Repeated core dumps with cuffdiff

[shurjo]

Dear Cufflinks user community,

I am repeatedly getting a segmentation fault with core dumping while running cuffdiff with the following parameters:

~sensh/bin/cuffdiff -b /home/sensh/bin/bowtie-0.12.7/indexes/hg18_inclusive.fa -M /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/ribosomal_RNA.filter.gtf -N -p 4 -u -v ./merged.gtf <replicates for group 1> <replicates for group 2>

The naming convention bug in cuffdiff previously discussed in this forum is unlikely to the cause for the segfault (cuffdiff still crashes when the default setting is used). The error log (pasted below) indicates that cuffdiff was processing roughly the same region on chr2 when the segfault happened for all my runs.

Has anyone else faced this problem? Or, to be optimistic, does anyone have a solution to suggest? While I have nothing but admiration for the team producing TopHat/Cufflinks, the number of bugs seems directly proportional to the added features in every new version.

Any help will be deeply appreciated,

Shurjo

[sensh@kirk cuffdiff]$ tail sh.cuffdiff.e769224 sh.cuffdiff.e768889 sh.cuffdiff.e767724
==> sh.cuffdiff.e769224 <==
Importance sampling posterior distribution
Warning: restimation failed, importance samples have zero weight.
        Resorting to MLE and observed Fisher
Testing for differential expression and regulation in locus [chr2:200878848-201055231]

Reduced 3881 frags to 105 (2.705488 percent)
Calculating intial MLE
Tossing likely garbage isoforms
Importance sampling posterior distribution
/opt/gridengine/default/Federation/spool/execd/kr03n25/job_scripts/769224: line 3: 12223 Segmentation fault      (core dumped) ~sensh/bin/cuffdiff -b /home/sensh/bin/bowtie-0.12.7/indexes/hg18_inclusive.fa -M /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/ribosomal_RNA.filter.gtf -N -p 4 -u -v /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/cuffmerge/merged_asm/merged.gtf 198564.LCL.PE51.tophat.bam,165583.LCL.PE51.tophat.bam,163383.LCL.PE51.tophat.bam,121424.LCL.PE51.tophat.bam,108971.LCL.PE51.tophat.bam,189793.LCL.PE51.tophat.bam,132306.LCL.PE51.tophat.bam,158592.LCL.PE51.tophat.bam 119657.LCL.PE51.tophat.bam,133237.LCL.PE51.tophat.bam,118655.LCL.PE51.tophat.bam,112916.LCL.PE51.tophat.bam,116099.LCL.PE51.tophat.bam,113235.LCL.PE51.tophat.bam,119522.LCL.PE51.tophat.bam

==> sh.cuffdiff.e768889 <==
Importance sampling posterior distribution
Warning: restimation failed, importance samples have zero weight.
        Resorting to MLE and observed Fisher
Testing for differential expression and regulation in locus [chr2:200878848-201055231]

Reduced 3881 frags to 105 (2.705488 percent)
Calculating intial MLE
Tossing likely garbage isoforms
Importance sampling posterior distribution
/opt/gridengine/default/Federation/spool/execd/kr03n24/job_scripts/768889: line 3: 27415 Segmentation fault      (core dumped) ~sensh/bin/cuffdiff -b /home/sensh/bin/bowtie-0.12.7/indexes/hg18_inclusive.fa -M /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/ribosomal_RNA.filter.gtf -N -o LCL15.riboF.cufflinks.1.0.2.cuffdiff -p 4 -u -v /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/cuffmerge/merged_asm/merged.gtf 198564.LCL.PE51.tophat.bam,165583.LCL.PE51.tophat.bam,163383.LCL.PE51.tophat.bam,121424.LCL.PE51.tophat.bam,108971.LCL.PE51.tophat.bam,189793.LCL.PE51.tophat.bam,132306.LCL.PE51.tophat.bam,158592.LCL.PE51.tophat.bam 119657.LCL.PE51.tophat.bam,133237.LCL.PE51.tophat.bam,118655.LCL.PE51.tophat.bam,112916.LCL.PE51.tophat.bam,116099.LCL.PE51.tophat.bam,113235.LCL.PE51.tophat.bam,119522.LCL.PE51.tophat.bam

==> sh.cuffdiff.e767724 <==
Tossing likely garbage isoforms
Importance sampling posterior distribution

Reduced 4907 frags to 1670 (34.033014 percent)
Calculating intial MLE
Convergence reached in 75 iterations
Tossing likely garbage isoforms
Importance sampling posterior distribution
Testing for differential expression and regulation in locus [chr2:200501878-200537090]
/opt/gridengine/default/Federation/spool/execd/kr03n15/job_scripts/767724: line 3: 19106 Segmentation fault      (core dumped) ~sensh/bin/cuffdiff -b /home/sensh/bin/bowtie-0.12.7/indexes/hg18_inclusive.fa --emit-count-tables -M /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/ribosomal_RNA.filter.gtf -N -o LCL15.riboF.cufflinks.1.0.2.cuffdiff -p 4 -u -v /home/sensh/expressseq/expressseq_ifs/cufflinks_LCL_PE/cuffmerge/merged_asm/merged.gtf 198564.LCL.PE51.tophat.bam,165583.LCL.PE51.tophat.bam,163383.LCL.PE51.tophat.bam,121424.LCL.PE51.tophat.bam,108971.LCL.PE51.tophat.bam,189793.LCL.PE51.tophat.bam,132306.LCL.PE51.tophat.bam,158592.LCL.PE51.tophat.bam 119657.LCL.PE51.tophat.bam,133237.LCL.PE51.tophat.bam,118655.LCL.PE51.tophat.bam,112916.LCL.PE51.tophat.bam,116099.LCL.PE51.tophat.bam,113235.LCL.PE51.tophat.bam,119522.LCL.PE51.tophat.bam

[shurjo]

Update: there is no segfault when cuffdiff is run without any options (just the merged GTF and the BAM files. This combination of options is still trigerring the error: -b -M -N -v . Trying 1.0.3 now.

Update: segfault persists with v.1.0.3