align_trim.py error using V3 scheme bed file

artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

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align_trim.py error using V3 scheme bed file #31

Closed lzhwin closed 3 years ago

lzhwin commented 4 years ago

When we update to V3 primmer , if we use V3/nCoV-2019.scheme.bed. the align_trim step has an error occured as following: line 96, in find_primer closest = min([(abs(p['start'] - pos), p['start'] - pos, p) for p in bed if p['direction'] == direction], key=itemgetter(0)) ValueError: min() arg is an empty sequence but if we change the bed file to V1/nCoV-2019.scheme.bed or V3/nCoV-2019.bed , there're no error occured. So, is there something wrong in my pipline?

will-rowe commented 4 years ago

This sounds like it might be due to an old version of the artic pipeline causing an incompatibility issue?

If updating to the most recent version of the pipeline doesn't work (conda install -c bioconda artic), can you post this as an issue on the artic pipeline repository please

will-rowe commented 3 years ago

Marking resolved and closing - please reopen if not fixed or you have a further question.