Segmentation Fault

[yoyosef]

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Hello,

I got this error while running RUFUS, I haven't had this problem before with any of my previous runs. I've run it around 7 times.

/net/apps/x86_64/RUFUS/scripts/Overlap.sh: line 92: 19299 Segmentation fault (core dumped) $OverlapRebion2 ./TempOverlap/$NameStub.3.fastqd .98 50 2 ./TempOverlap/$NameStub.4 $NameStub 1 $Threads > /dev/null

On a separate line:

starst with /net/apps/x86_64/RUFUS/scripts/Overlap.sh: line 216: 19105 Done samtools view ./$NameStub.overlap.hashcount.fastq.bam 19106 Segmentation fault (core dumped) | $RUFUSinterpret -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 8 -r $humanRef -hf $HashList -o ./$NameStub.overlap.hashcount.fastq.bam -m 1000000 $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash 8578338.55user 4592.68system 72:19:52elapsed 3296%CPU (0avgtext+0avgdata 41707244maxresident)k

Thank you,

Yosef

[jandrewrfarrell]

Thanks for letting me know about this. Rufus interpret is segfaulting because it’s not getting any input from OverlapRegion2. Its on the list of exceptions to handle when things go wrong that I haven’t fixed yet. Can you check that Overlap assembled contigs? Can you send me an “ls -l” of TempOverlap for that run and the full output.

================================= Andrew Farrell PhD
Director of Research and Science Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine​ 15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330
Email: [email protected] http://marthlab.org/

On Jul 29, 2019, at 7:38 PM, Yosef [email protected] wrote:

Hello,

I got this error while running RUFUS, I haven't had this problem before with any of my previous runs. I've run it around 7 times.

/net/apps/x86_64/RUFUS/scripts/Overlap.sh: line 92: 19299 Segmentation fault (core dumped) $OverlapRebion2 ./TempOverlap/$NameStub.3.fastqd .98 50 2 ./TempOverlap/$NameStub.4 $NameStub 1 $Threads > /dev/null

On a separate line:

starst with /net/apps/x86_64/RUFUS/scripts/Overlap.sh: line 216: 19105 Done samtools view ./$NameStub.overlap.hashcount.fastq.bam 19106 Segmentation fault (core dumped) | $RUFUSinterpret -mod Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -mQ 8 -r $humanRef -hf $HashList -o ./$NameStub.overlap.hashcount.fastq.bam -m 1000000 $(echo $parentCRString) -sR Intermediates/$NameStub.overlap.asembly.hash.fastq.Ref.sample -s Intermediates/$NameStub.overlap.asembly.hash.fastq.sample -e ./Intermediates/$NameStub.ref.RepRefHash 8578338.55user 4592.68system 72:19:52elapsed 3296%CPU (0avgtext+0avgdata 41707244maxresident)k

Thank you,

Yosef

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[yoyosef]

total 7041192 -rw-rw-r-- 1 username pgm 604500418 Jul 25 06:17 bgm0388a1.hg19.bam.generator.V2.1.fastq -rw-rw-r-- 1 username pgm 0 Jul 25 01:28 bgm0388a1.hg19.bam.generator.V2.1.fastqbad.fastq -rw-rw-r-- 1 username pgm 1390732711 Jul 25 06:17 bgm0388a1.hg19.bam.generator.V2.1.fastqd -rw-rw-r-- 1 username pgm 0 Jul 25 01:28 bgm0388a1.hg19.bam.generator.V2.1.fastqgood.fastq -rw-rw-r-- 1 username pgm 544231236 Jul 25 12:35 bgm0388a1.hg19.bam.generator.V2.2.fastq -rw-rw-r-- 1 username pgm 0 Jul 25 06:17 bgm0388a1.hg19.bam.generator.V2.2.fastqbad.fastq -rw-rw-r-- 1 username pgm 1274713185 Jul 25 12:35 bgm0388a1.hg19.bam.generator.V2.2.fastqd -rw-rw-r-- 1 username pgm 0 Jul 25 06:17 bgm0388a1.hg19.bam.generator.V2.2.fastqgood.fastq -rw-rw-r-- 1 username pgm 1274713185 Jul 25 12:41 bgm0388a1.hg19.bam.generator.V2.3.fastqd -rw-rw-r-- 1 username pgm 0 Jul 25 12:41 bgm0388a1.hg19.bam.generator.V2.4.fastq -rw-rw-r-- 1 username pgm 0 Jul 25 12:41 bgm0388a1.hg19.bam.generator.V2.4.fastqd -rw-rw-r-- 1 username pgm 0 Jul 27 13:10 bgm0388a1.hg19.bam.generator.V2.5.fastq -rw-rw-r-- 1 username pgm 0 Jul 27 13:10 bgm0388a1.hg19.bam.generator.V2.5.fastqd -rw-rw-r-- 1 username pgm 0 Jul 27 13:10 bgm0388a1.hg19.bam.generator.V2.overlap.asembly.hash.fastq -rw-rw-r-- 1 username pgm 0 Jul 27 13:21 bgm0388a1.hg19.bam.generator.V2.overlap.hashcount.fastq.bam.vcf.Big.bed -rw-rw-r-- 1 username pgm 0 Jul 27 13:21 bgm0388a1.hg19.bam.generator.V2.overlap.hashcount.fastq.bam.vcf.invertions.bed -rw-rw-r-- 1 username pgm 0 Jul 27 13:21 bgm0388a1.hg19.bam.generator.V2.overlap.hashcount.fastq.bam.vcf.NotHandled.bed -rw-rw-r-- 1 username pgm 0 Jul 27 13:21 bgm0388a1.hg19.bam.generator.V2.overlap.hashcount.fastq.bam.vcf.Translocations -rw-rw-r-- 1 username pgm 0 Jul 27 13:21 bgm0388a1.hg19.bam.generator.V2.overlap.hashcount.fastq.bam.vcf.Translocations.bed -rw-rw-r-- 1 username pgm 0 Jul 27 13:21 bgm0388a1.hg19.bam.generator.V2.overlap.hashcount.fastq.bamvcf.Unaligned -rw-rw-r-- 1 username pgm 658511796 Jul 25 01:28 bgm0388a1.hg19.bam.generator.V2.sam.fastq -rw-rw-r-- 1 username pgm 1462732060 Jul 25 01:28 bgm0388a1.hg19.bam.generator.V2.sam.fastqd

Thanks,

Yosef