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Old 06-03-2011, 09:18 AM   #1
biterbilen
Junior Member
 
Location: Basel

Join Date: Jun 2009
Posts: 6
Default bug in memory allocation in cuffdiff with bias correction

Hi,

I am using precompiled cuffdiff of version 1.0.3 for linux.

The following command runs wo problems.

cuffdiff --no-update-check -q -M maskfile.12051 -N -u -p 8 -o Cuffdiff merged_asm/merged.gtf TopHat_RepA/accepted_hits.sorted.sam TopHat_RepB/accepted_hits.sorted.sam

But when I set the bias correction option and run

cuffdiff --no-update-check -q -M maskfile.12051 -b hg18_chr19.fa -N -u -p 8 -o Cuffdiff merged_asm/merged.gtf TopHat_RepA/accepted_hits.sorted.sam TopHat_RepB/accepted_hits.sorted.sam

I get the following memory map problem:

cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff)
[bam_header_read] EOF marker is absent.
File TopHat_RepA/accepted_hits.sorted.sam doesn't appear to be a valid BAM file, trying SAM...
[bam_header_read] EOF marker is absent.
File TopHat_RepB/accepted_hits.sorted.sam doesn't appear to be a valid BAM file, trying SAM...
[18:57:27] Loading reference annotation and sequence.
Warning: couldn't find fasta record for 'chr1'!
This contig will not be bias corrected.
*** glibc detected *** cuffdiff: munmap_chunk(): invalid pointer: 0x0000000009078e88 ***
======= Backtrace: =========
/lib64/libc.so.6(cfree+0x166)[0x3e33472886]
cuffdiff[0x4e62ec]
cuffdiff[0x46ffdf]
cuffdiff[0x40a74a]
cuffdiff[0x4118e8]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x3e3341d994]
cuffdiff(sin+0xc9)[0x404c29]
======= Memory map: ========
00400000-005de000 r-xp 00000000 00:1b 54890239 /import/bc2/home/zavolan/bilebi00/bsoft/cufflinks-1.0.3.Linux_x86_64/bin/cuffdiff
007dd000-007df000 rw-p 001dd000 00:1b 54890239 /import/bc2/home/zavolan/bilebi00/bsoft/cufflinks-1.0.3.Linux_x86_64/bin/cuffdiff
007df000-007ff000 rw-p 007df000 00:00 0
09078000-121b7000 rw-p 09078000 00:00 0
3e33000000-3e3301c000 r-xp 00000000 08:09 753694 /lib64/ld-2.5.so
3e3321b000-3e3321c000 r--p 0001b000 08:09 753694 /lib64/ld-2.5.so
3e3321c000-3e3321d000 rw-p 0001c000 08:09 753694 /lib64/ld-2.5.so

Did anyone experience this problem before?

Biter

PS: The bias correction works for cufflinks.
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