CHECK_DESIGN terminated with an error #286
Comments
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I answered your query in slack, think that you are including an empty line at the end of the file. Let me know if this does not solve the problem. |
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Hi Jose, Thank you! The pipeline started properly in cluster after removing the empty line at the end of design.csv. But there is another error occured at CONSENSUS_PEAKS step. A similar issue #134 has been posted two years ago. I tried the suggested solution but still can't fix the problem. This is the error I receive: Caused by: Command executed: sort -T '.' -k1,1 -k2,2n TAL1_IP_R1_peaks.narrowPeak TAL1_IP_R2_peaks.narrowPeak macs2_merged_expand.py TAL1.consensus_peaks.txt awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $1, $2, $3, $4, "0", "+" }' TAL1.consensus_peaks.boolean.txt > TAL1.consensus_peaks.bed echo -e "GeneID Chr Start End Strand" > TAL1.consensus_peaks.saf plot_peak_intersect.r -i TAL1.consensus_peaks.boolean.intersect.txt -o TAL1.consensus_peaks.boolean.intersect.plot.pdf find * -type f -name "TAL1.consensus_peaks.bed" -exec echo -e "bwa/mergedLibrary/macs/narrowPeak/consensus/TAL1/"{}"\t0,0,0" ; > TAL1.consensus_peaks.bed.igv.txt Command exit status: Command output: Command error: Work dir: Tip: view the complete command output by changing to the process work dir and entering the command |
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I would say that the problem might be related to #128, maybe in some files no peaks are called. You could skip this process by adding the |
Hello,
I have been trying to run the nextflow/chipseq pipeline but failed due to the following error:
Error executing process > 'CHECK_DESIGN (design_combined.csv)'
Caused by:
Process
CHECK_DESIGN (design_combined.csv)terminated with an error exit status (1)Command executed:
check_design.py design_combined.csv design_reads.csv design_controls.csv
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/shared/ucl/depts/cancer/apps/nextflow_pipelines/nfcore_chipseq/chipseq-1.2.2/bin/check_design.py", line 186, in
reformat_design(DesignFile=args.DESIGN_FILE,ReadMappingFile=args.READ_MAPPING_FILE,ControlMappingFile=args.CONTROL_MAPPING_FILE)
File "/shared/ucl/depts/cancer/apps/nextflow_pipelines/nfcore_chipseq/chipseq-1.2.2/bin/check_design.py", line 55, in reformat_design
group,replicate,fastQFiles,antibody,control = lspl[0],lspl[1],[x for x in lspl[2:-2] if x],lspl[-2],lspl[-1]
IndexError: list index out of range
Here is my design:
group,replicate,fastq_1,fastq_2,antibody,control
TAL1_IP,1,path toSRR443847/SRR443847.fastq.gz,,TAL1,TAL1_INPUT
TAL1_IP,2,path to SRR443848.fastq.gz,,TAL1,TAL1_INPUT
MYB_IP,1,path to SRR1603647.fastq.gz,,MYB,MYB_INPUT
MYB_IP,2,path to SRR1603653.fastq.gz,,MYB,MYB_INPUT
MYB_IP,3,path to SRR1603651.fastq.gz,,MYB,MYB_INPUT
TAL1_INPUT,1,path toSRR443856.fastq.gz,,,
TAL1_INPUT,2,path toSRR443855.fastq.gz,,,
MYB_INPUT,1,path to SRR1603649.fastq.gz,,,
MYB_INPUT,2,path to SRR1603652.fastq.gz,,,
MYB_INPUT,3,path to SRR1603648.fastq.gz,,,
It seems the pipeline couldn't recogonize design.csv although I think I followed the structure required?
Many thanks.
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