cufflink 2.0.1 memory problems

[newbietonextgen]

hi

I am using cufflinks 2.0.1 and am getting this error after the re-estimation abundance with bias correction step.


2abe67183000-2abe67383000 rw-p 00000000 00:00 0
2abe67383000-2abe67384000 ---p 00000000 00:00 0
2abe67384000-2abe67584000 rw-p 00000000 00:00 0
2abe6759a000-2abe675b0000 r-xp 00000000 08:02 604349 /lib/libgcc_s.so.1
2abe675b0000-2abe677af000 ---p 00016000 08:02 604349 /lib/libgcc_s.so.1
2abe677af000-2abe677b0000 r--p 00015000 08:02 604349 /lib/libgcc_s.so.1
2abe677b0000-2abe677b1000 rw-p 00016000 08:02 604349 /lib/libgcc_s.so.1
2abe68000000-2abe6c000000 rw-p 00000000 00:00 0
2abe6c000000-2abe70000000 rw-p 00000000 00:00 0
2abe70000000-2abe74000000 rw-p 00000000 00:00 0
2abe74001000-2abe74002000 ---p 00000000 00:00 0
2abe74002000-2abe74202000 rw-p 00000000 00:00 0
2abe74202000-2abe74203000 ---p 00000000 00:00 0
2abe74203000-2abe74403000 rw-p 00000000 00:00 0
2abe78000000-2abe7c000000 rw-p 00000000 00:00 0
2abe7c000000-2abe7ff46000 rw-p 00000000 00:00 0
2abe7ff46000-2abe80000000 ---p 00000000 00:00 0
2abe80000000-2abe80001000 ---p 00000000 00:00 0
2abe80001000-2abe80201000 rw-p 00000000 00:00 0
7fffadde2000-7fffaddf8000 rw-p 00000000 00:00 0 [stack]
7fffaddff000-7fffade00000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted

Has any body encountered it? I am using the pre complied binary on linux. I have tried using the version 1.3.0 and i don't have any problems. Could any body help?

Thanks
sp

[jkorn]

cufflinks 2.0.1 -- same error / aborting

I get the same error; unfortunately I don't have a solution other than to revert to older versions.

Josh

[newbietonextgen]

can one use tophat 2.0.4 and Bowtie 2.0.6 for the initial part and go back to using cufflink 1.3.0?

[jkorn]

cufflinks 2.0.1 errors

I don't see why not...but I haven't tried that. I'm actually using a modified version of tophat 1.3. The input to cufflinks is just a bam file though; the alignment algorithm shouldn't matter (as long as the bam file has the XS tag that cufflinks requires.)