cufflinks error when processing locus

[Wallysb01]

Hi all,

So, I'm using cufflinks and give the command:

cufflinks -G Anolis_carolinensis.AnoCar2.0.61.gtf -r Anocarol2.0.61_toplevel.fa -o LANE1 LANE1/accepted_hits.bam

and I get a lot of warnings that cufflinks appears to handle, such as this:

GFF warning: merging adjacent/overlapping segments of ENSACAT00000023691 on AAWZ02035238 (15000-15041, 15044-16366)
GFF warning: merging adjacent/overlapping segments of ENSACAT00000009897 on AAWZ02035329 (27491-27562, 27565-27681)
GFF warning: merging adjacent/overlapping segments of ENSACAT00000000397 on AAWZ02035620 (33975-34634, 34637-35002)
GFF warning: merging adjacent/overlapping segments of ENSACAT00000025872 on AAWZ02035752 (26868-26957, 26960-27124)
GFF warning: merging adjacent/overlapping segments of ENSACAT00000001792 on AAWZ02035788 (5904-6164, 6167-7459)
GFF warning: merging adjacent/overlapping segments of ENSACAT00000002744 on AAWZ02035903 (34948-34986, 34989-35075)
GFF warning: merging adjacent/overlapping segments of ENSACAT00000011558 on AAWZ02036422 (20764-21103, 21108-21185)

Then I get through the inspecting reads part ok, however, I run into problems when it starts learning bias parameter giving me this:


[16:36:17] Learning bias parameters.
> Processing Locus AAWZ02037236:2088-2610 [************ ] 50%terminate called after throwing an instance of 'std::bad_alloc'
what(): St9bad_alloc
Aborted

Does anyone have some ideas?

Should I take out the reference genome?

[sciencewu]

I also encounter this problem, anybody has some suggestion?