piPipes_smallRNA_bed2_to_bw.sh: line 32: 73659 Segmentation fault

[YouCai626]

Recently, I used piPipes step by step using data in manual, I ran the small RNA-Seq part:
piPipes small -i Zamore.SRA.ago3_het.ox.ovary.trimmed.fastq.gz -g dm3 -o Zamore.SRA.ago3_het.ox.ovary.piPipes_out 1> Zamore.SRA.ago3_het.ox.ovary.piPipes.stdout 2> Zamore.SRA.ago3_het.ox.ovary.piPipes.stderr
But it showed errors:
cat Zamore.SRA.ago3_het.ox.ovary.piPipes.stderr
Rscript execution error: No such file or directory
/mnt/isilon/wang_lab/caiyou/piPipes/bin/piPipes_smallRNA_bed2_to_bw.sh: line 32: 73659 Segmentation fault (core dumped) piPipes_bed2_to_bedGraph -i $OUTDIR/${INPUT_BED_NAME%bed2}sorted.bed2 -c $CHROM -p $CPU -o $OUTDIR/${INPUT_BED_NAME%bed2}sorted.
/mnt/isilon/wang_lab/caiyou/piPipes/bin/piPipes_smallRNA_bed2_to_bw.sh: line 33: 73663 Segmentation fault (core dumped) 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.
[bam_header_read] EOF marker is absent. The input is probably truncated.
Rscript execution error: No such file or directory
[bam_header_read] EOF marker is absent. The input is probably truncated.
Rscript execution error: No such file or directory
[bam_header_read] EOF marker is absent. The input is probably truncated.
Rscript execution error: No such file or directory
GPL Ghostscript 9.07: Unrecoverable error, exit code 1

The files in /common/dm3/
Bowtie2Index
BowtieIndex
Brennecke.piRNAcluster.20A.bed6.gz
Brennecke.piRNAcluster.42AB.bed6.gz
Brennecke.piRNAcluster.bed6.gz
Brennecke.piRNAcluster.flam.bed6.gz
BWAIndex
chrU.fa
cisNATs.bed.gz
cytoBand.txt
dm3.ChromInfo.txt
dm3.fa
dm3.fa.fai
dm3.gap.bed
dm3.genes.bed12
dm3.genes.fa
dm3.genes.gp
dm3.genes.gtf
dm3.genes+repBase+piRNACluster.gtf
dm3.genes+transposon+piRNACluster.gtf
dm3.gene+transposon.fa
dm3.hairpin.fa
dm3.mature.fa
dm3.mature.multiMapper.fa
dm3.piRNAcluster.bed.gz
dm3.piRNAcluster.fa
dm3.repBase.eref
dm3.repBase.fa
dm3.transposon.fa
dm3.transposon.rm.bed
Drosophila_melanogaster
Drosophila_melanogaster_UCSC_dm3.tar.gz
genomic_features
hpRNA.bed.gz
lincRNA.Young.bed6.gz
Log.out
mature2hairpin.allMapper.bed
mature2hairpin.multi.bed
mature2hairpin.uniq.bed
mrFastIndex
README.txt
repBase
rRNA.fa
STARIndex
structured_loci.bed.gz
UCSC.flyBase.3UTR.bed.gz
UCSC.flyBase.5UTR.bed.gz
UCSC.flyBase.CDS.bed.gz
UCSC.flyBase.Exons.bed.gz
UCSC.flyBase.Genes.bed12.gz
UCSC.flyBase.Genes.bed6.gz
UCSC.flyBase.Introns.bed.gz
UCSC.flyBase.Introns_xRM.bed.gz
UCSC.flyBase.Noncoding.bed.gz
UCSC.refSeq.3UTR.bed.gz
UCSC.refSeq.5UTR.bed.gz
UCSC.refSeq.CDS.bed.gz
UCSC.refSeq.Exon.bed.gz
UCSC.refSeq.Genes.bed12.gz
UCSC.refSeq.Intron.bed.gz
UCSC.RepeatMask.bed
UCSC.RepeatMask.inCluster.bed.gz
UCSC.RepeatMask.outCluster.bed.gz
UCSC.RepeatMask.Satellite.bed
UCSC.rRNA+tRNA+nonCoding.bed6.gz
UCSC.SimpleRepeats.bed.gz
unannotated_genome.bed.gz
variables
X-TAS.fa
Zamore.transposon.bed.gz
Zamore.transposon.group0.bed.gz
Zamore.transposon.group1.bed.gz
Zamore.transposon.group2.bed.gz
Zamore.transposon.group3.bed.gz
Zamore.transposon.inCluster.bed.gz
Zamore.transposon.outCluster.bed.gz

Is there someone else met the same trouble?
Please give me some suggestion.

Thanks very much!

[yfu]

Could you cd into the genome_mapping dir and run ls -hl *.sorted.bed2? It could be that this file is empty, which causes piPipes_bed2_to_bedGraph to fail. If it is not empty, could you post the first 10 lines here?

[YouCai626]

Yes, in the genome_mapping dir, there is no *.sorted.bed2.
These are files in genome_mapping dir:
[caiy1@c-2-01 genome_mapping]$ ls
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.hairpin.dm3v0a.bed2
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.hairpin.dm3v0a.log
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.all.bed2
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.all.bed2.lendis
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.all.log
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.all.piRNA.bed2
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.all.siRNA.bed2
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.unique.bed2
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.unique.bed2.lendis
Zamore.SRA.ago3_het.ox.ovary.trimmed.x_rRNA.x_hairpin.dm3v0.unique.+hairpin.bed2

Thanks!

[yfu]

Could you try running piPipes_debug instead of piPipes and then attach the stderr and stdout here?

[YouCai626]

cat Zamore.SRA.ago3_het.ox.ovary.piPipes_debug.stdout
[2018-02-11 21:14:58 EST] sort is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/sort
[2018-02-11 21:14:58 EST] md5sum is using:
/usr/bin/md5sum
[2018-02-11 21:14:58 EST] awk is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/awk
[2018-02-11 21:14:58 EST] grep is using:
/usr/bin/grep
[2018-02-11 21:14:58 EST] python is using:
/usr/bin/python
[2018-02-11 21:14:58 EST] samtools is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/samtools
[2018-02-11 21:14:58 EST] gs is using:
/usr/bin/gs
[2018-02-11 21:14:58 EST] Rscript is using:
/mnt/isilon/wang_lab/caiyou/miniconda2/bin/Rscript
[2018-02-11 21:14:58 EST] bowtie is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/bowtie
[2018-02-11 21:14:58 EST] ParaFly is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/ParaFly
[2018-02-11 21:14:58 EST] bedtools_piPipes is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/bedtools_piPipes
[2018-02-11 21:14:58 EST] bedGraphToBigWig is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/bedGraphToBigWig
[2018-02-11 21:14:58 EST] piPipes_bed2Summary is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/piPipes_bed2Summary
[2018-02-11 21:14:58 EST] piPipes_fastq_to_insert is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/piPipes_fastq_to_insert
[2018-02-11 21:14:58 EST] piPipes_insertBed_to_bed2 is using:
/mnt/isilon/wang_lab/caiyou/piPipes/bin/piPipes_insertBed_to_bed2
[2018-02-11 21:14:58 EST] ---------------------------------------------------------------------------------
[2018-02-11 21:14:58 EST] Beginning running [piPipes] small RNA pipeline single library mode version 1.1.0
[2018-02-11 21:14:58 EST] Converting fastq format into insert format
[2018-02-11 21:15:00 EST] Mapping to rRNA, with 0 mismatch(es) allowed
[2018-02-11 21:15:02 EST] Mapping to microRNA Hairpin, with 0 mismatch(es) allowed; only keep unique mappers
[2018-02-11 21:15:03 EST] Calculate microRNA heterogeneity
[2018-02-11 21:15:03 EST] Mapping to genome, with 0 mismatch(es) allowed
[2018-02-11 21:15:22 EST] Separating unique and multiple mappers
[2018-02-11 21:15:31 EST] Separating siRNA, piRNA based on length
[2018-02-11 21:15:37 EST] Plotting length distribution
[2018-02-11 21:15:42 EST] Intersecting with genomic features, make length distribution, nucleotide fraction for siRNA/piRNA assigned to each feature
[2018-02-11 21:23:49 EST] Making bigWig files for genome browser
[2018-02-11 21:23:56 EST] Direct mapping to transposon and piRNA cluster and make distribution plot
[2018-02-11 21:24:33 EST] Merging pdfs
Error: /undefinedfilename in (/mnt/isilon/wang_lab/caiyou/piPipes/Zamore.SRA.ago3_het.ox.ovary.piPipes_debug_out/pdfs/Zamore.SRA.ago3_het.ox.ovary.trimmed.pie.pdf)
Operand stack:

Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push
Dictionary stack:
--dict:1165/1684(ro)(G)-- --dict:0/20(G)-- --dict:77/200(L)--
Current allocation mode is local
Last OS error: No such file or directory
[2018-02-11 21:24:33 EST] Finished running piPipes small RNA pipeline version 1.1.0

[YouCai626]

less Zamore.SRA.ago3_het.ox.ovary.piPipes_debug.stderr

• bash -x /mnt/isilon/wang_lab/caiyou/piPipes/piPipes.sh small -i Zamore.SRA.ago3_het.ox.ovary.trimmed.fastq.gz -g dm3 -o Zamore.SRA.ago3_het.ox.ovary.piPipes_debug_out
• export 'COLOR_RED=\e[31;40m'
• COLOR_RED='\e[31;40m'
• export 'COLOR_GREEN=\e[32;40m'
• COLOR_GREEN='\e[32;40m'
• export 'COLOR_YELLOW=\e[33;40m'
• COLOR_YELLOW='\e[33;40m'
• export 'COLOR_BLUE=\e[34;40m'
• COLOR_BLUE='\e[34;40m'
• export 'COLOR_MAGENTA=\e[35;40m'
• COLOR_MAGENTA='\e[35;40m'
• export 'COLOR_CYAN=\e[36;40m'
• COLOR_CYAN='\e[36;40m'
• export 'COLOR_RED_BOLD=\e[31;1m'
• COLOR_RED_BOLD='\e[31;1m'
• export 'COLOR_RED_LIGHT=\e[91m'
• COLOR_RED_LIGHT='\e[91m'
• export 'COLOR_GREEN_BOLD=\e[32;1m'
• COLOR_GREEN_BOLD='\e[32;1m'
• export 'COLOR_GREEN_LIGHT=\e[92m'
• COLOR_GREEN_LIGHT='\e[92m'
• export 'COLOR_YELLOW_BOLD=\e[33;1m'
• COLOR_YELLOW_BOLD='\e[33;1m'
• export 'COLOR_BLUE_BOLD=\e[34;1m'
• COLOR_BLUE_BOLD='\e[34;1m'
• export 'COLOR_MAGENTA_BOLD=\e[35;1m'
• COLOR_MAGENTA_BOLD='\e[35;1m'
• export 'COLOR_CYAN_BOLD=\e[36;1m'
• COLOR_CYAN_BOLD='\e[36;1m'
• export 'COLOR_END=\e[0m'
• COLOR_END='\e[0m'
  ++ echo -ne '\e[0m'
• export 'RESET=ESC[0m'
• RESET='ESC[0m'
  ++ echo -ne '\e[1m'
• PACKAGE_NAME=piPipes
• export 'CONTACT_EMAILS=ESC[[email protected][0m'
• CONTACT_EMAILS='ESC[[email protected][0m'
  +++ readlink -f /mnt/isilon/wang_lab/caiyou/piPipes/piPipes.sh
  ++ dirname /mnt/isilon/wang_lab/caiyou/piPipes/piPipes.sh
• export PIPELINE_DIRECTORY=/mnt/isilon/wang_lab/caiyou/piPipes
• PIPELINE_DIRECTORY=/mnt/isilon/wang_lab/caiyou/piPipes
• export PATH=/mnt/isilon/wang_lab/caiyou/piPipes/bin:/home/caiy1/mirdeep2_patch:/home/caiy1/.linuxbrew/bin:/home/caiy1/.linuxbrew/sbin:/home/caiy1/.linuxbrew/bin:/home/caiy1/.linuxbrew/sbin:/home/caiy1/mirdeep2_patch:/home/caiy1/mirdeep2_patch:/home/caiy1/software/subread-1.6.0-source/bin:/usr/bin:/mnt/isilon/wang_lab/caiyou/miniconda2/bin:/home/caiy1/software/cbbio-miarma-e1674d108b24/lib/CbBio/RNASeq:/home/caiy1/software/cbbio-miarma-e1674d108b24:/home/caiy1/software/sratoolkit.2.8.2-1-centos_linux64/bin:/cm/shared/apps_chop/R/3.4.1/bin:/cm/shared/apps_chop/bedtools/2.25.0/bin:/cm/local/apps/gcc/6.3.0/bin:/cm/shared/apps/uge/8.5.3/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/opt/dell/srvadmin/bin:/home/caiy1/bin:/home/caiy1/mirdeep2/bin
• PATH=/mnt/isilon/wang_lab/caiyou/piPipes/bin:/home/caiy1/mirdeep2_patch:/home/caiy1/.linuxbrew/bin:/home/caiy1/.linuxbrew/sbin:/home/caiy1/.linuxbrew/bin:/home/caiy1/.linuxbrew/sbin:/home/caiy1/mirdeep2_patch:/home/caiy1/mirdeep2_patch:/home/caiy1/software/subread-1.6.0-source/bin:/usr/bin:/mnt/isilon/wang_lab/caiyou/miniconda2/bin:/home/caiy1/software/cbbio-miarma-e1674d108b24/lib/CbBio/RNASeq:/home/caiy1/software/cbbio-miarma-e1674d108b24:/home/caiy1/software/sratoolkit.2.8.2-1-centos_linux64/bin:/cm/shared/apps_chop/R/3.4.1/bin:/cm/shared/apps_chop/bedtools/2.25.0/bin:/cm/local/apps/gcc/6.3.0/bin:/cm/shared/apps/uge/8.5.3/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/sbin:/cm/local/apps/environment-modules/3.2.10/bin:/opt/dell/srvadmin/bin:/home/caiy1/bin:/home/caiy1/mirdeep2/bin
• . /mnt/isilon/wang_lab/caiyou/piPipes/bin/piPipes_bash_functions
  ++ export -f echo2
  ++ export -f checkBin
  .............

There are so many sentences difficult to understand in debug.stderr.

[yfu]

You can attach a file directly here, by dragging your debug.stderr into the text box. ;-)

[YouCai626]

Okay! Thank you!

But it showed "do not support that file type"

[YouCai626]

Zamore.SRA.ago3_het.ox.ovary.piPipes.stderr.txt
Zamore.SRA.ago3_het.ox.ovary.piPipes.stdout.txt
Zamore.SRA.ago3_het.ox.ovary.piPipes_debug.stderr.txt
Zamore.SRA.ago3_het.ox.ovary.piPipes_debug.stdout.txt

I add .txt after each file.

[YouCai626]

By the way, I can not install package ‘parallel’ in R, because of the version of R. Is this the reason?

[yfu]

Thanks for the files. parallel is on longer necessary as it has been incorporated into R since v2.14.0.

It seems that mapping was done correctly. I am guessing that the binary piPipes_bed2_to_bedGraph does not work correctly in your environment.

@bowhan: Do you have any clues what went wrong with piPipes_bed2_to_bedGraph. Would recompile the program solve the issue? This issue seems to be the same with #28.

[edridgedsouza]

@yfu I am running into the same issue. I am running on a linux cluster but the binary keeps segfaulting. Has anyone figured out a fix for this?

[janoppelt]

I had a similar issue. In my case, the problem was with the pre-compiled binaries. After recompiling from source everything works as it should. The problem main problem was with the Boost library. In my case before recompiling, piPipes_bed2_to_bedGraph failed if used with -p/--thread. It worked fine when I didn't use the -p/--thread. Recompiling is simple, just go to the main piPipes directory and do make. If you see any error that's the thing most likely causing the error.