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dorbarker / voc-identify

Identify Variants of Concern from metagenomic samples of SARS-CoV-2
MIT License
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Output fails when using YAML files #43

Closed melohar closed 3 years ago

melohar commented 3 years ago

Hi,

I am not getting any output files when using YAML files instead of a mutations file. Please see error description below.

Thanks,

melohar

2021-09-09 00:08:02 Begin 2021-09-09 00:08:02 Loading reads from SRR15291230_trimmed.bam [E::idx_find_and_load] Could not retrieve index file for 'SRR15291230_trimmed.bam' 2021-09-09 00:08:03 Searching for reference signature mutations 2021-09-09 00:08:32 Searching for paragraph-footwork signature mutations 2021-09-09 00:08:40 Searching for slinky-antennae signature mutations 2021-09-09 00:08:48 Searching for perfume-sprint signature mutations 2021-09-09 00:08:56 Searching for cornstalk-handprint signature mutations 2021-09-09 00:09:02 Searching for spherical-trial signature mutations 2021-09-09 00:09:10 Searching for harbor-sprite signature mutations 2021-09-09 00:09:16 Searching for animating-thermos signature mutations 2021-09-09 00:09:24 Searching for empathy-serve signature mutations 2021-09-09 00:09:31 Searching for mushroom-android signature mutations 2021-09-09 00:09:39 Searching for carnival-shimmy signature mutations 2021-09-09 00:09:47 Searching for denture-daughter signature mutations 2021-09-09 00:09:55 Searching for marbling-doodle signature mutations 2021-09-09 00:10:01 Searching for unloved-crouton signature mutations 2021-09-09 00:10:07 Searching for dandelion-marshy signature mutations 2021-09-09 00:10:16 Searching for glorious-saucy signature mutations 2021-09-09 00:10:24 Searching for cheesy-styling signature mutations 2021-09-09 00:10:32 Searching for habitable-pasty signature mutations 2021-09-09 00:10:38 Searching for kelp-lesser signature mutations 2021-09-09 00:10:46 Formatting and writing reports 2021-09-09 00:10:46 Formatting summary Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.9/bin/mmmvi", line 8, in sys.exit(main()) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/mmmvi/mmmvi.py", line 134, in main reporting.write_reports(mutation_results, vocs, reads, args.outdir, args.delimiter) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/mmmvi/lib/reporting.py", line 541, in write_reports write_summary(voc_results, vocs, reads, outdir, delimiter) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/mmmvi/lib/reporting.py", line 485, in write_summary summary = format_summary(voc_results, vocs, reads) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/mmmvi/lib/reporting.py", line 80, in format_summary max_coverage = theoretical_maximum(reads, vocs) File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/mmmvi/lib/reporting.py", line 168, in theoretical_maximum position_ranges = sorted(vocs[voc].keys()) TypeError: '<' not supported between instances of 'NoneType' and 'int'

dorbarker commented 3 years ago

Hi melohar, thanks for the bug report. There was an issue when dealing with indel mutations that somehow escaped earlier testing. Should be fixed now in version 0.10.2