CHECK_DESIGN terminated with an error
CLAIRE-cuhk opened this issue · comments
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.
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.
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:
[33/ab3912] process > CHECK_DESIGN (design_combin... [100%] 1 of 1, cached: 1 ✔
[fa/056c77] process > MAKE_GENOME_FILTER (genome.fa) [100%] 1 of 1, cached: 1 ✔
[23/c215e6] process > FASTQC (MYB_INPUT_R2_T1) [100%] 10 of 10, cached:...
[ae/d850df] process > TRIMGALORE (TAL1_INPUT_R2_T1) [100%] 10 of 10, cached:...
[8c/402e85] process > BWA_MEM (MYB_INPUT_R3_T1) [100%] 10 of 10, cached:...
[a6/00a6fc] process > SORT_BAM (MYB_INPUT_R1_T1) [100%] 10 of 10, cached:...
[6e/9888cb] process > MERGED_BAM (MYB_INPUT_R3) [100%] 10 of 10, cached:...
[6b/f18bd3] process > MERGED_BAM_FILTER (MYB_INPU... [100%] 10 of 10, cached:...
[a6/e38657] process > PRESEQ (MYB_INPUT_R3) [100%] 10 of 10, cached:...
[4e/65961c] process > PICARD_METRICS (TAL1_IP_R2) [100%] 10 of 10, cached:...
[81/4702e2] process > BIGWIG (MYB_IP_R1) [100%] 10 of 10, cached:...
[6a/edf300] process > PLOTPROFILE (MYB_IP_R3) [100%] 10 of 10, cached:...
[78/dc61dc] process > PHANTOMPEAKQUALTOOLS (MYB_I... [100%] 10 of 10, cached:...
[97/87f6d2] process > PLOTFINGERPRINT (MYB_IP_R2 ... [100%] 5 of 5, cached: 4 ✔
[88/e67c93] process > MACS2 (TAL1_IP_R2 vs TAL1_I... [100%] 5 of 5, cached: 5 ✔
[2e/c28ae8] process > MACS2_ANNOTATE (MYB_IP_R3 v... [100%] 5 of 5, cached: 4 ✔
[- ] process > MACS2_QC -
[90/ff2f95] process > CONSENSUS_PEAKS (MYB) [100%] 2 of 2, failed: 1 ✘
[- ] process > CONSENSUS_PEAKS_ANNOTATE -
[- ] process > CONSENSUS_PEAKS_COUNTS -
[- ] process > CONSENSUS_PEAKS_DESEQ2 -
[- ] process > IGV -
[f1/b2b161] process > get_software_versions [100%] 1 of 1 ✔
[- ] process > MULTIQC -
[c4/765f6e] process > output_documentation [100%] 1 of 1, cached: 1 ✔
[nf-core/chipseq] Sent summary e-mail to wly.claire2022@gmail.com (sendmail)
-[nf-core/chipseq] Pipeline completed with errors-
Waiting files transfer to complete (1 files)
WARN: To render the execution DAG in the required format it is required to install Graphviz -- See http://www.graphviz.org for more info.
Error executing process > 'CONSENSUS_PEAKS (TAL1)'
Caused by:
Process CONSENSUS_PEAKS (TAL1) terminated with an error exit status (1)
Command executed:
sort -T '.' -k1,1 -k2,2n TAL1_IP_R1_peaks.narrowPeak TAL1_IP_R2_peaks.narrowPeak
| mergeBed -c 2,3,4,5,6,7,8,9,10 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > TAL1.consensus_peaks.txt
macs2_merged_expand.py TAL1.consensus_peaks.txt
TAL1_IP_R1,TAL1_IP_R2
TAL1.consensus_peaks.boolean.txt
--min_replicates 1
--is_narrow_peak
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
awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $4, $1, $2, $3, "+" }' TAL1.consensus_peaks.boolean.txt >> 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:
1
Command output:
(empty)
Command error:
Error in rowSums(Freqs[, 1:num_sets]) :
'x' must be an array of at least two dimensions
Calls: upset -> Counter -> [ -> [.data.frame -> rowSums
Execution halted
Work dir:
/lustre/scratch/scratch/ucnvlw0/TALL_Project/results_wly/CHIPSEQ_Yang/GSE29180_GSE59657_try3/work/a6/7421b82b3ad9749ba15fdd97b6c5d9
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
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 --skip_consensus_peaks parameter to your command. Otherwise, you could give a try to the dev branch where the files without peaks are filtered (see #268). The dev branch should be quite stable as we are about to release.