Question: Control-FREEC - Segmentation fault (core dumped)
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gravatar for igor
19 months ago by
igor7.1k
United States
igor7.1k wrote:

I am running Control-FREEC. I run into this error:

CG-content printed into ./GC_profile.targetedRegions.cnp
..using GC-content to normalize the control profile
file ./GC_profile.targetedRegions.cnp is read
..will remove all windows with read count in the control less than 50
Warning: control length is not equal to the sample length for chromosome 1
Warning: control length is not equal to the sample length for chromosome 2
Warning: control length is not equal to the sample length for chromosome 3
Warning: control length is not equal to the sample length for chromosome 4
Warning: control length is not equal to the sample length for chromosome 5
Warning: control length is not equal to the sample length for chromosome 6
Warning: control length is not equal to the sample length for chromosome 7
Warning: control length is not equal to the sample length for chromosome 8
Warning: control length is not equal to the sample length for chromosome 9
Warning: control length is not equal to the sample length for chromosome 10
Warning: control length is not equal to the sample length for chromosome 11
Warning: control length is not equal to the sample length for chromosome 12
Warning: control length is not equal to the sample length for chromosome 13
Warning: control length is not equal to the sample length for chromosome 14
Warning: control length is not equal to the sample length for chromosome 15
Warning: control length is not equal to the sample length for chromosome 16
Warning: control length is not equal to the sample length for chromosome 17
Warning: control length is not equal to the sample length for chromosome 18
Warning: control length is not equal to the sample length for chromosome 19
Warning: control length is not equal to the sample length for chromosome 20
Warning: control length is not equal to the sample length for chromosome 21
Warning: control length is not equal to the sample length for chromosome 22
Warning: control length is not equal to the sample length for chromosome X
Segmentation fault (core dumped)

I also tried compiling with a newer version of gcc (6.1 instead of 4.4), which produces a slightly different error message:

Warning: control length is not equal to the sample length for chromosome X
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)

Usually, a core dump happens when there is a memory issue, but it's only 45MB, so that can't be the reason.

If I repeat the analysis, but change from mateFile using BAM files to mateCopyNumberFile using the .cpn files from the failed analysis, the problem goes away:

CG-content printed into ./GC_profile.targetedRegions.cnp
..using GC-content to normalize the control profile
file ./GC_profile.targetedRegions.cnp is read
..will remove all windows with read count in the control less than 50
..will process the control file as well: removing all windows with read count in the control less than 50
..Set ploidy for the control genome equal to 2
..Running FREEC with ploidy set to 2

It's using the same .cpn files for doing that calculation as far as I can tell. Why does it get stuck depending on input? I tried multiple times with the same results.

This is based on the latest Control-FREEC 10.6. I used the same input files for older version 7.2 and that one works.

A similar problem was reported previously:

Unfortunately, those discussions don't actually have a solution posted. Has anyone run into this problem and solved it?

control-freec freec cnv cna • 1.2k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 19 months ago by igor7.1k
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