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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