search

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
Other
294 stars 89 forks source link

[Error] Docker exited with rc =1 #302

Closed namho4577 closed 2 months ago

namho4577 commented 2 months ago

I don't know how to write the code for the yaml file ~/PGAP$ ./pgap.py -r -o ecol1 -g $HOME/.pgap/non/input.yaml -s 'Escherichia coli' --ignore-all-errors

namho4577@Namho4577:~/PGAP$ ./pgap.py -r -o ecol1 -g $HOME/.pgap/non/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/ecol1 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 09:25:22] 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 09:25:22] 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 09:25:22] INFO [step Cache_WGS_contig_FASTA] start [2024-05-04 09:25:22] 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 09:25:22] 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 09:25:22] DEBUG [job Cache_WGS_contig_FASTA] path mappings is { "file:///pgap/user_input/input.yaml": [ "/pgap/user_input/input.yaml", "/tmp/kkusryk7/stgb5b94447-b5f6-4532-8e8d-7f1e3cf1a420/input.yaml", "File", true ] } [2024-05-04 09:25:22] 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/kkusryk7/stgb5b94447-b5f6-4532-8e8d-7f1e3cf1a420/input.yaml", "dirname": "/tmp/kkusryk7/stgb5b94447-b5f6-4532-8e8d-7f1e3cf1a420" } }, { "prefix": "-oseq-ids", "position": [ 0, "seq_ids_name" ], "datum": "oseq-ids.seqids" } ] [2024-05-04 09:25:22] DEBUG [job Cache_WGS_contig_FASTA] initial work dir {} [2024-05-04 09:25:22] INFO [job Cache_WGS_contig_FASTA] /tmp/m0auvq0j$ prime_cache \ -cache \ sequence_cache \ -ifmt \ fasta \ -i \ /tmp/kkusryk7/stgb5b94447-b5f6-4532-8e8d-7f1e3cf1a420/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=0x7f3f2e1ab23a /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=0x7f3f2e20f17b /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=0x7f3f26c75132 /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=0x7f3f26c7878c /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=0x7f3f24e89554 /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 0x7f3f24e89554, 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 [0x7f3f26c7878c]

9 Source "/export/home/gpipe/TeamCity/Agent3/work/427aceaa834ecbb6/ncbi_cxx/src/corelib/ncbiapp.cpp", line 711, in x_TryMain [0x7f3f26c75132]

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 [0x7f3f2e20f1c5]

5 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_throw.cc", line 93, in __cxa_throw [0x7f3f25a0b222]

4 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 57, in terminate [0x7f3f25a0afe0]

3 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/eh_terminate.cc", line 47, in __cxa_begin_catch [0x7f3f25a0af95]

2 Source "../../../../gcc-7.3.0/libstdc++-v3/libsupc++/vterminate.cc", line 95, in __verbose_terminate_handler [0x7f3f25a0d1a4]

1 Object "/usr/lib64/libc-2.17.so", at 0x7f3f24e9ea77, in abort

0 Object "/usr/lib64/libc-2.17.so", at 0x7f3f24e9d387, in raise

Aborted (Signal sent by tkill() 162 1000) [2024-05-04 09:25:23] DEBUG Could not collect memory usage, job ended before monitoring began. [2024-05-04 09:25:23] WARNING [job Cache_WGS_contig_FASTA] was terminated by signal: SIGABRT [2024-05-04 09:25:23] WARNING [job Cache_WGS_contig_FASTA] completed permanentFail [2024-05-04 09:25:23] DEBUG [job Cache_WGS_contig_FASTA] outputs { "asn_cache": { "location": "file:///tmp/m0auvq0j/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "oseq_ids": { "location": "file:///tmp/m0auvq0j/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 09:25:23] 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/m0auvq0j/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/m0auvq0j/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 09:25:23] WARNING [step Cache_WGS_contig_FASTA] completed permanentFail [2024-05-04 09:25:23] DEBUG [job Cache_WGS_contig_FASTA] Removing input staging directory /tmp/kkusryk7 [2024-05-04 09:25:23] DEBUG [job Cache_WGS_contig_FASTA] Removing temporary directory /tmp/_t08zxug [2024-05-04 09:25:23] INFO [workflow default_plane] completed permanentFail [2024-05-04 09:25:23] DEBUG [workflow default_plane] outputs { "adaptor_blastdb_dir": null, "contig_ids_out": { "location": "file:///tmp/m0auvq0j/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/m0auvq0j/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" } } [2024-05-04 09:25:23] 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/m0auvq0j/oseq-ids.seqids", "basename": "oseq-ids.seqids", "nameroot": "oseq-ids", "nameext": ".seqids", "class": "File", "checksum": "sha1$9639094c36326cfaa04bff33f2b24d20616cb905", "size": 14, "http://commonwl.org/cwltool#generation": 0 }, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/hits": null, "file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir": { "location": "file:///tmp/m0auvq0j/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" } } [2024-05-04 09:25:23] WARNING [step default_plane] completed permanentFail [2024-05-04 09:25:23] INFO [workflow vecscreen] completed permanentFail [2024-05-04 09:25:23] DEBUG [workflow vecscreen] outputs { "adaptor_blastdb_dir": null, "blast_align": null, "calls": null, "contamination_feats": null, "filtered_align": null, "foreign_feats": null, "hits": null, "out_cache_dir": { "location": "file:///tmp/m0auvq0j/sequence_cache", "basename": "sequence_cache", "nameroot": "sequence_cache", "nameext": "", "class": "Directory" }, "success": null } [2024-05-04 09:25:23] DEBUG [step vecscreen] produced output { "file:///pgap/pgap/pgap.cwl#vecscreen/success": null, "file:///pgap/pgap/pgap.cwl#vecscreen/calls": null } [2024-05-04 09:25:23] WARNING [step vecscreen] completed permanentFail [2024-05-04 09:25:23] INFO [workflow ] completed permanentFail [2024-05-04 09:25:23] DEBUG [workflow ] outputs { "calls": null, "cds_nucleotide_fasta": null, "cds_protein_fasta": null, "checkm_raw": null, "fastaval_errors": { "location": "file:///tmp/5pw7um17/fastaval.xml", "basename": "fastaval.xml", "nameroot": "fastaval", "nameext": ".xml", "class": "File", "checksum": "sha1$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_ovtxphhc.yaml", "size": 451, "basename": "pgap_submol_ovtxphhc.yaml", "nameroot": "pgap_submol_ovtxphhc", "nameext": ".yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null } [2024-05-04 09:25:23] DEBUG Moving /tmp/5pw7um17/fastaval.xml to /pgap/output/fastaval.xml [2024-05-04 09:25:23] DEBUG Copying /pgap/user_input/input.yaml to /pgap/output/input.yaml [2024-05-04 09:25:23] DEBUG Copying /pgap/user_input/pgap_submol_ovtxphhc.yaml to /pgap/output/pgap_submol_ovtxphhc.yaml [2024-05-04 09:25:23] DEBUG Removing intermediate output directory /tmp/gvskxfge [2024-05-04 09:25:23] DEBUG Removing intermediate output directory /tmp/lj2h0am7 [2024-05-04 09:25:23] DEBUG Removing intermediate output directory /tmp/6d8w3e5c [2024-05-04 09:25:23] DEBUG Removing intermediate output directory /tmp/m0auvq0j [2024-05-04 09:25:23] DEBUG Removing intermediate output directory /tmp/5pw7um17 [2024-05-04 09:25:23] 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_ovtxphhc.yaml", "size": 451, "basename": "pgap_submol_ovtxphhc.yaml", "checksum": "sha1$e38218f8dd835b9671a026c408adea10fba953ab", "path": "/pgap/output/pgap_submol_ovtxphhc.yaml" }, "nucleotide_fasta": null, "protein_fasta": null, "sqn": null

asd1864714 commented 2 months ago

same question

azat-badretdin commented 2 months ago

Thank you, user @namho4577 for your report!

As I said in a different ticket, this is incorrect: -g $HOME/.pgap/non/input.yaml, -g argument requires FASTA files, not YAML file.

YAML file is old school. You can still use it, but then -g and -s parameters should not be specified. Hope this helps

As for user @asd1864714 : I am afraid I need a little bit more information. Did you also specify YAML file with -g parameter?

If not, I anticipate the issue would be quite different and I recommend to open a new Issue for this.