search

jhuapl-bio / taxtriage

TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various use-cases of mNGS in mind.
MIT License
18 stars 4 forks source link

changed singularity container to include wget https support #23

Closed gunarsosis closed 11 months ago

gunarsosis commented 11 months ago

Container that is being used in the _downloadtaxtab.nf step uses older version of wget that doesn't support https resulting in error which aborts the pipeline. Changing the container to the one used in _get_assemblyrefs.nf fixes the issue.

Error information below:

Error executing process > 'NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB'

Caused by: Process NFCORE_TAXTRIAGE:TAXTRIAGE:DOWNLOAD_TAXTAB terminated with an error exit status (1)

Command executed:

wget https://github.com/jhuapl-bio/datasets/raw/main/databases/ncbi/taxonomy.tab.gz -O taxonomy.tab.gz && gzip -d >taxonomy.tab.gz

Command exit status: 1

Command output: (empty)

Command error: WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container wget: not an http or ftp url: https://github.com/jhuapl-bio/datasets/raw/main/databases/ncbi/taxonomy.tab.gz

Work dir: /scratch/72/022a2192978678f70ecad85676f995

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

Merritt-Brian commented 11 months ago

Correctly adjusted singularity location for download db