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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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samtools command failed (align-trim) #70

Closed bernardowerner closed 3 years ago

bernardowerner commented 3 years ago

Hello,

Following the nCoV-2019 novel coronavirus bioinformatics protocol, when I try to run the "Run the MinION pipeline" part

artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file run_name_barcode03.fastq --fast5-directory path_to_fast5 --sequencing-summary path_to_sequencing_summary.txt nCoV-2019/V3 samplename

...it stops with the following error message: "samtools sort: failed to read header from "-""

What could be the trouble here? A different samtools version maybe?

Best regards, Bernardo Werner

lt116 commented 9 months ago

Hi Bernardo Sorry to reopen a closed thread, but I was wondering if you managed to find a solution to this (or even if this was the issue)? I am getting the exact same error (running artic through nextflow) and this is literally the only thing to be found online regarding it.