search

kzeglinski / nabseq_nf

Nextflow pipeline for NAb-seq (analyses nanopore sequencing data from hybridomas and single B cells)
Other
5 stars 1 forks source link

Error executing nanocomp #3

Closed jagos01 closed 1 year ago

jagos01 commented 1 year ago

Hello, I am trying to analyze a small sequencing run with 3 samples. I get the following error:

Error executing process > 'nanocomp ([null, null, null])'

Caused by: Process nanocomp input file name collision -- There are multiple input files for each of the following file names: null.fastq.gz

The command I used is as follows: nextflow run /home/nabseq_nf/main.nf --fastq_dir /home/Data_Raw/mAbs20June2023/WA4_WH7_EA2/20230620_1432_MC-111382_FAW58338_f8d6ce5f/ --sample_sheet /home/Data_Analysis/mAbs_20June2023/sample_sheet.csv -profile standard

do you have and idea why nanocomp is failing? Thanks,

jagos01 commented 1 year ago

When I include only 1 of the 3 samples in the sample sheet, the following error is generated: Error executing process > 'nanocomp ([null])'

Caused by: Process nanocomp ([null]) terminated with an error exit status (1)

Command executed:

NanoComp \ \ -t 4 \ --fastq null.fastq.gz \ --prefix "reportnull"

Command exit status: 1

Command output: (empty)

jagos01 commented 1 year ago

Hello, The issue was improper format of the sample sheet. Somehow a quote was inserted. All is working fine now. Thanks,