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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: prepareReferenceFiles #86

Open yockping opened 3 years ago

yockping commented 3 years ago

Hi, facing the similar problem and encounter error when execute the pipeline. Could please advise? Error as below:

Error executing process > 'ncovIllumina:prepareReferenceFiles:indexReference ([nCoV-2019.reference.fasta, ZaireEbola.reference.fasta, nCoV-2019.reference.fasta])'

Caused by: Process ncovIllumina:prepareReferenceFiles:indexReference input file name collision -- There are multiple input files for each of the following file names: nCoV-2019.reference.fasta

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

Originally posted by @yockping in https://github.com/connor-lab/ncov2019-artic-nf/issues/71#issuecomment-751331915

rdeborja commented 3 years ago

The problem seems to be the primer-schemes directory which duplicates the nCoV-2019.reference.fasta in the nCoV-2019 directory and the SARS-CoV-2 symlink. To get around this, I specified the --ref primer-schemes/nCoV-2019/V3/nCoV-2019.reference.fasta and --bed primer-schemes/nCoV-2019/V3/nCoV-2019.bed options when running the pipeline. This way it doesn't recursively look for *reference.fasta files and duplicate the file for a collision in the list.

m-bull commented 3 years ago

I'm sorry but I can't replicate this - please can you try pulling the latest version and showing me the command that you ran to get this error?

rdeborja commented 3 years ago

I just did a complete clone from scratch and everything seems to be working fine now. The command I issued was nextflow run src/ncov2019-artic-nf/main.nf --schemeVersion V3 --directory data --illumina --prefix tester

yockping commented 3 years ago

great thanks! Finally it works!