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[Error] Docker exited with rc = 1 #301

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namho4577 opened this issue May 4, 2024 · 3 comments
Closed

[Error] Docker exited with rc = 1 #301

namho4577 opened this issue May 4, 2024 · 3 comments

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@namho4577
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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$9639094c36326cfaa04bff33f2b24d20616cb905",
"size": 14,
"http://commonwl.org/cwltool#generation": 0
},
"file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/feats": null,
"file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/hits": null,
"file:///pgap/pgap/vecscreen/vecscreen.cwl#vecscreen/default_plane/out_cache_dir": {
"location": "file:///tmp/rjjr7em7/sequence_cache",
"basename": "sequence_cache",
"nameroot": "sequence_cache",
"nameext": "",
"class": "Directory"
}
}
[2024-05-04 06:51:46] WARNING [step default_plane] completed permanentFail
[2024-05-04 06:51:46] INFO [workflow vecscreen] completed permanentFail
[2024-05-04 06:51:46] DEBUG [workflow vecscreen] outputs {
"adaptor_blastdb_dir": null,
"blast_align": null,
"calls": null,
"contamination_feats": null,
"filtered_align": null,
"foreign_feats": null,
"hits": null,
"out_cache_dir": {
"location": "file:///tmp/rjjr7em7/sequence_cache",
"basename": "sequence_cache",
"nameroot": "sequence_cache",
"nameext": "",
"class": "Directory"
},
"success": null
}
[2024-05-04 06:51:46] DEBUG [step vecscreen] produced output {
"file:///pgap/pgap/pgap.cwl#vecscreen/success": null,
"file:///pgap/pgap/pgap.cwl#vecscreen/calls": null
}
[2024-05-04 06:51:46] WARNING [step vecscreen] completed permanentFail
[2024-05-04 06:51:46] INFO [workflow ] completed permanentFail
[2024-05-04 06:51:46] DEBUG [workflow ] outputs {
"calls": null,
"cds_nucleotide_fasta": null,
"cds_protein_fasta": null,
"checkm_raw": null,
"fastaval_errors": {
"location": "file:///tmp/kpw057w/fastaval.xml",
"basename": "fastaval.xml",
"nameroot": "fastaval",
"nameext": ".xml",
"class": "File",
"checksum": "sha1$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,
"protein_fasta": 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_submol_ajzoocdl.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
@namho4577 namho4577 changed the title [Error] input.yaml error [Error] Docker exited with rc = 1 May 4, 2024
@azat-badretdin
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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
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namho4577 commented May 4, 2024 via email

@azat-badretdin
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If you would like to continue using YAML file replace -s and -g parameters with YAML file.

So this:

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

will become this

./pgap.py -r --ignore-all-errors -o E_coli_result9 $HOME/.pgap/test_genomes/MG37/input.yaml

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@azat-badretdin @namho4577