Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

UPDATE: propose update to blast #2

Open
wants to merge 4 commits into
base: master
Choose a base branch
from
Open

UPDATE: propose update to blast #2

wants to merge 4 commits into from

Conversation

kevinkle
Copy link
Member

Hey Matt,

Was getting this error https://rt.cpan.org/Public/Bug/Display.html?id=121336 when blast was running on - blast=2.5.0=0. I updated blast manually to 2.7.1 and it resolved the issue. The PR pins the newer blast ver. in our conda build, but we should check it isn't incompatible with another dep.

I've added a .travis config that should recreate the issue.

(phylotyper) kevin@kevin-ThinkPad-T510:~/Desktop$ phylotyper genome stx2 temp/ test_stx2_genome1.fasta
INFO:phylotyper.main:No config file argument. Using default settings.
You can provide a Phylotyper config file using enviroment variable PHYLOTYPER_CONFIG or command-line argument --config.
INFO:phylotyper.main:Settings:
{'alignment': ['/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_reference0.affn',
               '/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_reference1.affn'],
 'desc': 'Escherichia coli Shiga-toxin 2 (Stx2) subtype',
 'fast': False,
 'genomes': ['/home/kevin/Desktop/test_stx2_genome1.fasta'],
 'input': ['/home/kevin/Desktop/temp/search_results.locus0',
           '/home/kevin/Desktop/temp/search_results.locus1'],
 'lookup': '/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_dictionary.json',
 'ngenomes': 1,
 'nloci': 2,
 'noplots': False,
 'output_directory': '/home/kevin/Desktop/temp',
 'rate_matrix': '/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_rate_matrix.rds',
 'result': '/home/kevin/Desktop/temp/subtype_predictions.tsv',
 'search_database': '/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_search_database',
 'seq': 'aa',
 'subtype': '/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_subtypes.csv'}
INFO:phylotyper.main:Config:
R:
    rscript: Rscript
    repo: None
    lib: None
external:
    blastx: blastx
    blastdbcmd: blastdbcmd
    makeblastdb: makeblastdb
    fasttree: FastTree
    trimal: trimal
    blastn: blastn
    mafft: mafft
phylotyper:
    prediction_threshold: 0.9

Traceback (most recent call last):
  File "/home/kevin/miniconda2/envs/phylotyper/bin/phylotyper", line 11, in <module>
    sys.exit(main())
  File "/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/run.py", line 698, in main
    subtype_pipeline(subtype_options, config)
  File "/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/run.py", line 205, in subtype_pipeline
    detector = LociSearch(config, options['search_database'], None, seqtype, options['nloci'])
  File "/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/genome/loci.py", line 123, in __init__
    self.load_db(database)
  File "/home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/genome/loci.py", line 209, in load_db
    raise Exception(msg)
Exception: LociSearch command blastdbcmd -db /home/kevin/miniconda2/envs/phylotyper/lib/python2.7/site-packages/phylotyper-0.1.0-py2.7.egg/phylotyper/data/stx2/stx2_search_database -entry all -outfmt "%t	%l" failed: Error: [blastdbcmd] CObject_id::GetId(): Invalid choice selection: NCBI-General::Object-id.str
ptloci1|Stx2a-E-cloacae-95MV2	320
ptloci1|Stx2a-O101-EBC201	320
ptloci1|Stx2a-O104-G5506	320
ptloci1|Stx2a-O111-928-91	320
ptloci1|Stx2a-O113-CL-3	320
ptloci1|Stx2a-O113-TS17-08	320
ptloci1|Stx2a-O113-TS17-08-1	320
ptloci1|Stx2a-O113-TS17-08-2	320
ptloci1|Stx2a-O113-TS17-08-3	320
ptloci1|Stx2a-O113-TS17-08-4	320
ptloci1|Stx2a-O113-TS17-08-5	320
ptloci1|Stx2a-O136-VTB60	320
ptloci1|Stx2a-O157-16581	320
ptloci1|Stx2a-O157-93-111	320
ptloci1|Stx2a-O157-A397	320
ptloci1|Stx2a-O157-EDL933	320
ptloci1|Stx2a-O157-EDL933-1	320
ptloci1|Stx2a-O157-EDL933-2	320
ptloci1|Stx2a-O157-SF-258-98	320
ptloci1|Stx2a-O178-TS22-08	320
ptloci1|Stx2a-O22-EBC217	320
ptloci1|Stx2a-O26-126814	320
ptloci1|Stx2a-O26-FD930	320
ptloci1|Stx2a-O48-94C	320
ptloci1|Stx2a-O48-94C-1	320
ptloci1|Stx2a-O48-94C-2	320
ptloci1|Stx2a-O48-94C-3	320
ptloci1|Stx2a-O48-94C-4	320
ptloci1|Stx2a-O48-94C-5	320
ptloci1|Stx2a-O8-VTB178	320
ptloci1|Stx2a-O8-VTB178-1	320
ptloci1|Stx2a-ONT-23765	320
ptloci1|Stx2a-ONT-EBC210	320
ptloci1|Stx2b-O111-PH	320
ptloci1|Stx2b-O111-S-1	320
ptloci1|Stx2b-O111-S-3	320
ptloci1|Stx2b-O118-EH250	320
ptloci1|Stx2b-O128-24196-97	320
ptloci1|Stx2b-O174-031	320
ptloci1|Stx2b-O22-3143-97	320
ptloci1|Stx2b-O40-5293-98	320
ptloci1|Stx2b-O8-S-9	320
ptloci1|Stx2b-O93-S-5	320
ptloci1|Stx2b-O96-S-10	320
ptloci1|Stx2b-O96-S-6	320
ptloci1|Stx2b-O96-S-7	320
ptloci1|Stx2b-ONT-I7606	318
ptloci1|Stx2b-Out-HI-N	320
ptloci1|Stx2b-Out-S-4	320
ptloci1|Stx2c-O157-020324	320
ptloci1|Stx2c-O157-310	320
ptloci1|Stx2c-O157-310-1	320
ptloci1|Stx2c-O157-469	320
ptloci1|Stx2c-O157-A75	320
ptloci1|Stx2c-O157-C394-03	320
ptloci1|Stx2c-O157-E32511	320
ptloci1|Stx2c-O157-FLY16	320
ptloci1|Stx2c-O157-FLY16-1	320
ptloci1|Stx2c-O157-FLY16-2	320
ptloci1|Stx2c-O157-FLY16-3	320
ptloci1|Stx2c-O157-G5101	320
ptloci1|Stx2c-O157-V20	320
ptloci1|Stx2c-O157-Y350-1	320
ptloci1|Stx2c-O171-EBC287	320
ptloci1|Stx2c-O174-031	320
ptloci1|Stx2c-O177-06-5121	320
ptloci1|Stx2c-O177-06-5121-1	320
ptloci1|Stx2c-O177-CB7126	320
ptloci1|Stx2c-ONT-EBC219	320
ptloci1|Stx2c-ONT-EBC289	320
ptloci1|Stx2c-ONT-pVTEC9	320
ptloci1|Stx2c-OR-TS27-08	320
ptloci1|Stx2c-OR-TS27-08-1	320
ptloci1|Stx2d-O91-B2F1-1	320
ptloci1|Stx2d-O91-B2F1-2	320
ptloci1|Stx2d-C-freundii-LM76	321
ptloci1|Stx2d-O103-pVTEC7	320
ptloci1|Stx2d-O113-TS03-07	320
ptloci1|Stx2d-O113-TS21-08	320
ptloci1|Stx2d-O113-TS21-08-1	320
ptloci1|Stx2d-O157-7279	320
ptloci1|Stx2d-O174-EC1720a	320
ptloci1|Stx2d-O174-EC173b	320
ptloci1|Stx2d-O174-EC173b-1	320
ptloci1|Stx2d-O174-EC173b-2	320
ptloci1|Stx2d-O174-EC173b-3	320
ptloci1|Stx2d-O174-EC173b-4	320
ptloci1|Stx2d-O174-EC173b-5	320
ptloci1|Stx2d-O174-EC173b-6	320
ptloci1|Stx2d-O174-EC173b-7	320
ptloci1|Stx2d-O2-EC604a	320
ptloci1|Stx2d-O55-5905	320
ptloci1|Stx2d-O6-NV206	320
ptloci1|Stx2d-O73-C165-02	320
ptloci1|Stx2d-O8-C466-01B	320
ptloci1|Stx2d-ONT-EBC275	320
ptloci1|Stx2d-ONT-EC1871a	320
ptloci1|Stx2d-O28-MT71	320
ptloci1|Stx2e-O8-FHI-1106-1092	320
ptloci1|Stx2e-O100-TS01-07	320
ptloci1|Stx2e-O101-E-D42	320
ptloci1|Stx2e-O101-E-D43	320
ptloci1|Stx2e-O101-E-D53	320
ptloci1|Stx2e-O101-E-D68	320
ptloci1|Stx2e-O121-NP9621	320
ptloci1|Stx2e-O139-S1191	320
ptloci1|Stx2e-O22-3615-99	320
ptloci1|Stx2e-O22-3615-99-1	320
ptloci1|Stx2e-O22-3615-99-2	320
ptloci1|Stx2e-O22-3615-99-3	320
ptloci1|Stx2e-O26-R107	320
ptloci1|Stx2e-ONT-2771	320
ptloci1|Stx2e-ONT-TS03-08	320
ptloci1|Stx2e-ONT-TS29-08	320
ptloci1|Stx2e-OR-TS09-07	320
ptloci1|Stx2f-O115-F08-101-31	320
ptloci1|Stx2f-O128-T4-97	320
ptloci1|Stx2f-O128-T4-97-1	320
ptloci1|Stx2g-O2-7v	320
ptloci1|Stx2g-O2-HI-11	320
ptloci1|Stx2g-O2-S86	320
ptloci1|Stx2g-Out-S-8	320
ptloci2|Stx2a-Acinetobacter_haemolyticus	90
ptloci2|Stx2a-E-cloacae-95MV2	90
ptloci2|Stx2a-O101-EBC201	90
ptloci2|Stx2a-O104-G5506	90
ptloci2|Stx2a-O111-928-91	90
ptloci2|Stx2a-O113-CL-3	90
ptloci2|Stx2a-O113-TS17-08	90
ptloci2|Stx2a-O113-TS17-08-1	90
ptloci2|Stx2a-O113-TS17-08-2	90
ptloci2|Stx2a-O113-TS17-08-3	90
ptloci2|Stx2a-O113-TS17-08-4	90
ptloci2|Stx2a-O113-TS17-08-5	90
ptloci2|Stx2a-O136-VTB60	90
ptloci2|Stx2a-O157-16581	90
ptloci2|Stx2a-O157-93-111	90
ptloci2|Stx2a-O157-A397	90
ptloci2|Stx2a-O157-EDL933	90
ptloci2|Stx2a-O157-EDL933-1	90
ptloci2|Stx2a-O157-EDL933-2	90
ptloci2|Stx2a-O157-SF-258-98	90
ptloci2|Stx2a-O178-TS22-08	90
ptloci2|Stx2a-O22-EBC217	90
ptloci2|Stx2a-O26-126814	90
ptloci2|Stx2a-O26-FD930	90
ptloci2|Stx2a-O48-94C	90
ptloci2|Stx2a-O48-94C-1	90
ptloci2|Stx2a-O48-94C-2	90
ptloci2|Stx2a-O48-94C-3	90
ptloci2|Stx2a-O48-94C-4	90
ptloci2|Stx2a-O48-94C-5	90
ptloci2|Stx2a-O8-VTB178	90
ptloci2|Stx2a-O8-VTB178-1	90
ptloci2|Stx2a-ONT-23765	90
ptloci2|Stx2a-ONT-EBC210	90
ptloci2|Stx2b-O111-PH	88
ptloci2|Stx2b-O111-S-1	90
ptloci2|Stx2b-O111-S-3	90
ptloci2|Stx2b-O118-EH250	88
ptloci2|Stx2b-O128-24196-97	88
ptloci2|Stx2b-O174-031	88
ptloci2|Stx2b-O22-3143-97	88
ptloci2|Stx2b-O40-5293-98	88
ptloci2|Stx2b-O8-S-9	90
ptloci2|Stx2b-O93-S-5	90
ptloci2|Stx2b-O96-S-10	90
ptloci2|Stx2b-O96-S-6	90
ptloci2|Stx2b-O96-S-7	90
ptloci2|Stx2b-ONT-I7606	90
ptloci2|Stx2b-Out-HI-N	90
ptloci2|Stx2b-Out-S-4	90
ptloci2|Stx2c-O157-020324	90
ptloci2|Stx2c-O157-310	90
ptloci2|Stx2c-O157-310-1	90
ptloci2|Stx2c-O157-469	90
ptloci2|Stx2c-O157-A75	90
ptloci2|Stx2c-O157-C394-03	90
ptloci2|Stx2c-O157-E32511	90
ptloci2|Stx2c-O157-FLY16	90
ptloci2|Stx2c-O157-FLY16-1	90
ptloci2|Stx2c-O157-FLY16-2	90
ptloci2|Stx2c-O157-FLY16-3	90
ptloci2|Stx2c-O157-G5101	90
ptloci2|Stx2c-O157-V20	90
ptloci2|Stx2c-O157-Y350-1	90
ptloci2|Stx2c-O171-EBC287	90
ptloci2|Stx2c-O174-031	90
ptloci2|Stx2c-O177-06-5121	90
ptloci2|Stx2c-O177-06-5121-1	90
ptloci2|Stx2c-O177-CB7126	90
ptloci2|Stx2c-ONT-EBC219	90
ptloci2|Stx2c-ONT-EBC289	90
ptloci2|Stx2c-ONT-pVTEC9	90
ptloci2|Stx2c-OR-TS27-08	90
ptloci2|Stx2c-OR-TS27-08-1	90
ptloci2|Stx2d-O91-B2F1-1	90
ptloci2|Stx2d-O91-B2F1-2	90
ptloci2|Stx2d-C-freundii-LM76	90
ptloci2|Stx2d-O103-pVTEC7	90
ptloci2|Stx2d-O113-TS03-07	90
ptloci2|Stx2d-O113-TS21-08	90
ptloci2|Stx2d-O113-TS21-08-1	90
ptloci2|Stx2d-O157-7279	90
ptloci2|Stx2d-O174-EC1720a	90
ptloci2|Stx2d-O174-EC173b	90
ptloci2|Stx2d-O174-EC173b-1	90
ptloci2|Stx2d-O174-EC173b-2	90
ptloci2|Stx2d-O174-EC173b-3	90
ptloci2|Stx2d-O174-EC173b-4	90
ptloci2|Stx2d-O174-EC173b-5	90
ptloci2|Stx2d-O174-EC173b-6	90
ptloci2|Stx2d-O174-EC173b-7	90
ptloci2|Stx2d-O2-EC604a	90
ptloci2|Stx2d-O55-5905	90
ptloci2|Stx2d-O6-NV206	90
ptloci2|Stx2d-O73-C165-02	90
ptloci2|Stx2d-O8-C466-01B	90
ptloci2|Stx2d-ONT-EBC275	90
ptloci2|Stx2d-ONT-EC1871a	90
ptloci2|Stx2d-O28-MT71	90
ptloci2|Stx2e-O8-FHI-1106-1092	90
ptloci2|Stx2e-O100-TS01-07	88
ptloci2|Stx2e-O101-E-D42	88
ptloci2|Stx2e-O101-E-D43	88
ptloci2|Stx2e-O101-E-D53	88
ptloci2|Stx2e-O101-E-D68	88
ptloci2|Stx2e-O121-NP9621	88
ptloci2|Stx2e-O139-S1191	88
ptloci2|Stx2e-O22-3615-99	88
ptloci2|Stx2e-O22-3615-99-1	88
ptloci2|Stx2e-O22-3615-99-2	88
ptloci2|Stx2e-O22-3615-99-3	88
ptloci2|Stx2e-O26-R107	88
ptloci2|Stx2e-ONT-2771	88
ptloci2|Stx2e-ONT-TS03-08	88
ptloci2|Stx2e-ONT-TS29-08	88
ptloci2|Stx2e-OR-TS09-07	88
ptloci2|Stx2f-O115-F08-101-31	88
ptloci2|Stx2f-O128-T4-97	88
ptloci2|Stx2f-O128-T4-97-1	88
ptloci2|Stx2g-O2-7v	90
ptloci2|Stx2g-O2-HI-11	90
ptloci2|Stx2g-O2-S86	90
ptloci2|Stx2g-Out-S-8	90
 (return code: 1).

@kevinkle kevinkle requested a review from mwhitesi March 11, 2018 22:27
@kevinkle
Copy link
Member Author

https://travis-ci.org/superphy/insilico-subtyping/builds/352108707?utm_source=github_status&utm_medium=notification (the latest build) is correct.

@kevinkle kevinkle mentioned this pull request Mar 12, 2018
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mwhitesi mwhitesi Awaiting requested review from mwhitesi

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
1 participant
@kevinkle