Finder test issue

[tomh1lll]

I'm having the same issue several other people have found, but I couldn't see a solution so I was wondering if you've found one.

I run the example command as follows, using singularity instead of docker:

module load singularity samtools STAR

run_finder \
-no_cleanup -om PLANTS -gml ${PWD}/gm_key_64 -gm ${PWD}/gmes_linux_64 \
-mf ${PWD}/example/Arabidopsis_thaliana_metadata.csv --framework singularity \
-n 16 -out_dir $PWD/example/FINDER_test_ARATH \
-g $PWD/example/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa -p $PWD/example/uniprot_ARATH.fasta \
-preserve 1> $PWD/example/FINDER_test_ARATH.output 2> $PWD/example/FINDER_test_ARATH.error 

And get the attached error report. I can't make heads nor tails of it & it seems the error is within finder, but it could be a singularity issue. I'm using singularity version 3.10.3

FINDER_test_ARATH.error.txt

Any help with this would be great, thanks

[BenAawf]

Hi @tomh1lll and @sagnikbanerjee15 I'm facing the issue. Could you share any updates regarding this? isn't it related to the containers update issues?

[sagnikbanerjee15]

Hello @tomh1lll,

Very sorry for the late reply. There seems to be an issue with STAR execution. Also, you do not require to module load STAR and samtools. Both software will be executed via singularity framework. Could you please check if the provided fastq files are present in the path and the genome file is correct?

Thank you.