml_ctl [2024-05-01 11:30:00] DEBUG [job pgapx_yaml_ctl] { "ignore_all_errors": true, "input": { "location": "file:///tmp/6b_9y3_s/submol.json", "basename": "submol.json", "nameroot": "submol", "nameext": ".json", "class": "File", "checksum": "sha1$556fc658cd60a5504f673333a51469998eb149d5", "size": 404, "http://commonwl.org/cwltool#generation": 0 }, "input_fasta": { "class": "File", "location": "file:///pgap/user_input/E_coli_seq1.fasta", "size": 67004, "basename": "E_coli_seq1.fasta", "nameroot": "E_coli_seq1", "nameext": ".fasta" }, "no_internet": null, "taxon_db": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1112997888, "nameroot": "taxonomy", "nameext": ".sqlite3" }, "ifmt": "JSON", "ofmt": "JSON", "output_annotation_name": "input.asn", "output_input_asn_type_name": "input_asn_type.txt", "output_ltp_name": "genome.ltp.txt", "output_taxid_name": "taxid.txt" } [2024-05-01 11:30:00] DEBUG [job pgapx_yaml_ctl] path mappings is { "file:///tmp/6b_9y3_s/submol.json": [ "/tmp/6b_9y3_s/submol.json", "/tmp/ld3k632o/stg18850ff6-b66f-4136-9523-78cca2f8e426/submol.json", "File", true ], "file:///pgap/user_input/E_coli_seq1.fasta": [ "/pgap/user_input/E_coli_seq1.fasta", "/tmp/ld3k632o/stgb125db4e-63e1-45c1-bd6d-7668dfd7fefe/E_coli_seq1.fasta", "File", true ], "file:///pgap/input/uniColl_path/taxonomy.sqlite3": [ "/pgap/input/uniColl_path/taxonomy.sqlite3", "/tmp/ld3k632o/stg3d6ce5af-1fb1-43b6-900d-388b5eb499db/taxonomy.sqlite3", "File", true ] } [2024-05-01 11:30:00] DEBUG [job pgapx_yaml_ctl] command line bindings is [ { "position": [ -1000000, 0 ], "datum": "pgapx_yaml_ctl" }, { "prefix": "-ifmt", "position": [ 0, "ifmt" ], "datum": "JSON" }, { "prefix": "-ignore-all-errors", "position": [ 0, "ignore_all_errors" ], "datum": true }, { "prefix": "-input", "position": [ 0, "input" ], "datum": { "location": "file:///tmp/6b_9y3_s/submol.json", "basename": "submol.json", "nameroot": "submol", "nameext": ".json", "class": "File", "checksum": "sha1$556fc658cd60a5504f673333a51469998eb149d5", "size": 404, "http://commonwl.org/cwltool#generation": 0, "path": "/tmp/ld3k632o/stg18850ff6-b66f-4136-9523-78cca2f8e426/submol.json", "dirname": "/tmp/ld3k632o/stg18850ff6-b66f-4136-9523-78cca2f8e426" } }, { "prefix": "-input-fasta", "position": [ 0, "input_fasta" ], "datum": { "class": "File", "location": "file:///pgap/user_input/E_coli_seq1.fasta", "size": 67004, "basename": "E_coli_seq1.fasta", "nameroot": "E_coli_seq1", "nameext": ".fasta", "path": "/tmp/ld3k632o/stgb125db4e-63e1-45c1-bd6d-7668dfd7fefe/E_coli_seq1.fasta", "dirname": "/tmp/ld3k632o/stgb125db4e-63e1-45c1-bd6d-7668dfd7fefe" } }, { "prefix": "-ofmt", "position": [ 0, "ofmt" ], "datum": "JSON" }, { "prefix": "-output-annotation", "position": [ 0, "output_annotation_name" ], "datum": "input.asn" }, { "prefix": "-output-asn-type", "position": [ 0, "output_input_asn_type_name" ], "datum": "input_asn_type.txt" }, { "prefix": "-output-ltp", "position": [ 0, "output_ltp_name" ], "datum": "genome.ltp.txt" }, { "prefix": "-output-taxid", "position": [ 0, "output_taxid_name" ], "datum": "taxid.txt" }, { "prefix": "-taxon-db", "position": [ 0, "taxon_db" ], "datum": { "class": "File", "location": "file:///pgap/input/uniColl_path/taxonomy.sqlite3", "basename": "taxonomy.sqlite3", "size": 1112997888, "nameroot": "taxonomy", "nameext": ".sqlite3", "path": "/tmp/ld3k632o/stg3d6ce5af-1fb1-43b6-900d-388b5eb499db/taxonomy.sqlite3", "dirname": "/tmp/ld3k632o/stg3d6ce5af-1fb1-43b6-900d-388b5eb499db" } } ] [2024-05-01 11:30:00] DEBUG [job pgapx_yaml_ctl] initial work dir {} [2024-05-01 11:30:00] INFO [job pgapx_yaml_ctl] /tmp/sw3hmub6$ pgapx_yaml_ctl \ -ifmt \ JSON \ -ignore-all-errors \ -input \ /tmp/ld3k632o/stg18850ff6-b66f-4136-9523-78cca2f8e426/submol.json \ -input-fasta \ /tmp/ld3k632o/stgb125db4e-63e1-45c1-bd6d-7668dfd7fefe/E_coli_seq1.fasta \ -ofmt \ JSON \ -output-annotation \ input.asn \ -output-asn-type \ input_asn_type.txt \ -output-ltp \ genome.ltp.txt \ -output-taxid \ taxid.txt \ -taxon-db \ /tmp/ld3k632o/stg3d6ce5af-1fb1-43b6-900d-388b5eb499db/taxonomy.sqlite3 ignoring failure of pgapx_yaml_input.GetFasta terminate called after throwing an instance of 'ncbi::CException' what(): NCBI C++ Exception: Error: CWL(CException::eUnknown) "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/internal/gpipe/app/cloud/cwl/pgapx_yaml_ctl.cpp", line 251: CPgapxYamlCtlApplication::Run() --- Unknown organism Eschericahi coli Stack trace: /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/pgapx_yaml_ctl :0 offset=0x0 addr=0x41a060 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp:711 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const, int, bool) offset=0x0 addr=0x7fd8943a9132 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp:1023 ncbi::CNcbiApplicationAPI::AppMain(int, char const const, char const const, ncbi::EAppDiagStream, char const, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) offset=0x0 addr=0x7fd8943ac78c /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/pgapx_yaml_ctl :0 offset=0x0 addr=0x40c7b9 /usr/lib64/libc-2.17.so :0 offset=0x0 addr=0x7fd892dd5554 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/pgapx_yaml_ctl :0 offset=0x0 addr=0x40c989 :0 offset=0x0 addr=0xffffffffffffffff

Stack trace (most recent call last):

12 Object "", at 0xffffffffffffffff, in

11 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/pgapx_yaml_ctl", at 0x40c989, in _start

10 Object "/usr/lib64/libc-2.17.so", at 0x7fd892dd5554, in __libc_start_main

9 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/pgapx_yaml_ctl", at 0x40c7b9, in main

8 Source "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 1023, in AppMain [0x7fd8943ac78c]

7 Source "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 711, in x_TryMain [0x7fd8943a9132]

6 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/pgapx_yaml_ctl", at 0x41a0c0, in CPgapxYamlCtlApplication::Run()

5 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x7fd893957222]

4 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x7fd893956fe0]

3 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x7fd893956f95]

2 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x7fd8939591a4]

1 Object "/usr/lib64/libc-2.17.so", at 0x7fd892deaa77, in abort

0 Object "/usr/lib64/libc-2.17.so", at 0x7fd892de9387, in raise

Aborted (Signal sent by tkill() 229 1000) [2024-05-01 11:30:10] INFO [job pgapx_yaml_ctl] Max memory used: 35MiB [2024-05-01 11:30:10] WARNING [job pgapx_yaml_ctl] was terminated by signal: SIGABRT [2024-05-01 11:30:10] ERROR [job pgapx_yaml_ctl] Job error: ("Error collecting output for parameter 'input_asn_type': pgap/progs/pgapx_yaml_ctl.cwl:75:13: Did not find output file with glob pattern: ['input_asn_type.txt'].", {}) [2024-05-01 11:30:10] WARNING [job pgapx_yaml_ctl] completed permanentFail [2024-05-01 11:30:10] DEBUG [job pgapx_yaml_ctl] outputs {} [2024-05-01 11:30:10] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/output_annotation [2024-05-01 11:30:10] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/output_ltp [2024-05-01 11:30:10] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/input_asn_type [2024-05-01 11:30:10] ERROR [step pgapx_yaml_ctl] Output is missing expected field file:///pgap/pgap/prepare_user_input2.cwl#pgapx_yaml_ctl/taxid [2024-05-01 11:30:10] DEBUG [step pgapx_yaml_ctl] produced output {} [2024-05-01 11:30:10] WARNING [step pgapx_yaml_ctl] completed permanentFail [2024-05-01 11:30:10] DEBUG [job pgapx_yaml_ctl] Removing input staging directory /tmp/ld3k632o [2024-05-01 11:30:10] DEBUG [job pgapx_yaml_ctl] Removing temporary directory /tmp/6bmhf4xg [2024-05-01 11:30:10] INFO [workflow prepare_input_template] completed permanentFail [2024-05-01 11:30:10] DEBUG [workflow prepare_input_template] outputs { "input_asn_type": null, "locus_tag_prefix": null, "output_entries": null, "output_seq_submit": null, "submol_block_json": { "location": "file:///tmp/6b_9y3_s/submol.json", "basename": "submol.json", "nameroot": "submol", "nameext": ".json", "class": "File", "checksum": "sha1$556fc658cd60a5504f673333a51469998eb149d5", "size": 404, "http://commonwl.org/cwltool#generation": 0 }, "taxid": null } [2024-05-01 11:30:10] DEBUG [step prepare_input_template] produced output { "file:///pgap/pgap/pgap.cwl#prepare_input_template/output_seq_submit": null, "file:///pgap/pgap/pgap.cwl#prepare_input_template/output_entries": null, "file:///pgap/pgap/pgap.cwl#prepare_input_template/locus_tag_prefix": null, "file:///pgap/pgap/pgap.cwl#prepare_input_template/submol_block_json": { "location": "file:///tmp/6b_9y3_s/submol.json", "basename": "submol.json", "nameroot": "submol", "nameext": ".json", "class": "File", "checksum": "sha1$556fc658cd60a5504f673333a51469998eb149d5", "size": 404, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/pgap.cwl#prepare_input_template/taxid": null } [2024-05-01 11:30:10] WARNING [step prepare_input_template] completed permanentFail [2024-05-01 11:30:10] INFO [workflow ] completed permanentFail [2024-05-01 11:30:10] DEBUG [workflow ] outputs { "calls": { "location": "file:///tmp/8r895kud/calls.tab", "basename": "calls.tab", "nameroot": "calls", "nameext": ".tab", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "http://commonwl.org/cwltool#generation": 0 }, "cds_nucleotide_fasta": null, "cds_protein_fasta": null, "checkm_raw": null, "fastaval_errors": { "location": "file:///tmp/vfqc8wrk/fastaval.xml", "basename": "fastaval.xml", "nameroot": "fastaval", "nameext": ".xml", "class": "File", "checksum": "sha1$53b6a99a8edd78b64bd27eec6ebf928fa44f75d9", "size": 143, "http://commonwl.org/cwltool#generation": 0 }, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbk": null, "gff": null, "gff_enhanced": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "input_fasta": { "class": "File", "location": "file:///pgap/user_input/E_coli_seq1.fasta", "size": 67004, "basename": "E_coli_seq1.fasta", "nameroot": "E_coli_seq1", "nameext": ".fasta" }, "input_submol": { "class": "File", "location": "file:///pgap/user_input/pgap_submol_yogpv0es.yaml", "size": 451, "basename": "pgap_submol_yogpv0es.yaml", "nameroot": "pgap_submol_yogpv0es", "nameext": ".yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null } [2024-05-01 11:30:10] DEBUG Moving /tmp/8r895kud/calls.tab to /pgap/output/calls.tab [2024-05-01 11:30:10] DEBUG Moving /tmp/vfqc8wrk/fastaval.xml to /pgap/output/fastaval.xml [2024-05-01 11:30:10] DEBUG Copying /pgap/user_input/E_coli_seq1.fasta to /pgap/output/E_coli_seq1.fasta [2024-05-01 11:30:10] DEBUG Copying /pgap/user_input/pgap_submol_yogpv0es.yaml to /pgap/output/pgap_submol_yogpv0es.yaml [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/xc0_bplj [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/ryuo8qxg [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/sw3hmub6 [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/6b_9y3_s [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/6gwzbcxa [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/d7hzsw_ [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/u25axrc4 [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/v3r0astn [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/3vft0pt [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/rkf4jecx [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/aghzpe_u [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/uzlmf87h [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/vfqc8wrk [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/uut_1wfy [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/c18hgbj1 [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/oj3g7feb [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/8r895kud [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/evf773ja [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/oz6shcs3 [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/xrpeum2u [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/zlwty7bm [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/whiy5gea [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/_ggjpkdq [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/5ztz53me [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/u7g0x5om [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/vge8di3q [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/5cx4w7nh [2024-05-01 11:30:10] DEBUG Removing intermediate output directory /tmp/kho11b1a { "calls": { "location": "file:///pgap/output/calls.tab", "basename": "calls.tab", "class": "File", "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709", "size": 0, "path": "/pgap/output/calls.tab" }, "cds_nucleotide_fasta": null, "cds_protein_fasta": null, "checkm_raw": null, "fastaval_errors": { "location": "file:///pgap/output/fastaval.xml", "basename": "fastaval.xml", "class": "File", "checksum": "sha1$53b6a99a8edd78b64bd27eec6ebf928fa44f75d9", "size": 143, "path": "/pgap/output/fastaval.xml" }, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbk": null, "gff": null, "gff_enhanced": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "input_fasta": { "class": "File", "location": "file:///pgap/output/E_coli_seq1.fasta", "size": 67004, "basename": "E_coli_seq1.fasta", "checksum": "sha1$198ce434adeef2a9749c164edb41e2ecf36d1c3e", "path": "/pgap/output/E_coli_seq1.fasta" }, "input_submol": { "class": "File", "location": "file:///pgap/output/pgap_submol_yogpv0es.yaml", "size": 451, "basename": "pgap_submol_yogpv0es.yaml", "checksum": "sha1$078362e438bc4db768e2ba6fb4fc00b7a26f012a", "path": "/pgap/output/pgap_submol_yogpv0es.yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null }[2024-05-01 11:30:10] WARNING Final process status is permanentFail

ncbi / pgap

[BUG] Final process status is permanentFail #300