Fail test annotation

[ncbi]

Fail test annotation

[azat-badretdin]

Could you please run this with --debug option and post the content of the file submol.json and pgapx_yaml_ctl.*.log. You might want to use find, but before running please chmod -R u+rx .

Thanks!

[azat-badretdin]

Internal ticket PGAPX-429 opened

[scubapenn]

topology: circular
organism:
taxon: 243273
strain: 'replaceme'
contact_info:
last_name: 'Doe'
first_name: 'Jane'
email: '[email protected]'
organization: 'Institute of Klebsiella foobarensis research'
department: 'Department of Using NCBI'
phone: '301-555-0245'
street: '1234 Main St'
city: 'Docker'
postal_code: '12345'
country: 'Lappland'

authors:
- author:
first_name: 'Arnold'
last_name: 'Schwarzenegger'
middle_initial: 'T800'
- author:
first_name: 'Linda'
last_name: 'Hamilton'
bioproject: 'PRJNA9999999'
biosample: 'SAMN99999999'

-- Locus tag prefix - optional. Limited to 9 letters. Unless the locus tag prefix was officially assigned by NCBI, ENA, or DDBJ, it will be replaced upon submission of the annotation to NCBI and is therefore temporary and not to be

used in publications. If not provided, pgaptmp will be used.
locus_tag_prefix: 'tmp'
publications:
- publication:
pmid: 16397293
title: 'Discrete CHARMm of Klebsiella foobarensis. Journal of Improbable Results, vol. 34, issue 13, pages: 10001-100005, 2018'
status: published # this is enum: controlled vocabulary
authors:
- author:
first_name: 'Arnold'
last_name: 'Schwarzenegger'
middle_initial: 'T800'
- author:
first_name: 'Linda'
last_name: 'Hamilton'

[scubapenn]

more ./mg37_results.2/debug/log/pgapx_yaml_ctl.1502.log
00184/000/0000/PB DCBE00B8CF678141 0001/0001 2019-06-04T13:54:28.109697 59830e92b933 UNK_CLIENT UNK_SESSION pgapx_yaml_ctl start /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2019-05-1
3.build3740/arch/x86_64/bin/pgapx_yaml_ctl -ifmt JSON -input /tmp/tmpksgcayt2/stg65cfc086-9c3a-4d7c-a85d-919ed58e1a7b/submol.json -input-fasta /tmp/tmpksgcayt2/stgc7bdbf29-53b2-406d-9c58-d62a489ab08d/ASM2732v1.annotation.nucleotide.1.
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/tmpksgcayt2/stg048e1799-576e-4f29-8c21-652ae604acb9/taxonomy.sqlite3
00184/000/0000/PB DCBE00B8CF678141 0002/0002 2019-06-04T13:54:28.111951 59830e92b933 UNK_CLIENT UNK_SESSION pgapx_yaml_ctl extra ncbi_app_username=&ncbi_app_path=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ba
cterial_pipeline/system/2019-05-13.build3740/arch/x86_64/bin/pgapx_yaml_ctl&ncbi_app_build_date=May+13+2019+12:55:23&ncbi_app_version=0.0.0&ncbi_app_sc_version=22&ncbi_app_vcs_revision=586246
00184/000/0000/P DCBE00B8CF678141 0003/0003 2019-06-04T13:54:28.119035 59830e92b933 UNK_CLIENT UNK_SESSION pgapx_yaml_ctl Error: CORELIB(106.16) "ncbiapp.cpp", line 529: ncbi::CNcbiApplication::x_TryMain() --- Ap
plication's execution failed (CSerialException::eFormatError) line 1: '}' expected ( at JsonValue.organism)
00184/000/0000/PE DCBE00B8CF678141 0004/0004 2019-06-04T13:54:28.125527 59830e92b933 UNK_CLIENT UNK_SESSION pgapx_yaml_ctl stop 3 0.054496049

[scubapenn]

more ./mg37_results.3/debug/log/pgapx_yaml_ctl.1502.log
00182/000/0000/PB AEC700B6CF6789C1 0001/0001 2019-06-04T13:56:44.719894 62dafcb80f9d UNK_CLIENT UNK_SESSION pgapx_yaml_ctl start /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2019-05-1
3.build3740/arch/x86_64/bin/pgapx_yaml_ctl -ifmt JSON -input /tmp/tmp7f52gsqh/stg86d1f0cf-ef4e-4cfa-b32e-ab4b6ce16022/submol.json -input-fasta /tmp/tmp7f52gsqh/stg3ee35762-cf22-47df-b0a7-360d0d62e82d/ASM2732v1.annotation.nucleotide.1.
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/tmp7f52gsqh/stg474e3300-ccbe-4a9c-b563-2ba804881282/taxonomy.sqlite3
00182/000/0000/PB AEC700B6CF6789C1 0002/0002 2019-06-04T13:56:44.721278 62dafcb80f9d UNK_CLIENT UNK_SESSION pgapx_yaml_ctl extra ncbi_app_username=&ncbi_app_path=/panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/ba
cterial_pipeline/system/2019-05-13.build3740/arch/x86_64/bin/pgapx_yaml_ctl&ncbi_app_build_date=May+13+2019+12:55:23&ncbi_app_version=0.0.0&ncbi_app_sc_version=22&ncbi_app_vcs_revision=586246
00182/000/0000/P AEC700B6CF6789C1 0003/0003 2019-06-04T13:56:44.728124 62dafcb80f9d UNK_CLIENT UNK_SESSION pgapx_yaml_ctl Error: CORELIB(106.16) "ncbiapp.cpp", line 529: ncbi::CNcbiApplication::x_TryMain() --- Ap
plication's execution failed (CSerialException::eFormatError) line 1: '}' expected ( at JsonValue.organism)
00182/000/0000/PE AEC700B6CF6789C1 0004/0004 2019-06-04T13:56:44.734471 62dafcb80f9d UNK_CLIENT UNK_SESSION pgapx_yaml_ctl stop 3 0.051583051

[scubapenn]

Any word on this error yet?

[azat-badretdin]

taxon: 243273 presence of this input field in your input submol.yaml file indicates that you are using a bit outdated format for YAML. We are using now combo:

organism:
    genus_species: 'Mycoplasma genitalium' 
    strain: 'replaceme'

under organism field in input submol.yaml

I suggest to freshen up your installation as it is suggested in https://github.com/ncbi/pgap/wiki/Quick-Start

curl -OL https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py
time nohup ./pgap.py --update  > pgap.py.update.log &
watch -n 1 tail -c40 pgap.py.update.log

and try to rerun the "tutorial" case (MG37) again.

[scubapenn]

I am still getting this same error. I just ran ./pgap.py --update > pgap.py.update.log & and it says:
PGAP version 2019-05-13.build3740 is up to date.

[scubapenn]

time nohup ./pgap.py --update > pgap.py.update.log &
[1] 48662
(11:44 kpenn@ActinodeC ~/bin/PGAP.dir) $ nohup: ignoring input and redirecting stderr to stdout

real 0m0.271s
user 0m0.113s
sys 0m0.031s

[slottad]

Please delete the old files and try again.

rm -rf test_genomes* input*

[scubapenn]

This did not fix the problem

[YU-DENG]

I encountered the same problem, has this been solved yet?