Runs fail at barcode22 about porecov

[replikation]

since the error is from:

Running: artic-tools check_vcf --summaryOut barcode22.vcfreport.txt barcode22.merged.vcf.gz external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.scheme.bed 2> barcode22.vcfcheck.log
Command failed:artic-tools check_vcf --summaryOut barcode22.vcfreport.txt barcode22.merged.vcf.gz external_primer_schemes/nCoV-2019/VarSkipV2/nCoV-2019.scheme.bed 2> barcode22.vcfcheck.log

can you visually inspect if all the files from the artic-tools check_vcf are present in /home/minion/Sequenzierung/Analysis/poreCov/results/20220328-01/alignment_data/work/15/5de05280883000c5dd16c97d531a15

my first guess would be that maybe something is wrong with this file (e.g. not enough reads or something).

usually, we ignore these errors by default. i just noticed that this "ignore" was deactivated and I forgot to activate this so the workflow is not failing if some less good barcodes are fed into artic

[JaMaack]

The /home/minion/Sequenzierung/Analysis/poreCov/results/20220328-01/alignment_data/work/15/5de05280883000c5dd16c97d531a15 folder contains these files/folders (via ls command):

20220328-01                  barcode22_filtered.fastq.gz.index         barcode22.merged.vcf.gz      barcode22.nCoV-2019_2.vcf              barcode22.primertrimmed.rg.sorted.bam.bai  barcode22.trimmed.rg.sorted.bam.bai
barcode22.alignreport.er     barcode22_filtered.fastq.gz.index.fai     barcode22.merged.vcf.gz.tbi  barcode22.primersitereport.txt         barcode22.sorted.bam                       barcode22.vcfcheck.log
barcode22.alignreport.txt    barcode22_filtered.fastq.gz.index.gzi     barcode22.minion.log.txt     barcode22.primers.vcf                  barcode22.sorted.bam.bai                   external_primer_schemes
barcode22_filtered.fastq.gz  barcode22_filtered.fastq.gz.index.readdb  barcode22.nCoV-2019_1.vcf    barcode22.primertrimmed.rg.sorted.bam  barcode22.trimmed.rg.sorted.bam            sequencing_summary_FAT41443_4eceb848.txt
`

[JaMaack]

Looks like barcode22.vcfreport.txt isn't present.

[replikation]

okay probably not enough reads or coverage. the next release will ignore these errors again so it wont fail (is currently in the testing phase). for now I recommend excluding the barcode. We had a few exit 20 errors previously in older poreCov versions and it was always due to bad samples (reads too short, not enough coverage, too many human reads and not enough viral, etc.)

[JaMaack]

Is there some way to exclude a specific barcode via the command line?

[replikation]

@JaMaack not really. the new porecov release will be out today in a few hours. this would automatically ignore and skip this barcode. if you want it now you can update porecov and run the latest master:

# update
nextflow pull replikation/poreCov
# run poreCov via master
nextflow run replikation/poreCov -r master    <your commands>

[JaMaack]

Thanks, I'll update poreCov and repeat the runs later.

[replikation]

1.4.1 available now