Error when running with too few reads/very low coverage about fieldbioinformatics HOT 3 OPEN

Running with artic-tools==0.3.1 fixes the artic-tools check_vcf error on artic==1.3.0-dev. It might be just a matter of updating the artic-tools dependency to the newest version.

from fieldbioinformatics.

On v1.2.1, the problem is on Longshot

On v1.3.0, this is actually a duplicate of #88

from fieldbioinformatics.

The above error is occurring regularly using ARTIC v1.2.4 in samples with very low coverage (roughly 0 to 5 aligned reads).

Command failed:longshot -P 0 -F -A --no_haps --bam sample_name.primertrimmed.rg.sorted.bam --ref primer-schemes/SARS-CoV-2/V5.3.2/SARS-CoV-2.reference.fasta --out sample_name.merged.vcf --potential_variants sample_name.merged.vcf.gz

As mentioned above, a solution would be to remove the '-A' (automatic max coverage) flag from the longshot command or to make it optional.

from fieldbioinformatics.