Sam-Sims
commented
1 year ago I think this is a similar issue I outlined in more detail here https://github.com/artic-network/fieldbioinformatics/issues/125 with the artic minion step.
You could examine your vcf files and see if it seems similar.
Essentially it seems there are overlapping variants in the fail.vcf and pass.vcf which causes preconsensus fasta file to be masked and thus bcftools complains when applying the "pass" variant as it expects the reference but instead finds the masked "N".
Typically I have seen this happen in indels when an amplicon drops out - when medaka variant is run on the pool containing the dropped amplicon it prodcues variants that should be filtered out - but dont seem to be.
I was wondering if it was something odd/bug happening with the longshot annotation and dropped amplicons (as it doesnt happen when medaka annotate is used via the --no-longshot flag in minion) causing the artifact variants to be kept from the dropped amplicon. Unforunately I havent had to time to look further.
One way around the issue is to run minion manually using the --no-longshot flag or use bcftools norm with the --check-ref x flag to exclude those sites.
maxulysse
MOISECHRIST
Description of the bug
It is my first time running nf-core/viralrecon pipeline using a sequence from nanopore (Minion). I used the following script but th Pipeline completed with errors. Is there anyone who can help me in troubleshooting the problem? when I try to view the complete command output by changing to the process work dir and entering the command
cat .command.out, nothing is shown.Command used and terminal output
WHEN i RE-RUN THE COMMAND USING THE FOLLOWING SCRIPT
!/bin/bash
nextflow run nf-core/viralrecon -profile singularity \ --max_memory '32.GB' --max_cpus 12 \ --input /home/dej/SARS/data105/samplesheet.csv \ --outdir results_105/viralrecon \ --platform nanopore \ --protocol amplicon \ --genome 'MN908947.3' \ --primer_set artic \ --primer_set_version 3 \ --skip_assembly \ --fastq_dir data105/fastq_pass/ \ --artic_minion_caller medaka \ --artic_minion_medaka_model r941_min_fast_g303
ERROR:
-[nf-core/viralrecon] Pipeline completed with errors- WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta (try 1) -- Cause: github.com WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed (try 1) -- Cause: github.com WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta (try 2) -- Cause: github.com WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed (try 2) -- Cause: github.com WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed (try 3) -- Cause: github.com WARN: Unable to stage foreign file: https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.reference.fasta (try 3) -- Cause: github.com Error executing process > 'NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION (SRX12622371)'
Caused by: Can't stage file https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed -- reason: github.com
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.runRelevant files
No response
System information
No response