nf-core/hlatyping

configbuilder: command not found

Closed this issue · 3 comments

pandyark commented

I am using the offline version of hlatyping pipeline, when I run the pipeline using the following command in lsf script I get the error : .command.sh: line 2: configbuilder: command not found

Command used to run the pipeline:
nextflow run /nf-core-Pipelines/nf-core-hlatyping-1.1.5/workflow/ -profile singularity -with-singularity nf-core-Pipelines/nf-core-hlatyping-1.1.5/singularity-images/nf-core-hlatyping-1.1.5.img --singleEnd --bam --reads /exome/HLA-Typing/BAM_Files/*.bam' --fasta Analysis_Tools/Homo_sapiens_NCBI_GRCh38/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa --outdir 'exome/HLA-Typing/BAM_Files/results'

Error:
image

Any help will be appreciated!

christopher-mohr commented

Hi, this might be related to Singularity and it might not be able to find the container. Can you make sure that Singularity is working properly?

  • 👍1
christopher-mohr commented

I guess we can close this due to missing feedback

apeltzer commented

Looks like a singularity issue indeed