Hi,
I had the bad idea of switching to Cufflinks 2.2.0 and the new format with a sample sheet and a contrasts file. I'm now getting segmentation faults in all my analyses at the testing for differential expression stage. Any clues as to what is wrong with my command, which I've posted below, or if it might be a problem with the program or the cluster?
***
tail cuffdiff.sh_error
> Processing Locus 1:3102015-3102125 [ ] 0%/var/spool/pbs/mom_priv/jobs/15151606.gm-1r16-n04.guillimin.clumeq.ca.SC: line 36: 23285 Segmentation fault (core dumped) cuffdiff --use-sample-sheet -C contrasts.txt -p 12 --library-type fr-firststrand -u -b /sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa -o ../../cuffdiff /sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/Mus_musculus.GRCm38.75.gtf sample_sheet.txt
***
cuffdiff.sh
#PBS -l nodes=1pn=12
#PBS -l walltime=4:00:00:00
#PBS -o ${PBS_JOBNAME}_output
#PBS -e ${PBS_JOBNAME}_error
#PBS -V
#PBS -N cuffdiff.sh
#PBS -q sw
#PBS -m bae
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=12
cuffdiff \
--use-sample-sheet \
-C contrasts.txt \
-p 12 \
--library-type fr-firststrand \
-u -b /sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa \
-o ../../cuffdiff \
/sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/Mus_musculus.GRCm38.75.gtf \
sample_sheet.txt
***
sample_sheet.txt
sample_id group_label
../../tophat/DNAM_NE/accepted_hits.bam DNAM_NE
../../tophat/DNAM_PO/accepted_hits.bam DNAM_PO
***
contrasts.txt
condition_A condition_B
DNAM_NE DNAM_PO
***
cuffdiff.sh_output
----------------------------------------
Begin PBS Prologue Sun Apr 13 08:47:14 EDT 2014 1397393234
Job ID: 15151606.gm-1r16-n04.guillimin.clumeq.ca
Username: blancha
Group: afb-431-01
Nodes: sw-2r15-n32
End PBS Prologue Sun Apr 13 08:47:14 EDT 2014 1397393234
----------------------------------------
----------------------------------------
Begin PBS Epilogue Sun Apr 13 11:12:36 EDT 2014 1397401956
Job ID: 15151606.gm-1r16-n04.guillimin.clumeq.ca
Username: blancha
Group: afb-431-01
Job Name: cuffdiff.sh
Session: 23131
Limits: neednodes=1pn=12,nodes=1pn=12,pmem=2700mb,walltime=96:00:00
Resources: cput=05:11:19,mem=9762812kb,vmem=10809000kb,walltime=02:25:22
Queue: sw-parallel
Account: afb-431-ac
Exit code: 139
Nodes: sw-2r15-n32
Killing leftovers...
End PBS Epilogue Sun Apr 13 11:12:37 EDT 2014 1397401957
***
Thank you for your help,
Alexis
I had the bad idea of switching to Cufflinks 2.2.0 and the new format with a sample sheet and a contrasts file. I'm now getting segmentation faults in all my analyses at the testing for differential expression stage. Any clues as to what is wrong with my command, which I've posted below, or if it might be a problem with the program or the cluster?
***
tail cuffdiff.sh_error
> Processing Locus 1:3102015-3102125 [ ] 0%/var/spool/pbs/mom_priv/jobs/15151606.gm-1r16-n04.guillimin.clumeq.ca.SC: line 36: 23285 Segmentation fault (core dumped) cuffdiff --use-sample-sheet -C contrasts.txt -p 12 --library-type fr-firststrand -u -b /sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa -o ../../cuffdiff /sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/Mus_musculus.GRCm38.75.gtf sample_sheet.txt
***
cuffdiff.sh
#PBS -l nodes=1pn=12
#PBS -l walltime=4:00:00:00
#PBS -o ${PBS_JOBNAME}_output
#PBS -e ${PBS_JOBNAME}_error
#PBS -V
#PBS -N cuffdiff.sh
#PBS -q sw
#PBS -m bae
cd $PBS_O_WORKDIR
export OMP_NUM_THREADS=12
cuffdiff \
--use-sample-sheet \
-C contrasts.txt \
-p 12 \
--library-type fr-firststrand \
-u -b /sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa \
-o ../../cuffdiff \
/sb/project/afb-431/genomes/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/Mus_musculus.GRCm38.75.gtf \
sample_sheet.txt
***
sample_sheet.txt
sample_id group_label
../../tophat/DNAM_NE/accepted_hits.bam DNAM_NE
../../tophat/DNAM_PO/accepted_hits.bam DNAM_PO
***
contrasts.txt
condition_A condition_B
DNAM_NE DNAM_PO
***
cuffdiff.sh_output
----------------------------------------
Begin PBS Prologue Sun Apr 13 08:47:14 EDT 2014 1397393234
Job ID: 15151606.gm-1r16-n04.guillimin.clumeq.ca
Username: blancha
Group: afb-431-01
Nodes: sw-2r15-n32
End PBS Prologue Sun Apr 13 08:47:14 EDT 2014 1397393234
----------------------------------------
----------------------------------------
Begin PBS Epilogue Sun Apr 13 11:12:36 EDT 2014 1397401956
Job ID: 15151606.gm-1r16-n04.guillimin.clumeq.ca
Username: blancha
Group: afb-431-01
Job Name: cuffdiff.sh
Session: 23131
Limits: neednodes=1pn=12,nodes=1pn=12,pmem=2700mb,walltime=96:00:00
Resources: cput=05:11:19,mem=9762812kb,vmem=10809000kb,walltime=02:25:22
Queue: sw-parallel
Account: afb-431-ac
Exit code: 139
Nodes: sw-2r15-n32
Killing leftovers...
End PBS Epilogue Sun Apr 13 11:12:37 EDT 2014 1397401957
***
Thank you for your help,
Alexis
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