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`).
Using the any design matrix with more then 3 samples there pipeline exists from Magick MLE with the following error.
Command error:
INFO @ Wed, 16 Oct 2024 15:53:18: Parameters: /usr/local/bin/mageck mle --threads 6 -k count_table.count.txt -n designmatrix-anh004 -d designmatrix-anh004.txt
INFO @ Wed, 16 Oct 2024 15:53:23: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Wed, 16 Oct 2024 15:53:23: Design matrix:
INFO @ Wed, 16 Oct 2024 15:53:23: [[1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]]
INFO @ Wed, 16 Oct 2024 15:53:23: Beta labels:baseline,common,hypoxiaVsNormoxia
INFO @ Wed, 16 Oct 2024 15:53:23: Included samples:day0-1,day0-2,control1,control2,hypoxia1,hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded samples:day0-1;day0-2;control1;control2;hypoxia1;hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Sample index: 4;5;2;3;0;1
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded 182 genes.
Error loading line 218
Error loading line 521
Error loading line 907
Traceback (most recent call last):
File "/usr/local/bin/mageck", line 66, in
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 74, in mageckmle_main
allgenedict=read_gene_from_file(args.count_table,includesamples=args.include_samples)
File "/usr/local/lib/python3.9/site-packages/mageck/mleinstanceio.py", line 84, in read_gene_from_file
ginst.nb_count=np.matrix(ginst.nb_count)
File "/usr/local/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py", line 145, in new
arr = N.array(data, dtype=dtype, copy=copy)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (6,) + inhomogeneous part.
N E X T F L O W ~ version 23.10.0
Launching https://github.com/nf-core/crisprseq [loving_planck] DSL2 - revision: b2c583a3fd [master]
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-validation@1.1.3
WARN: Access to undefined parameter reference_fasta -- Initialise it to a default value eg. params.reference_fasta = some_value
WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value
Command output:
Error loading line 218
Error loading line 521
Error loading line 907
Command error:
INFO @ Wed, 16 Oct 2024 15:53:18: Parameters: /usr/local/bin/mageck mle --threads 6 -k count_table.count.txt -n designmatrix-anh004 -d designmatrix-anh004.txt
INFO @ Wed, 16 Oct 2024 15:53:23: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Wed, 16 Oct 2024 15:53:23: Design matrix:
INFO @ Wed, 16 Oct 2024 15:53:23: [[1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]]
INFO @ Wed, 16 Oct 2024 15:53:23: Beta labels:baseline,common,hypoxiaVsNormoxia
INFO @ Wed, 16 Oct 2024 15:53:23: Included samples:day0-1,day0-2,control1,control2,hypoxia1,hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded samples:day0-1;day0-2;control1;control2;hypoxia1;hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Sample index: 4;5;2;3;0;1
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded 182 genes.
Error loading line 218
Error loading line 521
Error loading line 907
Traceback (most recent call last):
File "/usr/local/bin/mageck", line 66, in
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 74, in mageckmle_main
allgenedict=read_gene_from_file(args.count_table,includesamples=args.include_samples)
File "/usr/local/lib/python3.9/site-packages/mageck/mleinstanceio.py", line 84, in read_gene_from_file
ginst.nb_count=np.matrix(ginst.nb_count)
File "/usr/local/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py", line 145, in new
arr = N.array(data, dtype=dtype, copy=copy)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (6,) + inhomogeneous part.
Work dir:
/mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM/work-combined-day0/20/ebfc47d70920ccc3aa3c2ea08f6da1
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
Description of the bug
Using the any design matrix with more then 3 samples there pipeline exists from Magick MLE with the following error.
Command error: INFO @ Wed, 16 Oct 2024 15:53:18: Parameters: /usr/local/bin/mageck mle --threads 6 -k count_table.count.txt -n designmatrix-anh004 -d designmatrix-anh004.txt INFO @ Wed, 16 Oct 2024 15:53:23: Cannot parse design matrix as a string; try to parse it as a file name ... INFO @ Wed, 16 Oct 2024 15:53:23: Design matrix: INFO @ Wed, 16 Oct 2024 15:53:23: [[1. 1. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]] INFO @ Wed, 16 Oct 2024 15:53:23: Beta labels:baseline,common,hypoxiaVsNormoxia INFO @ Wed, 16 Oct 2024 15:53:23: Included samples:day0-1,day0-2,control1,control2,hypoxia1,hypoxia2 INFO @ Wed, 16 Oct 2024 15:53:23: Loaded samples:day0-1;day0-2;control1;control2;hypoxia1;hypoxia2 INFO @ Wed, 16 Oct 2024 15:53:23: Sample index: 4;5;2;3;0;1 INFO @ Wed, 16 Oct 2024 15:53:23: Loaded 182 genes. Error loading line 218 Error loading line 521 Error loading line 907 Traceback (most recent call last): File "/usr/local/bin/mageck", line 66, in
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 74, in mageckmle_main
allgenedict=read_gene_from_file(args.count_table,includesamples=args.include_samples)
File "/usr/local/lib/python3.9/site-packages/mageck/mleinstanceio.py", line 84, in read_gene_from_file
ginst.nb_count=np.matrix(ginst.nb_count)
File "/usr/local/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py", line 145, in new
arr = N.array(data, dtype=dtype, copy=copy)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (6,) + inhomogeneous part.
The follow inputs were used:
Sample sheet sample,fastq_1,fastq_2,condition RM-231Hxn1,./seqdata231/RM-231Hxn1_R1_001.fastq.gz,,hypoxia1 RM-231Hxn2,./seqdata231/RM-231Hxn2_R1_001.fastq.gz,,hypoxia2 RM-231Nxn1,./seqdata231/RM-231Nxn1_R1_001.fastq.gz,,control1 RM-231Nxn2,./seqdata231/RM-231Nxn2_R1_001.fastq.gz,,control2 RM-231T0n1,./seqdata231/RM-231T0n1_R1_001.fastq.gz,,day0-1 RM-231T0n2,./seqdata231/RM-231T0n2_R1_001.fastq.gz,,day0-2
Guide library (head): id target transcript gene symbol 1 ACCAGGGGAGCCAAGTGGA ATP1A1 2 GAAGGAGCCCCGAACCCGG ATP1A1 3 ggcggacacgtggcaacag ATP1A1 4 GAGGGAGCGCAGTAACGGG ATP1A1 5 acagcggtagcagcccggg ATP1A1 6 CCAGCCCGTCTGGGACAGT ATP1A2 7 GGGCTGTGGGTCTAACTGT ATP1A2 8 AGGGAAGGACTAGAGATGT ATP1A2 9 AGCCCACACCAGCCCGTCT ATP1A2
Design Matrix: Samples baseline common hypoxiaVsNormoxia day0-1 1 1 0 day0-2 1 1 0 control1 1 0 0 control2 1 0 0 hypoxia1 1 1 1 hypoxia2 1 1 1
Command used and terminal output
nextflow run nf-core/crisprseq --analysis screening --input $sampleSheet -profile apptainer\ --library $guideLibrary --outdir $output \ --mle_design_matrix $designMatrix\ -w work-combined-day0
Relevant files
N E X T F L O W ~ version 23.10.0 Launching
https://github.com/nf-core/crisprseq[loving_planck] DSL2 - revision: b2c583a3fd [master] WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: nf-validation@1.1.3 WARN: Access to undefined parameterreference_fasta-- Initialise it to a default value eg.params.reference_fasta = some_valueWARN: Access to undefined parametermonochromeLogs-- Initialise it to a default value eg.params.monochromeLogs = some_value|\ | | /
/ \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--,.,._,' nf-core/crisprseq v2.2.1-gb2c583aCore Nextflow options revision : master runName : loving_planck containerEngine : apptainer launchDir : /mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM workDir : /mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM/work-combined-day0 projectDir : /users/anh524/.nextflow/assets/nf-core/crisprseq userName : anh524 profile : apptainer configFiles :
Input/output options input : settings/samplesheet-anh003.csv outdir : anh231-mle-day0 analysis : screening
Screening parameters library : settings/guide_library-anh001.tsv mle_design_matrix: settings/designmatrix-anh004.txt
!! Only displaying parameters that differ from the pipeline defaults !!
If you use nf-core/crisprseq for your analysis please cite:
The pipeline https://doi.org/10.5281/zenodo.7598496
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/nf-core/crisprseq/blob/master/CITATIONS.md
executor > local (8) [93/ee583d] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:FASTQC (RM-231T0n2) [100%] 6 of 6 ✔ [99/4c6443] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_COUNT (hypoxia1,hypoxia2,control1,control2,day0-1,day0-2) [100%] 1 of 1 ✔ [20/ebfc47] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (designmatrix-anh004) [100%] 1 of 1, failed: 1 ✘ [- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE - [- ] process > 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_MLE_MATRIX (designmatrix-anh004)'
Caused by: Process
NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (designmatrix-anh004)terminated with an error exit status (1)Command executed:
mageck \ mle \ \ --threads 6 \ -k count_table.count.txt \ -n designmatrix-anh004 \ -d designmatrix-anh004.txt
cat <<-END_VERSIONS > versions.yml "NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX": mageck: $(mageck -v) END_VERSIONS
Command exit status: 1
Command output: Error loading line 218 Error loading line 521 Error loading line 907
Command error: INFO @ Wed, 16 Oct 2024 15:53:18: Parameters: /usr/local/bin/mageck mle --threads 6 -k count_table.count.txt -n designmatrix-anh004 -d designmatrix-anh004.txt INFO @ Wed, 16 Oct 2024 15:53:23: Cannot parse design matrix as a string; try to parse it as a file name ... INFO @ Wed, 16 Oct 2024 15:53:23: Design matrix: INFO @ Wed, 16 Oct 2024 15:53:23: [[1. 1. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.] INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]] INFO @ Wed, 16 Oct 2024 15:53:23: Beta labels:baseline,common,hypoxiaVsNormoxia INFO @ Wed, 16 Oct 2024 15:53:23: Included samples:day0-1,day0-2,control1,control2,hypoxia1,hypoxia2 INFO @ Wed, 16 Oct 2024 15:53:23: Loaded samples:day0-1;day0-2;control1;control2;hypoxia1;hypoxia2 INFO @ Wed, 16 Oct 2024 15:53:23: Sample index: 4;5;2;3;0;1 INFO @ Wed, 16 Oct 2024 15:53:23: Loaded 182 genes. Error loading line 218 Error loading line 521 Error loading line 907 Traceback (most recent call last): File "/usr/local/bin/mageck", line 66, in
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 74, in mageckmle_main
allgenedict=read_gene_from_file(args.count_table,includesamples=args.include_samples)
File "/usr/local/lib/python3.9/site-packages/mageck/mleinstanceio.py", line 84, in read_gene_from_file
ginst.nb_count=np.matrix(ginst.nb_count)
File "/usr/local/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py", line 145, in new
arr = N.array(data, dtype=dtype, copy=copy)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (6,) + inhomogeneous part.
Work dir: /mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM/work-combined-day0/20/ebfc47d70920ccc3aa3c2ea08f6da1
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