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Old 10-25-2009, 05:02 PM   #1
drio
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Default aligning solid data with bwa -- Seg Fault

I am trying to align some SOLiD data with bwa and there are two reads
that cause bwa to crash:

Code:
@1_10_531
T.11011..010..31...20..300..301.00.0.30...200..0...
+
"7=<<8"":8:""28"""&%""62$""))&"%6"2"10"""7,1""#"""
@1_10_536
T.01300.3100..00...12..0000.000.0030.010.0300..0...
+
"77+03"9/,4""&4"""&+""1:)9"&)/"67&5">5'",5*2""="""
I am using bwa (0.5.4).

The indexing of the reference (human) was created using:

bwa index -a bwtsw -c -p "cs" ./indexes

For the alignment I used:

bwa aln -t 8 -c $ref $reads > aln.fr.solid.sai
bwa samse $ref aln.fr.solid.sai $reads > aln.fr.solid.sam

bwa crashes dumping: 22550 Segmentation fault

The original qualities are:

>1_10_531_F3
-1 22 28 27 27 23 -1 -1 25 23 25 -1 -1 17 23 -1 -1 -1 5 4 -1 -1 21 17 3 -1 -1 8 8 5 -1 4 21 -1 17 -1 16 15 -1 -1 -1 22 11 16 -1 -1 2 -1 -1 -1
>1_10_536_F3
-1 22 22 10 15 18 -1 24 14 11 19 -1 -1 5 19 -1 -1 -1 5 10 -1 -1 16 25 8 24 -1 5 8 14 -1 21 22 5 20 -1 29 20 6 -1 11 20 9 17 -1 -1 28 -1 -1 -1

The original reads:
>1_10_531_F3
T.11011..010..31...20..300..301.00.0.30...200..0...
>1_10_536_F3
T.01300.3100..00...12..0000.000.0030.010.0300..0...
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Old 10-26-2009, 01:15 AM   #2
Chipper
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Default

You need to remove the sign from the quality files (add "s/-//g;" after reading from the quality file in solid2fastq.pl).
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Old 10-26-2009, 04:38 AM   #3
drio
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That's not it. there are other reads with -1 in the quals that bwa process without problems.
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