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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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Error: Nextflow #67

Closed yockping closed 3 years ago

yockping commented 4 years ago

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 process ncovIllumina: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

m-bull commented 4 years ago

Should be fixed by https://github.com/connor-lab/ncov2019-artic-nf/commit/bc9884de54445eeeb5a73cb2f50fc2f10c9f3b4a.