These days I was analyzing my RNASeq data by cufflinks,then I found some problems when I run cuffdiff.The program always died with "Segmental fault" after runing some time,my command likes below，
"cuffdiff -C pairwise_compare_list -o cuff_diff -p 30 -b genome.fa -u --labels 0.5hDex,0.5hNaCl,2hDex,2hNaCl,0 genome.gtf 0.5hDex/abundances.cxb 0.5hNaCl/abundances.cxb 2hDex/abundances.cxb 2hNaCl/abundances.cxb 0/abundances.cxb".
But cuffdif runned successfulled when I runned with
"cuffdiff -C pairwise_compare_list -o cuff_diff -p 30 -b genome.fa -u --labels 0,0.5hDex,0.5hNaCl,2hDex,2hNaCl genome.gtf 0/abundances.cxb 0.5hDex/abundances.cxb 0.5hNaCl/abundances.cxb 2hDex/abundances.cxb 2hNaCl/abundances.cxb",
the only diff is I changed the labels order. I don't known why.
Does the sample named by interger can't appear at the end of sample labels ？
Even it runned successfulled,when I check results I found that all five comparisons in contrast file "pairwise_compare_list" were done in "genes_exp.diff", but only three comparisons in "isoforms_exp.diff". I don't known why,because everything looks well. I have met this problem befor,too.
Try to allocate the virtual memory and see if it works, might be the bam files are insanely big and the reason it is not being able to work wit the allocated memory. But the label order should be the pointing to the files that are being compared