A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Earlier, I managed to execute the code:
./nextflow run connor-lab/ncov2019-artic-nf -profile conda --illumina --prefix run1_result --directory run1
However, when I try to rerun the same code, I encountered the following error:
_Error executing process > 'ncovIllumina:prepareReferenceFiles:articDownloadScheme (https://github.com/artic-network/artic-ncov2019.git)'
Caused by:
Missing output file(s) scheme/**/V2/*.reference.fasta expected by process ncovIllumina:prepareReferenceFiles:articDownloadScheme (https://github.com/artic-network/artic-ncov2019.git)
Hi,
Earlier, I managed to execute the code: ./nextflow run connor-lab/ncov2019-artic-nf -profile conda --illumina --prefix run1_result --directory run1
However, when I try to rerun the same code, I encountered the following error: _Error executing process > 'ncovIllumina:prepareReferenceFiles:articDownloadScheme (https://github.com/artic-network/artic-ncov2019.git)'
Caused by: Missing output file(s)
scheme/**/V2/*.reference.fasta
expected by processncovIllumina:prepareReferenceFiles:articDownloadScheme (https://github.com/artic-network/artic-ncov2019.git)
Command executed:
git clone https://github.com/artic-network/artic-ncov2019.git scheme
Command exit status: 0
Command output: (empty)
Command error: Cloning into 'scheme'...
Work dir: /home/yp/work/a5/5dddf7b46f7974ef772b1545611245
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.run
Please need your advice to fix this problem._
Many thanks