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Old 03-13-2013, 04:48 AM   #5
simsalabim
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Location: Germany

Join Date: Mar 2013
Posts: 4
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Hi,
I realize this thread is older but I get a similar error message while using bfast for colorspace alignment.

My data consists of colorreads of length 75, dynamically trimmed down to >30 in case of bad sequencing quality. But the majority of reads still has length 75.

When I use the 10 masks from the bfast manual to build 10 (primary) indexes, the alignment works fine. But many of the shorter trimmed reads are not aligned. So I used 10 more masks to build indexes for shorter reads, which I want to use as secondary indexes. They should only be used for unaligned, (= mostly trimmed) reads. Right?
Anyway, when I try to run bfast as follows:
Quote:
bfast match -f $reference -i 1,2,3,4,5,6,7,8,9,10 -I 11,12,13,14,15,16,17,18,19,20 -r $infile -w 0 -n $nc -A 1 -z -t
I receive the error:
Quote:
Copying unmatched reads for secondary index search.
Splitting unmatched reads into temp files.
*** glibc detected *** bfast: double free or corruption (!prev): 0x000000000065f290 ***
I rebuild all indexfiles, but it didn't have any effect.

Is it not possible to use this many indexes? Everything works fine if I only use 10 primary ones... Or doesn't it make sense to use this combination of indexes since bfast is not designed to align reads with variable lengths?

Does anybody have suggestions what I did wrong? Thanks a lot in advance...
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