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.
Anybody can help me?
"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.
Anybody can help me?