Comments (3)
Could you provide the whole error message or the .nextflow.log
. Also, are you using Conda to run the pipeline?
from chipseq.
I'm not using conda. Here is the whole error message:
Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS (H3K9)'
Caused by:
Process NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS (H3K9)
terminated with an error exit status (1)
Command executed:
sort -T '.' -k1,1 -k2,2n CONTR1_H3K9_peaks.broadPeak CONTR2_H3K9_peaks.broadPeak CONTR3_H3K9_peaks.broadPeak frim7_1_H3K9_peaks.broadPeak frim7_2_H3K9_peaks.broadPeak frim7_3_H3K9_peaks.broadPeak pom_1_H3K9_peaks.broadPeak pom_2_H3K9_peaks.broadPeak pom_3_H3K9_peaks.broadPeak
| mergeBed -c 2,3,4,5,6,7,8,9 -o collapse,collapse,collapse,collapse,collapse,collapse,collapse,collapse > H3K9.consensus_peaks.txt
macs2_merged_expand.py
H3K9.consensus_peaks.txt
CONTR1_H3K9,CONTR2_H3K9,CONTR3_H3K9,frim7_1_H3K9,frim7_2_H3K9,frim7_3_H3K9,pom_1_H3K9,pom_2_H3K9,pom_3_H3K9
H3K9.consensus_peaks.boolean.txt
--min_replicates 1 \
awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $1, $2, $3, $4, "0", "+" }' H3K9.consensus_peaks.boolean.txt > H3K9.consensus_peaks.bed
echo -e "GeneID Chr Start End Strand" > H3K9.consensus_peaks.saf
awk -v FS=' ' -v OFS=' ' 'FNR > 1 { print $4, $1, $2, $3, "+" }' H3K9.consensus_peaks.boolean.txt >> H3K9.consensus_peaks.saf
plot_peak_intersect.r -i H3K9.consensus_peaks.boolean.intersect.txt -o H3K9.consensus_peaks.boolean.intersect.plot.pdf
echo "H3K9.consensus_peaks.bed H3K9/H3K9.consensus_peaks.bed" > H3K9.consensus_peaks.antibody.txt
cat <<-END_VERSIONS > versions.yml
"NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CONSENSUS":
python: $(python --version | sed 's/Python //g')
r-base:
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Error: package or namespace load failed for ‘UpSetR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
namespace ‘scales’ 1.1.1 is being loaded, but >= 1.2.0 is required
Execution halted
Work dir:
/shared/ifbstor1/projects/project_nbouche/frim7_ChIP_CONTR/work/d0/c9bf0fd655e9a11bbae24e711026ab
Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out
from chipseq.
I think that it could be that you have a local version of the R package installed in your environment which overwrites the one in the image (which actually meets the requirements since is 1.14). If this is the case, maybe it will be worth to remove the local version of the UpSetR
package.
from chipseq.
Related Issues (20)
- Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1) HOT 3
- mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9. HOT 18
- Normalisation of bigwig files
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR
- Get rid of checkIfExists for params paths
- minor "samplesheet_pe.csv" format issue
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model!
- Error with NextSeq trimming
- Error running the pipline test in the BWA index step
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3
- There are multiple files for each of the following file names
- Can't run if there is no control
- Improve website on parameters section Alignment Options for argument --save_unaligned
- IDR analysis
- Remove lib folder to get ready for v2.13.1 template merge
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from chipseq.