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PHANTOMPEAKQUALTOOLS throws a stack overflow exception on certain types of input data. This issue suggests a fix by increasing the default --max-ppsize. This is already implemented in MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS and should be added to PHANTOMPEAKQUALTOOLS as well.
Command used and terminal output
nextflow run main.nf -profile janelia --input samples.csv --read_length 50 --outdir ./results --fasta internal.fasta --gff internal.gffERROR ~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (neg_rep1)'Caused by: Process `NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS (neg_rep1)` terminated with an error exit status (1)Command executed: RUN_SPP=`which run_spp.R` Rscript -e "library(caTools); source(\"$RUN_SPP\")" -c="neg_rep1.mLb.clN.sorted.bam" -savp="neg_rep1.spp.pdf" -savd="neg_rep1.spp.Rdata" -out="neg_rep1.spp.out" -p=6 cat <<-END_VERSIONS > versions.yml "NFCORE_CHIPSEQ:CHIPSEQ:PHANTOMPEAKQUALTOOLS": phantompeakqualtools: 1.2.2 END_VERSIONSCommand exit status: 1Command output: ################ ChIP data: neg_rep1.mLb.clN.sorted.bam Control data: NA strandshift(min): -500 strandshift(step): 5 strandshift(max) 1500 user-defined peak shift NA exclusion(min): 10 exclusion(max): NaN num parallel nodes: 6 FDR threshold: 0.01 NumPeaks Threshold: NA Output Directory: . narrowPeak output file name: NA regionPeak output file name: NA Rdata filename: neg_rep1.spp.Rdata plot pdf filename: neg_rep1.spp.pdf result filename: neg_rep1.spp.out Overwrite files?: FALSE Reading ChIP tagAlign/BAM file neg_rep1.mLb.clN.sorted.bam opened /tmp/RtmpEulNd9/neg_rep1.mLb.clN.sorted.tagAlign2961e49a6f done. read 326050 fragmentsCommand error: INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred WARNING: Skipping mount /var/apptainer/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container Loading required package: Rcpp Error: protect(): protection stack overflow Execution halted
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered:
Description of the bug
PHANTOMPEAKQUALTOOLS throws a stack overflow exception on certain types of input data. This issue suggests a fix by increasing the default
--max-ppsize
. This is already implemented in MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS and should be added to PHANTOMPEAKQUALTOOLS as well.Command used and terminal output
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: