Question: Error In Running Cuffcompare
0
vasu punj • 360 wrote:
I get the error message run Cuff compare with Cufflinks- GTF file and
Ensembl file downloaded to Galaxy. To download Ensembl file Is used
following procedure:
Get Data --> UCSC Main
select clade/genome/assembly
for group, use 'Genes and Gene Prediction Tracks'
for track, use Ensembl
for table, choose the default (enGene)
region: genome
output format: GTF
The error message is:Error in cuffcompare:
[Errno 2] No such file or directory: '/tmp/9935868.hpc-
pbs.usc.edu/tmpGXnESn/input1.tmap'
Begin PBS Prologue Thu Dec 23 16:29:09 PST 2010
Job ID: 9935868.hpc-pbs.usc.edu
Username: ramjan
Group: hsc-ar
Name: 84_cuffcompare_ramjan@usc.edu
Queue: laird
Shared Access: yes
Nodes: hpc2712
TMPDIR: /tmp/9935868.hpc-pbs.usc.edu
End PBS Prologue Thu Dec 23 16:29:09 PST 2010
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
Begin PBS Epilogue Thu Dec 23 16:29:21 PST 2010
Job ID: 9935868.hpc-pbs.usc.edu
Username: ramjan
Group: hsc-ar
Job Name: 84_cuffcompare_ramjan@usc.edu
Session: 29712
Limits: neednodes=1:ppn=8,nodes=1:ppn=8,walltime=100:00:00
Resources:
cput=00:00:09,mem=62512kb,vmem=288372kb,walltime=00:00:12
Queue: laird
End PBS Epilogue Thu Dec 23 16:29:21 PST 2010
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modified 7.9 years ago
by
Nate Coraor ♦ 3.2k
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written
7.9 years ago by
vasu punj • 360
