View Single Post
Old 04-23-2012, 11:02 AM   #2
Kcornelius
Member
 
Location: Los Angeles

Join Date: Apr 2012
Posts: 14
Default no luck with cuffdiff either

So, when using cuffdiff and say :

cuffdiff -N -o diff_out -p 1 -L C1,C2 -u Homo_sapiens.GRCh37.62.gtf ~/s_1_sequence_gtf_tophat_accepted_hits.bam ~/s_2_sequence_gtf_tophat_accepted_hits.bam

I got the error:
[11:29:30] Loading reference annotation.
/opt/sge-6_2u4/default/spool/sunnode30/job_scripts/86547: line 12: 16032 Segmentation fault (core dumped) cuffdiff -N -o diff_out -p $NSLOTS -L C1,C2 -u Homo_sapiens.GRCh37.62.filter1.sorted3.gtf ~/s_1_sequence_gtf_tophat_accepted_hits.bam ~/s_2_sequence_gtf_tophat_accepted_hits.bam

For some reasons, the problem always points down to my reference. Funny enough, when I leave out chrX chrY and chrM, it is running beyond the Loading reference step and probably cuffmerge would as well.
Could anyone provide me a reference for human, which worked, given that your bowtie index is:
bowtie-inspect hg19 --names
chr1
chr2
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr20
chr21
chr22
chrX
chrY
chrM

Marc
Kcornelius is offline   Reply With Quote