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nf-core / crisprseq

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
https://nf-co.re/crisprseq
MIT License
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error in NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE file is not in PNG format #161

Open bolenala opened 6 days ago

bolenala commented 6 days ago

Description of the bug

The process NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE starts the FluteMLE command using the data of the gene_summary.txt file. It downloads several pathway files until pathway 'hsa05213' were it stops due to the error shown below.

The error did not occur when running only the 2.2.0/templates/template_fluteMLE.R script on my computer using the gene_summary.txt file. I also tried to use the latest image of mageckflute in the 2.2.0/modules/local/mageck/flutemle.nf with the same output.

Command used and terminal output

nextflow run 2.2.0 -params-file params.yaml -profile normal,singularity -resume -with-report -with-trace -with-timeline > log.txt

params.yaml
input: 'sample_sheet.csv'
outdir: 'results'
analysis: 'screening'
library: 'sgRNA_library.txt'
mle_design_matrix: 'design_matrices/T0_vs_T1_or_T2.txt' 
crisprcleanr: 'library_targets.csv'
min_reads: 3

error message:
  'select()' returned 1:1 mapping between keys and columns
  Info: Working in directory /dnext/project/78/a60432643daa4e4bad087f59d46236
  Info: Writing image file hsa05213.pathview.multi.png
  Error in png::readPNG(figure, native = FALSE) : file is not in PNG format
  Calls: FluteMLE ... arrangePathview -> lapply -> FUN -> <Anonymous> -> <Anonymous>
  In addition: There were 24 warnings (use warnings() to see them)
  Execution halted

Relevant files

No response

System information

Nextflow version: 23.04.0 Hardware: HPC Executor: slurm Container engine: Singularity Version of nf-core/crisprseq: 2.2.0

LaurenceKuhl commented 3 days ago

Hi @bolenala, would you mind giving me your mle output and count table so i can also try locally to see if i can reproduce locally + on the pipeline? I wonder if this issue happens if you run it with conda or docker?