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 ----------------------------------------