namho4577 commented 5 months ago

I don't know why this input.yaml doesn't work.

This is my code.

namho4577@Namho4577:~/PGAP$ ./pgap.py -r -o E_coli_result9 -g $HOME/.pgap/test_genomes/MG37/input.yaml -s 'Escherichia coli' --ignore-all-errors The latest version of PGAP is 2024-04-27.build7426, you are using version 2023-10-03.build7061, please update. Output will be placed in: /home/namho4577/PGAP/E_coli_result9 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:

[2024-05-04 06:51:46] DEBUG [step Cache_WGS_contig_FASTA] job input { "file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input": { "class": "File", "location": "file:///pgap/user_input/input.yaml", "size": 98, "basename": "input.yaml", "nameroot": "input", "nameext": ".yaml" } } [2024-05-04 06:51:46] DEBUG [step Cache_WGS_contig_FASTA] evaluated job input to { "file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/input": { "class": "File", "location": "file:///pgap/user_input/input.yaml", "size": 98, "basename": "input.yaml", "nameroot": "input", "nameext": ".yaml" } } [2024-05-04 06:51:46] INFO [step Cache_WGS_contig_FASTA] start [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] initializing from file:///pgap/pgap/progs/prime_cache.cwl as part of step Cache_WGS_contig_FASTA [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] { "input": { "class": "File", "location": "file:///pgap/user_input/input.yaml", "size": 98, "basename": "input.yaml", "nameroot": "input", "nameext": ".yaml" }, "biosource": null, "cache_dir": "sequence_cache", "ifmt": "fasta", "inst_mol": null, "molinfo": null, "seq_ids_name": "oseq-ids.seqids", "submit_block_template": null, "taxid": null, "taxon_db": null } [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] path mappings is { "file:///pgap/user_input/input.yaml": [ "/pgap/user_input/input.yaml", "/tmp/xozn3euv/stg2364a5fe-da2f-4e0e-8a62-4c49fd27060d/input.yaml", "File", true ] } [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] command line bindings is [ { "position": [ -1000000, 0 ], "datum": "prime_cache" }, { "prefix": "-cache", "position": [ 0, "cache_dir" ], "datum": "sequence_cache" }, { "prefix": "-ifmt", "position": [ 0, "ifmt" ], "datum": "fasta" }, { "prefix": "-i", "position": [ 0, "input" ], "datum": { "class": "File", "location": "file:///pgap/user_input/input.yaml", "size": 98, "basename": "input.yaml", "nameroot": "input", "nameext": ".yaml", "path": "/tmp/xozn3euv/stg2364a5fe-da2f-4e0e-8a62-4c49fd27060d/input.yaml", "dirname": "/tmp/xozn3euv/stg2364a5fe-da2f-4e0e-8a62-4c49fd27060d" } }, { "prefix": "-oseq-ids", "position": [ 0, "seq_ids_name" ], "datum": "oseq-ids.seqids" } ] [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] initial work dir {} [2024-05-04 06:51:46] INFO [job Cache_WGS_contig_FASTA] /tmp/rjjr7em7$ prime_cache \ -cache \ sequence_cache \ -ifmt \ fasta \ -i \ /tmp/xozn3euv/stg2364a5fe-da2f-4e0e-8a62-4c49fd27060d/input.yaml \ -oseq-ids \ oseq-ids.seqids terminate called after throwing an instance of 'ncbi::CObjReaderParseException' what(): NCBI C++ Exception: Error: READERS(CObjReaderParseException::eNoDefline) "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/objtools/readers/fasta.cpp", line 396: ncbi::objects::CFastaReader::ReadOneSeq() --- CFastaReader: Input doesn't start with a defline or comment around line 1 (m_Pos = 1) Stack trace: /export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/include/corelib/ncbistr.hpp:4455 CObjReaderException offset=0x0 addr=(nil) /export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/include/objtools/readers/reader_exception.hpp:82 CParseTemplException offset=0x0 addr=(nil) /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/lib/libxobjread.so /export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/include/objtools/readers/reader_exception.hpp:43 ncbi::CObjReaderParseException::CObjReaderParseException(ncbi::CDiagCompileInfo const&, ncbi::CException const, ncbi::CObjReaderParseException::EErrCode, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned long, ncbi::EDiagSev) offset=0x0 addr=0x7fc5e769223a /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/lib/libxobjread.so /export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/objtools/readers/fasta.cpp:393 ncbi::objects::CFastaReader::ReadOneSeq(ncbi::objects::ILineErrorListener) offset=0x0 addr=0x7fc5e76f617b /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache :0 offset=0x0 addr=0x415d67 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache :0 offset=0x0 addr=0x41c50b /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=0x7fc5e015c132 /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=0x7fc5e015f78c /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache :0 offset=0x0 addr=0x4118eb /usr/lib64/libc-2.17.so :0 offset=0x0 addr=0x7fc5de370554 /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache :0 offset=0x0 addr=0x411ad9 :0 offset=0x0 addr=0xffffffffffffffff

Stack trace (most recent call last):

14 Object "", at 0xffffffffffffffff, in

13 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache", at 0x411ad9, in _start

12 Object "/usr/lib64/libc-2.17.so", at 0x7fc5de370554, in __libc_start_main

11 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache", at 0x4118eb, in main

10 Source "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 1023, in AppMain [0x7fc5e015f78c]

9 Source "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 711, in x_TryMain [0x7fc5e015c132]

8 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache", at 0x41c50b, in CPrimeCacheApplication::Run()

7 Object "/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2023-10-03.build7061/arch/x86_64/bin/prime_cache", at 0x415d67, in CPrimeCacheApplication::x_Process_Fasta(std::istream&, std::ostream&)

6 Source "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/objtools/readers/fasta.cpp", line 393, in ReadOneSeq [0x7fc5e76f61c5]

5 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x7fc5deef2222]

4 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x7fc5deef1fe0]

3 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x7fc5deef1f95]

2 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x7fc5deef41a4]

1 Object "/usr/lib64/libc-2.17.so", at 0x7fc5de385a77, in abort

0 Object "/usr/lib64/libc-2.17.so", at 0x7fc5de384387, in raise

Aborted (Signal sent by tkill() 161 1000) [2024-05-04 06:51:46] DEBUG Could not collect memory usage, job ended before monitoring began. [2024-05-04 06:51:46] WARNING [job Cache_WGS_contig_FASTA] was terminated by signal: SIGABRT [2024-05-04 06:51:46] WARNING [job Cache_WGS_contig_FASTA] completed permanentFail [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] outputs { "asn_cache": { "location": "file:///tmp/rjjr7em7/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "oseq_ids": { "location": "file:///tmp/rjjr7em7/oseq-ids.seqids", "basename": "oseq-ids.seqids", "nameroot": "oseq-ids", "nameext": ".seqids", "class": "File", "checksum": "sha1$9639094c36326cfaa04bff33f2b24d20616cb905", "size": 14, "http://commonwl.org/cwltool#generation": 0 } } [2024-05-04 06:51:46] DEBUG [step Cache_WGS_contig_FASTA] produced output { "file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/asn_cache": { "location": "file:///tmp/rjjr7em7/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "file:///pgap/pgap/vecscreen/foreign_screening.cwl#foreign_screening/Cache_WGS_contig_FASTA/oseq_ids": { "location": "file:///tmp/rjjr7em7/oseq-ids.seqids", "basename": "oseq-ids.seqids", "nameroot": "oseq-ids", "nameext": ".seqids", "class": "File", "checksum": "sha1$9639094c36326cfaa04bff33f2b24d20616cb905", "size": 14, "http://commonwl.org/cwltool#generation": 0 } } [2024-05-04 06:51:46] WARNING [step Cache_WGS_contig_FASTA] completed permanentFail [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] Removing input staging directory /tmp/xozn3euv [2024-05-04 06:51:46] DEBUG [job Cache_WGS_contig_FASTA] Removing temporary directory /tmp/kxqk9s7i [2024-05-04 06:51:46] INFO [workflow default_plane] completed permanentFail [2024-05-04 06:51:46] DEBUG [workflow default_plane] outputs { "adaptor_blastdb_dir": null, "contig_ids_out": { "location": "file:///tmp/rjjr7em7/oseq-ids.seqids", "basename": "oseq-ids.seqids", "nameroot": "oseq-ids", "nameext": ".seqids", "class": "File", "checksum": "sha1$9639094c36326cfaa04bff33f2b24d20616cb905", "size": 14, "http://commonwl.org/cwltool#generation": 0 }, "feats": null, "hits": null, "out_cache_dir": { "location": "file:///tmp/rjjr7em7/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" } } [2024-05-04 06:51:46] DEBUG [step default_plane] produced output { "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/adaptor_blastdb_dir": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/contig_ids_out": { "location": "file:///tmp/rjjr7em7/oseq-ids.seqids", "basename": "oseq-ids.seqids", "nameroot": "oseq-ids", "nameext": ".seqids", "class": "File", "checksum": "sha1$9639094c36326cfaa04bff33f2b24d20616cb905", "size": 14, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/hits": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir": { "location": "file:///tmp/rjjr7em7/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" } } [2024-05-04 06:51:46] WARNING [step default_plane] completed permanentFail [2024-05-04 06:51:46] INFO [workflow vecscreen] completed permanentFail [2024-05-04 06:51:46] DEBUG [workflow vecscreen] outputs { "adaptor_blastdb_dir": null, "blast_align": null, "calls": null, "contamination_feats": null, "filtered_align": null, "foreign_feats": null, "hits": null, "out_cache_dir": { "location": "file:///tmp/rjjr7em7/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "success": null } [2024-05-04 06:51:46] DEBUG [step vecscreen] produced output { "file:///pgap/pgap/pgap.cwl#vecscreen/success": null, "file:///pgap/pgap/pgap.cwl#vecscreen/calls": null } [2024-05-04 06:51:46] WARNING [step vecscreen] completed permanentFail [2024-05-04 06:51:46] INFO [workflow ] completed permanentFail [2024-05-04 06:51:46] DEBUG [workflow ] outputs { "calls": null, "cds_nucleotide_fasta": null, "cds_protein_fasta": null, "checkm_raw": null, "fastavalerrors": { "location": "file:///tmp/kpw057w/fastaval.xml", "basename": "fastaval.xml", "nameroot": "fastaval", "nameext": ".xml", "class": "File", "checksum": "sha1$de6c0ec7d75456516c3b24dc8dea7e3380673a8c", "size": 636, "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/input.yaml", "size": 98, "basename": "input.yaml", "nameroot": "input", "nameext": ".yaml" }, "input_submol": { "class": "File", "location": "file:///pgap/user_input/pgap_submol_ajzoocdl.yaml", "size": 451, "basename": "pgap_submol_ajzoocdl.yaml", "nameroot": "pgap_submol_ajzoocdl", "nameext": ".yaml" }, "nucleotide_fasta": null, "proteinfasta": null, "sqn": null } [2024-05-04 06:51:46] DEBUG Moving /tmp/kpw057w/fastaval.xml to /pgap/output/fastaval.xml [2024-05-04 06:51:46] DEBUG Copying /pgap/user_input/input.yaml to /pgap/output/input.yaml [2024-05-04 06:51:46] DEBUG Copying /pgap/user_input/pgap_submol_ajzoocdl.yaml to /pgap/output/pgap_submolajzoocdl.yaml [2024-05-04 06:51:46] DEBUG Removing intermediate output directory /tmp/kpw057w [2024-05-04 06:51:46] DEBUG Removing intermediate output directory /tmp/rjjr7em7 [2024-05-04 06:51:46] DEBUG Removing intermediate output directory /tmp/726r70ss [2024-05-04 06:51:46] DEBUG Removing intermediate output directory /tmp/62nqoe3i [2024-05-04 06:51:46] DEBUG Removing intermediate output directory /tmp/m6femmbq [2024-05-04 06:51:46] WARNING Final process status is permanentFail { "calls": null, "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$de6c0ec7d75456516c3b24dc8dea7e3380673a8c", "size": 636, "path": "/pgap/output/fastaval.xml" }, "final_asndisc_error_diag": null, "final_asnval_error_diag": null, "gbk": null, "gff": null, "gff_enhanced": null, "initial_asndisc_error_diag": null, "initial_asnval_error_diag": null, "input_fasta": { "class": "File", "location": "file:///pgap/output/input.yaml", "size": 98, "basename": "input.yaml", "checksum": "sha1$b5c03fd011f22ad9a2d4a280ca36da6c9bfd2dae", "path": "/pgap/output/input.yaml" }, "input_submol": { "class": "File", "location": "file:///pgap/output/pgap_submol_ajzoocdl.yaml", "size": 451, "basename": "pgap_submol_ajzoocdl.yaml", "checksum": "sha1$e38218f8dd835b9671a026c408adea10fba953ab", "path": "/pgap/output/pgap_submol_ajzoocdl.yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null

azat-badretdin commented 5 months ago

Thank you for your report, user @namho4577 !

Your command line says:

./pgap.py -r -o E_coli_result9 -g $HOME/.pgap/test_genomes/MG37/input.yaml -s 'Escherichia coli' --ignore-all-errors

When you are using -g option it requires a FASTA file, not a YAML file.

namho4577 commented 5 months ago

Then what code should I write for the yaml file? iOS용 Outlookhttps://aka.ms/o0ukef 다운로드

보낸 사람: Azat Badretdin @.> 보낸 날짜: Saturday, May 4, 2024 5:57:13 PM 받는 사람: ncbi/pgap @.> 참조: charmantflower @.>; Mention @.> 제목: Re: [ncbi/pgap] [Error] Docker exited with rc = 1 (Issue #301)

Closed #301https://github.com/ncbi/pgap/issues/301 as completed.

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