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Old 02-12-2013, 05:00 AM   #1
Junior Member
Location: Germany

Join Date: Nov 2008
Posts: 5
Default Pindel Segmentation fault with -Q

I got Segmentation fault when using -Q. Have any idea about this?
Everything works fine if not using -Q.

there is what I got:

pindel -f $REF -i config_foo.txt -c chr8 -o pdel.out.chr8 -b foo.bkd -Q confirmed.chr8

Pindel version 0.2.4t, August 13 2012.
BreakDancer events: 22908
Processing chromosome: chr1
Skipping chromosome: chr1
Processing chromosome: chr2
Skipping chromosome: chr2
Processing chromosome: chr3
Skipping chromosome: chr3
Processing chromosome: chr4
Skipping chromosome: chr4
Processing chromosome: chr5
Skipping chromosome: chr5
Processing chromosome: chr6
Skipping chromosome: chr6
Processing chromosome: chr7
Skipping chromosome: chr7
Processing chromosome: chr8
Chromosome Size: 175793759
NumBoxes: 60005 BoxSize: 6526

Looking at chromosome chr8 bases 0 to 10000000.
Possible translocation from chromosome chr8 to chromosome chr1

getReads chr8 195793759
Insertsize in bamreads: 295
Number of reads in current window: 127044, + 63457 - 63587
Number of reads where the close end could be mapped: 33926, + 16994 - 16918
Percentage of reads which could be mapped: + 26.78% - 26.61%

BAM file index 0 33926
There are 33926 reads for this chromosome region.
Far end searching completed for this window.
Reads already used: 0
Far ends already mapped 22423
Checksum of far ends: 76402982
Searching some type of variant, replace this with the correct name in child class ...
Total: 6336 +3243 -3093
Sorting and outputing deletions ...
Segmentation fault

Last edited by schönblick; 02-12-2013 at 05:02 AM.
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Old 02-18-2013, 06:13 AM   #2
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Location: amsterdam

Join Date: Jun 2009
Posts: 133

An internal data structure was notified but not all modules have been updated for it. sorry for the inconvenience. We are working on this.

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