search

artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
110 stars 69 forks source link

artic_get_stats fails because V4 primer names in align_trim report don't match names in .bed file #93

Closed KatSteinke closed 2 years ago

KatSteinke commented 2 years ago

I'm running a pipeline which uses artic minion for consensus generation and then artic _get_stats for quality control. When trying to run this with the V4 primers, artic_get_stats fails with the following error:

amplicon in align_trim report but not in primer scheme SARSCoV2120_1_LEFT_SARSCoV2120_1_RIGHT

I used the V4 primer scheme in the primer-schemes repository, where the primers are named "SARS-CoV-2_1_LEFT" and "SARS-CoV-2_1_RIGHT" respectively; the other names are also affected. I suspect the error either gets introduced in parsing the bed file in read_bed_file in vcftagprimersites.py or in outputting the report in align_trim.py.

KatSteinke commented 2 years ago

Turns out to have been a different issue altogether - ARTIC ran with the wrong primer scheme.