ERROR picard container for NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS -> setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory

[grendon]

Description of the bug

I am running release 2.6.0 of the viralrecon pipeline. It aborts when it gets to this step

NFCORE_VIRALRECON:ILLUMINA:PICARD_COLLECTMULTIPLEMETRICS.

It looks like the problem is with the picard singularity container. It is not setting up a bunch of global variables.

I had to rerun the pipeline with skip_picard_metrics: true in order to force it to skip this step and complete the rest of the analyses. But it was just a temporary fix.

I am appending .command.err .command.run .command.sh for this failed process to help with troubleshooting.

Thanks in advance for your help.

Command used and terminal output

No response

Relevant files

command.err.txt
command.run.txt
command.sh.txt

System information

Nextflow version: 22.10.1
Hardware: HPC
Executor: slurm
Container engine: Singularity
OS: Rocky Linux 8.5 (Green Obsidian)
Version of nf-core/viralrecon: 2.6.0

[maxulysse]

Hi @grendon, I'm not sure this is due to the singularity container.
These WARNINGS in the .command.err seems concerning to me:

WARNING	2023-04-18 15:20:56	CollectAlignmentSummaryMetrics	No Read length histograms to plot.
WARNING	2023-04-18 15:20:56	CollectBaseDistributionByCycle	No valid bases found in input file. No plot will be produced.
WARNING	2023-04-18 15:20:56	CollectInsertSizeMetrics	All data categories were discarded because they contained < 0.05 of the total aligned paired data.
WARNING	2023-04-18 15:20:56	CollectInsertSizeMetrics	Total mapped pairs in all categories: 0.0
WARNING	2023-04-18 15:20:56	MeanQualityByCycle	No valid bases found in input file. No plot will be produced.
WARNING	2023-04-18 15:20:56	QualityScoreDistribution	No valid bases found in input file. No plot will be produced.
[Tue Apr 18 15:20:56 GMT 2023] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.

Can you check if the files are not empty, and if not, that singularity is properly configured so that Nextflow can read the files properly?

[asp8200]

I also got the warning

setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory

from this old Singularity-container for picard. I got rid of the warning by building my own Singularity-container with locales installed, that is, I added the following to the Singularity-recipe:

apt-get clean && apt-get update
apt-get install locales
locale-gen en_US.UTF-8

I got the fix from here.