Comments (2)
Error in database - no serotype hit for 39 - match to phenotype was 38 hence no hits. . Added catch and CtvdbError:
Traceback (most recent call last):
File "", line 1, in
File "/home/phe.gov.uk/carmen.sheppard/.pycharm_helpers/pydev/_pydev_bundle/pydev_umd.py", line 197, in runfile
pydev_imports.execfile(filename, global_vars, local_vars) # execute the script
File "/home/phe.gov.uk/carmen.sheppard/.pycharm_helpers/pydev/_pydev_imps/_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/pneumocat2.py", line 80, in
main(args, version)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/pneumocat2.py", line 38, in main
run_parse(analysis, tsvfile)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/run_scripts/run_stage1.py", line 164, in run_parse
group_check(filtered_df, analysis.database)
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/run_scripts/run_stage1.py", line 96, in group_check
stage1_result = list(get_pheno_list(results, session))
File "/home/phe.gov.uk/carmen.sheppard/PneumoCaT2/run_scripts/run_stage1.py", line 40, in get_pheno_list
raise CtvdbError(f"No phenotype found for hit {hit} check CTVdb integrity")
exceptions.CtvdbError: CtvdbError: No phenotype found for hit 39 check CTVdb integrity
Update to CTVdb to be done shortly to fix issue.
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Database fixed in development - merge to master.
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Related Issues (20)
- add sample ID to stdout HOT 1
- Filename checking for read 1 and read 2 HOT 1
- Add stage 2 for serogroup 25F/25A HOT 2
- Median multiplicity as quality metric HOT 1
- Update outputs to suit "pneumoKity" HOT 1
- False Ctvdberror HOT 4
- onscreen info for serotype within groups HOT 1
- "mixed serotypes" for 19F and 32F/A when not mixed HOT 1
- 18F reference sequence failing with <70% hit RED rag status HOT 1
- Add feature to create % for mixture multiplicities HOT 1
- Remove text from "predicted phenotype" field for group level detemination HOT 1
- Check Mixed serotype determination - for hit and group in mix. HOT 1
- Check 25FA determination from ENA panel HOT 1
- df.append() depreciated HOT 1
- raise KeyError(f"{not_found} not in index") HOT 2
- singularity image HOT 1
- Collation not correctly collating all data HOT 2
- Error writing empty dataframe HOT 2
- Stop low hits in stage 2 being flagged amber when gene not present" HOT 1
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