Cufflinks Run Error

Question

[Rm]

I have below cufflinks error message? Any suggestions to overmome this Thanks:

Cufflinks options used:

/tools/cufflinks-1.2.1.Linux_x86_64/cufflinks  --verbose --total-hits-norm --no-update-check --max-intron-length 300000 --min-isoform-fraction 0.15 --junc-alpha 0.001 --small-anchor-fraction 0.12 --pre-mrna-fraction 0.05 --num-threads 8 --label CUFFLI --num-importance-samples 1000 --max-mle-iterations 5000 --library-type fr-unstranded --min-frags-per-transfrag 10 --overhang-tolerance 8 --max-bundle-length 3500000 --trim-3-avgcov-thresh 10 --trim-3-dropoff-frac 0.1 --3-overhang-tolerance 600 --intron-overhang-tolerance 30 --frag-len-mean 285 --frag-len-std-dev 250 /tophat/accepted_hits.bam

Error message:

...
...
Inspecting bundle Y:59028562-59028929 with 23 reads
Inspecting bundle Y:59030375-59030571 with 2 reads
Inspecting bundle Y:59031182-59031502 with 11 reads
Bad intron table has 837 introns: (14928 alloc'd, 10044 used)
Map has 2601383 hits, 2187638 are non-redundant
Processed 260139 loci.                      
*** glibc detected *** /tools/cufflinks-1.2.1.Linux_x86_64/cufflinks: malloc(): memory corruption: 0x0000000002801510 ***
======= Backtrace: =========
/lib64/libc.so.6[0x35eb2730fe]
/lib64/libc.so.6(__libc_malloc+0x6e)[0x35eb274e2e]
/tools/cufflinks-1.2.1.Linux_x86_64/cufflinks[0x5a00fe]
/tools/cufflinks-1.2.1.Linux_x86_64/cufflinks[0x42e850]
/tools/cufflinks-1.2.1.Linux_x86_64/cufflinks[0x4134d5]
/tools/cufflinks-1.2.1.Linux_x86_64/cufflinks[0x41465e]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x35eb21d994]
/tools/cufflinks-1.2.1.Linux_x86_64/cufflinks(sin+0xd1)[0x404cd9]
======= Memory map: ========
00400000-00621000 r-xp 00000000 00:1b 25996492                           /tools/cufflinks-1.2.1.Linux_x86_64/cufflinks
00821000-00823000 rw-p 00221000 00:1b 25996492                           /tools/cufflinks-1.2.1.Linux_x86_64/cufflinks
00823000-02832000 rw-p 00823000 00:00 0                                  [heap]
35eae00000-35eae1c000 r-xp 00000000 fd:01 1063107                        /lib64/ld-2.5.so
35eb01c000-35eb01d000 r--p 0001c000 fd:01 1063107                        /lib64/ld-2.5.so
35eb01d000-35eb01e000 rw-p 0001d000 fd:01 1063107                        /lib64/ld-2.5.so

Answer 1

[ALchEmiXt]

Probably the obvious. Have you tried reinstalling the glibc libraries? They might have corrupted. Otherwise check that the versions match the specifications. Did it work before or is this after some upgrade?

[Rm]

thanks, Same pipeline earlier ran for more than 10 other samples..just failed for this one...

[ALchEmiXt]

Did it fail after processing them in a row or is this particular one larger in size? It could point to a memory leak/bug in cufflinks since the malloc seems to detect a write in memory beyond its allocated space. No clue how to fix it though... Cehck the cufflinks site if anything is known and/or file a bug?!

[Rm]

bam file is small ~2GB. I need to write to th eauthors and see...

Answer 2

[Nick]

Did you get anywhere with this?

[Rm]

@nick: not yet...