The number of labels (['KO14', 'KO-control']) must be equal to the number of fastq files provided.

[zhouzhendiao]

Description of the bug

command:

nextflow run /path-to/nf-core-crisprseq-2.0.0/workflow \
    -preview \
    --analysis screening \
    --library library.csv \
    --genome GRCh37 \
    -profile singularity \
    --igenomes_base /path-to/references \
    -offline \
    --outdir . \
    --input samplesheet.csv \
    -resume \
    --max_cpus 16 \
    --max_memory 64.GB \
    --max_time 256.h

samplesheet.csv

sample,fastq_1,fastq_2,condition
KO14,KO14_S1_L003_R1_001.fastq.gz,KO14_S1_L003_R2_001.fastq.gz,KO14
KO-control,KO-control_S6_L005_R1_001.fastq.gz,KO-control_S6_L005_R2_001.fastq.gz,KO-control

Error:

Command error:
  WARNING: Skipping mount /var/lib/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  INFO  @ Mon, 31 Jul 2023 18:09:46: Parameters: /usr/local/bin/mageck count -l library.csv -n count_table --sample-label KO14,KO-control --fastq KO14_S1_L003_R1_001.fastq.gz KO14_S1_L003_R2_001.fastq.gz KO-control_S6_L005_R1_001.fastq.gz KO-control_S6_L005_R2_001.fastq.gz
  INFO  @ Mon, 31 Jul 2023 18:09:46: Welcome to MAGeCK v0.5.9. Command: count
  ERROR @ Mon, 31 Jul 2023 18:09:46: The number of labels (['KO14', 'KO-control']) must be equal to the number of fastq files provided.

In megeck count --fastq, replicates seperated by comma, and samples with different condition seperated by space. However, crisprseq pipeline wrongly seperated fastq1 and fastq2 by comma, which fastq2 should be passed to --fastq-2.

  --fastq-2 FASTQ_2 [FASTQ_2 ...]
                        Paired sample fastq files (or fastq.gz files), the
                        order of which should be consistent with that in fastq
                        option.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[LaurenceKuhl]

Hi @zhouzhendiao,

thanks for adding the bug, working on the solution right now :)
Thanks a lot for taking the time to open these issues, it really is helpful!
Laurence

[zhouzhendiao]

Hi @LaurenceKuhl ，

Thanks for your contribution!

[zhouzhendiao]

Hi @LaurenceKuhl ,

I left fastq2 empty and run everything successfully. Is it not necessary using fastq2 since sgRNA usually way shorter than read1? I tried add fastq2, however mageck failed to estimated trim length of 5' adatpter of read2.

[LaurenceKuhl]

Hi @zhouzhendiao
could you please try rerunning this now with our new version 2.1.0?
Let me know if everything works smoothly :)

[LaurenceKuhl]

Hi, I will close this feel free to reopen if you have any updates