chipseq - samplesheet doesn't have minimum number of columns

[BalajiVenkadakrishnan]

Description of the bug

Error with the samplesheet input

Command used and terminal output

This is the command that I am using



sudo nextflow run nf-core/chipseq \
       -resume 2dcf3c47-880c-429d-937e-a93a3c0a3f39 \
       --input samplesheet_chip_seq.csv \
       --outdir chip_seq \
       -profile docker \
       --genome GRCh38 \
       --read_length 200 \
       --max_cpus 16 \
       --max_memory '100.GB' 


The error I am recieving is




Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_chip_seq.csv)'

Caused by:
  Process `NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_chip_seq.csv)` terminated with an error exit status (1)

Command executed:

  check_samplesheet.py \
      samplesheet_chip_seq.csv \
      samplesheet.valid.csv

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  ERROR: Please check samplesheet -> Invalid number of columns (minimum = 5)!
  Line: ''

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.

Work dir:
  /home/balaji/work/d5/015746a0a2448ae6c83952f4ebf86d

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Relevant files

This is the sample sheet that I am using:

sample,fastq_1,fastq_2,antibody,control
abl_h3k4me3,fastq/SRR524714.fastq.gz,,h3k4me3,abl_input
abl_h3k27me3,fastq/SRR524708_pass.fastq.gz,,h3k27me3,abl_input
abl_input,fastq/SRR524712.fastq.gz,,,
pm154_h3k4me3,fastq/SRR8816211.fastq.gz,,h3k4me3,pm154_input
pm154_h3k27me3,fastq/SRR8816210.fastq.gz,,h3k27me3,pm154_input
pm154_input,fastq/SRR7536856.fastq.gz,,,

System information

No response

[bjlang]

Is it possible that you have an empty line in the sample sheet?

[JoseEspinosa]

Close as stale