CHECK_DESIGN terminated with an error

[CLAIRE-cuhk]

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.

[JoseEspinosa]

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.

[CLAIRE-cuhk]

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 [email protected] (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

[JoseEspinosa]

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.