Hi I am trying to run the pipeline am getting two different errors. I have run it a couple times and I think the difference just depends on which process it tries to run first but the issues are with diffm6APeak and PeaksMotifReport. For PeaksMotifReport, it seems to copy the Peaks_Motif_Report.rmd file but must be having an issue with the R script because the PeakMotifPlot.RData file is not in the working directory. For diffm6APeak
Any ideas what could be causing these errors?
PeaksMotifReport error:
[- ] process > BWAAlign -
[ff/f6a0eb] process > StarAlign (SRX9973063_SRR13574981) [100%] 12 of 12 ✔
[a7/543845] process > SortRename (transgene_rep1.ip_transgene) [100%] 12 of 12 ✔
[48/0d1da9] process > RSeQC (transgene_rep1.ip_transgene) [100%] 12 of 12 ✔
[- ] process > CreateBedgraph -
[00/9aeb09] process > multiqc [100%] 1 of 1 ✔
[38/f820ef] process > FeatureCount [100%] 1 of 1 ✔
[32/1045b9] process > DESeq2 (transgenemut_vs_control) [100%] 2 of 2 ✔
[- ] process > EdgeR -
[7b/195bae] process > Metpeak (WT_rep2) [100%] 6 of 6 ✔
[77/c13c08] process > Macs2 (transgene_rep1) [100%] 6 of 6 ✔
[- ] process > MATKpeakCalling -
[- ] process > MeyerPrepration -
[- ] process > Meyer -
[18/6b35da] process > PeakMerge [100%] 1 of 1 ✔
[46/38c775] process > BedAnnotated (macs2_WT_rep2_normalized) [100%] 16 of 16 ✔
[3d/17b8d7] process > MotifSearching (rank_merged_group_control) [100%] 4 of 4 ✔
[f7/ce2e75] process > PeaksMotifReport [100%] 1 of 1, failed: 1 ✘
[52/b8634e] process > PeaksQuantification [100%] 1 of 1 ✔
[- ] process > diffm6APeak -
[b8/3d5ca7] process > SingleNucleotidePrediction [100%] 1 of 1 ✔
[- ] process > DiffReport -
[- ] process > CreateIGVjs -
[c6/82fd5a] process > get_software_versions [100%] 1 of 1 ✔
Error executing process > 'PeaksMotifReport'
Caused by:
Process `PeaksMotifReport` terminated with an error exit status (1)
Command executed:
cp /software/MeRIPseqPipe/bin/Peaks_Motif_Report.rmd ./
Rscript /software/MeRIPseqPipe/bin/Peaks_Motif_Report.R formatted_designfile.txt rank independence PeakMotifPlot.RData
R -e "load(\"PeakMotifPlot.RData\");rmarkdown::render('Peaks_Motif_Report.rmd',output_file='Peaks_Motif_Report_rank.html')"
Command exit status:
1
Command output:
(empty)
Command error:
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 2705 did not have 17 elements
Calls: read.table -> scan
Execution halted
Work dir:
/merip/work/f7/ce2e757763c249b7a87262e96eff89
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
diffm6aPeak error:
Differential m6A analysis is going on by bedtools
Differential m6A analysis is going on by bedtools
Execution cancelled -- Finishing pending tasks before exit
[MeRIPseqPpipe] Pipeline completed with errors
WARN: There's no process matching config selector: fastp -- Did you mean: Fastp?
WARN: There's no process matching config selector: sort
WARN: Failed to render execution report -- see the log file for details
WARN: Failed to render execution timeline -- see the log file for details
WARN: Graphviz is required to render the execution DAG in the given format -- See http://www.graphviz.org for more info.
Error executing process > 'diffm6APeak (transgenemut_vs_control)'
Caused by:
Process `diffm6APeak (transgenemut_vs_control)` terminated with an error exit status (1)
Command executed:
case Wilcox-test in
Wilcox-test)
Rscript /opt/software/MeRIPseqPipe/bin/bedtools_diffm6A.R formatted_designfile.txt bedtools_quantification.matrix transgenemut_vs_control
;;
QNB)
Rscript /opt/software/MeRIPseqPipe/bin/QNB_diffm6A.R formatted_designfile.txt rank_merged_allpeaks.bed transgenemut_vs_control
;;
MATK)
export OMP_NUM_THREADS=15
if [ ! -f "/MATK-1.0.jar" ]; then
echo "Cannot find matk.jar. Please check the param of matk_jar" 1>&2
exit 1
fi
bash /opt/software/MeRIPseqPipe/bin/MATK_diffm6A.sh /MATK-1.0.jar formatted_designfile.txt Oryza_sativa.IRGSP-1.0.56.chr.gtf transgenemut_vs_control rank_merged_allpeaks.bed
;;
edgeR)
Rscript /opt/software/MeRIPseqPipe/bin/GLM_edgeR_DM.R formatted_designfile.txt transgenemut_vs_control bedtools_quantification.matrix expression.star.count.matrix
;;
DESeq2)
Rscript /opt/software/MeRIPseqPipe/bin/GLM_DESeq2_DM.R formatted_designfile.txt transgenemut_vs_control 15 bedtools_quantification.matrix expression.star.count.matrix
;;
*)
echo Wilcox-test" is not Wilcox-test, QNB, MATK, DESeq2 or edgeR"
exit 1
;;
esac
Command exit status:
1
Command output:
(empty)
Command error:
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 3240 did not have 9 elements
Calls: read.table -> scan
Execution halted
Hi I am trying to run the pipeline am getting two different errors. I have run it a couple times and I think the difference just depends on which process it tries to run first but the issues are with diffm6APeak and PeaksMotifReport. For PeaksMotifReport, it seems to copy the Peaks_Motif_Report.rmd file but must be having an issue with the R script because the PeakMotifPlot.RData file is not in the working directory. For diffm6APeak Any ideas what could be causing these errors?
PeaksMotifReport error:
diffm6aPeak error:
design file contents: