piPipes_smallRNA_bed2_to_bw.sh: line 32: 21799 Segmentation fault

[edridgedsouza]

I'm trying to run a smallRNA pipeline before running a degradome-seq pipeline. I've installed the ce10 genome and am running this on the MGHPCC cluster, which uses an x86_64 architecture.

When I run the smallRNA pipeline, it finishes in 0.422 seconds, and the error output says that there are two segmentation faults when running piPipes_smallRNA_bed2_to_bw.sh. Specifically, this occurs when running the binary piPipes_bed2_to_bedGraph.

Below is the full output:

[ed40a@ghpcc06 degradome_seq]$ time ~/software/piPipes/piPipes small -i smallRNA_datasets/N2_all/N2_all.fa -g ce10 -o ./piPipes/smallRNA/N2_all -c 8
[2018-07-25 14:16:59 EDT] sort is using: 	
/home/ed40a/software/piPipes/bin/sort
[2018-07-25 14:16:59 EDT] md5sum is using: 	
/usr/bin/md5sum
[2018-07-25 14:16:59 EDT] awk is using: 	
/bin/awk
[2018-07-25 14:16:59 EDT] grep is using: 	
/bin/grep
[2018-07-25 14:16:59 EDT] python is using: 	
/share/pkg/python/2.7.9/bin/python
[2018-07-25 14:16:59 EDT] samtools is using: 	
/home/ed40a/software/piPipes/bin/samtools
[2018-07-25 14:16:59 EDT] gs is using: 	
/usr/bin/gs
[2018-07-25 14:16:59 EDT] Rscript is using: 	
/share/pkg/R/3.5.0/bin/Rscript
[2018-07-25 14:16:59 EDT] bowtie is using: 	
/home/ed40a/software/piPipes/bin/bowtie
[2018-07-25 14:16:59 EDT] ParaFly is using: 	
/home/ed40a/software/piPipes/bin/ParaFly
[2018-07-25 14:16:59 EDT] bedtools_piPipes is using: 	
/home/ed40a/software/piPipes/bin/bedtools_piPipes
[2018-07-25 14:16:59 EDT] bedGraphToBigWig is using: 	
/home/ed40a/software/piPipes/bin/bedGraphToBigWig
[2018-07-25 14:16:59 EDT] piPipes_bed2Summary is using: 	
/home/ed40a/software/piPipes/bin/piPipes_bed2Summary
[2018-07-25 14:16:59 EDT] piPipes_fastq_to_insert is using: 	
/home/ed40a/software/piPipes/bin/piPipes_fastq_to_insert
[2018-07-25 14:16:59 EDT] piPipes_insertBed_to_bed2 is using: 	
/home/ed40a/software/piPipes/bin/piPipes_insertBed_to_bed2
[2018-07-25 14:16:59 EDT] ---------------------------------------------------------------------------------
[2018-07-25 14:16:59 EDT] Beginning running [piPipes] small RNA pipeline single library mode version 1.1.0
[2018-07-25 14:16:59 EDT] Converting fastq format into insert format
[2018-07-25 14:16:59 EDT] Mapping to rRNA, with 2 mismatch(es) allowed
[2018-07-25 14:16:59 EDT] Mapping to microRNA Hairpin, with 1 mismatch(es) allowed; only keep unique mappers
[2018-07-25 14:16:59 EDT] Calculate microRNA heterogeneity
[2018-07-25 14:16:59 EDT] Mapping to genome, with 1 mismatch(es) allowed
[2018-07-25 14:16:59 EDT] Separating unique and multiple mappers
[2018-07-25 14:16:59 EDT] Separating siRNA, piRNA based on length
[2018-07-25 14:16:59 EDT] Plotting length distribution
[2018-07-25 14:16:59 EDT] Intersecting with genomic features, make length distribution, nucleotide fraction for siRNA/piRNA assigned to each feature
[2018-07-25 14:16:59 EDT] Making bigWig files for genome browser
/home/ed40a/software/piPipes/bin/piPipes_smallRNA_bed2_to_bw.sh: line 32: 43365 Segmentation fault      piPipes_bed2_to_bedGraph -i $OUTDIR/${INPUT_BED_NAME%bed2}sorted.bed2 -c $CHROM -p $CPU -o $OUTDIR/${INPUT_BED_NAME%bed2}sorted.
/home/ed40a/software/piPipes/bin/piPipes_smallRNA_bed2_to_bw.sh: line 33: 43368 Segmentation fault      piPipes_bed2_to_bedGraph -i $OUTDIR/${INPUT_BED_NAME%bed2}sorted.uniq.bed2 -c $CHROM -p $CPU -o $OUTDIR/${INPUT_BED_NAME%bed2}sorted.uniq.
[2018-07-25 14:16:59 EDT] Direct mapping to transposon and piRNA cluster and make distribution plot
[2018-07-25 14:16:59 EDT] Merging pdfs
[2018-07-25 14:16:59 EDT] Finished running piPipes small RNA pipeline version 1.1.0
[2018-07-25 14:16:59 EDT] ---------------------------------------------------------------------------------

real	0m0.422s
user	0m0.109s
sys	0m0.155s

I'm noticing other users are experiencing this same issue. Has anyone been able to fix this? What is the reason for the error, and what are potential workarounds?

[edridgedsouza]

Attached stderr output:

pipipes.stderr.txt