LaurenceKuhl
commented
3 months ago Hi @AASTHAPAL9 sorry for getting back to you so late! Is there any chance you could run it with docker instead of conda? We're experiencing some difficulties:
nextflow run nf-core/crisprseq -r 2.1.1 --input samplesheet_w_control.csv --mle_design_matrix design_matrix.txt --library final_input_sgrna.tsv --analysis screening --outdir /home/ap764/mageck/output -profile docker
let me know if this is possible :)
Description of the bug
Hi,
I am not sure if this any compatibility issue but I couldn't run the pipeline with -r 2.1.1 which was suggested by one of the nfcore crisprseq developer. However when I did get something using -r dev it failed at some other step. I haven't been able to traceback the error and would appreciate any help in debugging.
Command used and terminal output
Relevant files
The error when I ran the same command with -r dev :
`executor > local (8) [90/f186a3] NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:FASTQC (POST-KCNM-CDR-O) | 5 of 5 ✔ [ad/da22ac] NFC…R-O,PRE-CDR-O,POST-EGF-CDR-O,POST-KCNM-CDR-O,POST-PTPRZ-CDR-O) | 1 of 1 ✔ [7b/c72af1] NFC…RISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (design_matrix) | 1 of 1 ✔ [8d/013eae] NFC…_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE (design_matrix) | 1 of 1, failed: 1 ✘ [- ] NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MULTIQC - Execution cancelled -- Finishing pending tasks before exit -[nf-core/crisprseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE (design_matrix)'
Caused by: Process
NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE (design_matrix)terminated with an error exit status (127)Command executed [/home/ap764/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]:
!/usr/bin/env Rscript
author: Laurence Kuhlburger
Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text.
graphs mageck MLE
library(MAGeCKFlute) library(clusterProfiler) library(ggplot2)
library(pathview) options(ggrepel.max.overlaps = Inf) mle <- read.table("design_matrix.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE)
if("design_matrix" == "day0") { beta_strings <- grep("\.beta", colnames(mle), value = TRUE) before_beta <- sub("\.beta.", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { tryCatch( { FluteMLE(mle, treatname= i, proj=i, pathview.top=5) }, error=function(e) { print(paste("Could not run FluteMLE with project",i)) } ) } } else { beta_strings <- grep("\.beta", colnames(mle), value = TRUE) before_beta <- sub("\.beta.", "", beta_strings) unique_strings <- unique(before_beta) for(i in unique_strings) { tryCatch( { FluteMLE(mle, treatname= i, proj=i, , pathview.top=5) }, error=function(e) { print(paste("Could not run FluteMLE with project",i)) } ) } }
version_file_path <- "versions.yml" version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".") version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".") version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".") version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".")
f <- file(version_file_path, "w") writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE":', f) writeLines(" MAGeCKFlute: ", f, sep = "") writeLines(version_flute, f) writeLines(" ggplot2: ", f, sep = "") writeLines(version_ggplot, f) writeLines(" clusterProfiler: ", f, sep = "") writeLines(version_clusterprofiler, f) writeLines(" pathview: ", f, sep = "") writeLines(version_pathview, f) close(f)
Command exit status: 127
Command output: (empty)
Command error: /usr/bin/env: 'Rscript': No such file or directory
Work dir: /home/ap764/mageck/work/8d/013eae9d1032316baef01978a208a4
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named
.command.sh-- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details`
System information
No response