Hi everyone,
I'm trying to run gsnap programm with paired-end Illumina data. This is the command:
gsnap -D /data/database -d hg19 s_5.1.fastq .s_5.2.fastq -A sam >> s_5__hg19.sam
After two hours of running and 1,000,000 lines in the resulting sam file I get the following error:
========================
Signal received: Segmentation fault
Problem sequence: DD7DT8Q1:4:1101:20988:58254#ACACAA (100 bp)
>DD7DT8Q1:4:1101:20988:58254#ACACAA
GATGAAGGGAGGGATAGAGGGAGAATGGATGAAGGGAGAGTGGATGGATGGATGGGTGTAGGGTGGATGTGTGGAGGGCAGGTCGGAAGAGCACACGCCT
TCCATCCATACATGCACCCTTCATCCATCCATTCATCCACTCTCCCTTCATCCATTCTCCCTCTATCCCTCCCTTCATCAGATCGGAAGAGCGTCGTGTA
/usr/local/gridengine/default/spool/makoshark/job_scripts/225677: line 12: 30062 Aborted (core dumped)
========================
This sequence looks like this:
========================
@DD7DT8Q1:4:1101:20988:58254#ACACAA/1
GATGAAGGGAGGGATAGAGGGAGAATGGATGAAGGGAGAGTGGATGGATGGATGGGTGTAGGGTGGATGTGTGGAGGGCAGGTCGGAAGAGCACACGCCT
+DD7DT8Q1:4:1101:20988:58254#ACACAA/1
c\_b`[ddd`ddd`_`dXddZQcccf^^TeYTTV[cT]`^`a`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
========================
I don't see the problem with this sequence, but anyway gsnap doesn't accept it. Does anyone know what the problem might be?
Thanks in advance,
Irina
I'm trying to run gsnap programm with paired-end Illumina data. This is the command:
gsnap -D /data/database -d hg19 s_5.1.fastq .s_5.2.fastq -A sam >> s_5__hg19.sam
After two hours of running and 1,000,000 lines in the resulting sam file I get the following error:
========================
Signal received: Segmentation fault
Problem sequence: DD7DT8Q1:4:1101:20988:58254#ACACAA (100 bp)
>DD7DT8Q1:4:1101:20988:58254#ACACAA
GATGAAGGGAGGGATAGAGGGAGAATGGATGAAGGGAGAGTGGATGGATGGATGGGTGTAGGGTGGATGTGTGGAGGGCAGGTCGGAAGAGCACACGCCT
TCCATCCATACATGCACCCTTCATCCATCCATTCATCCACTCTCCCTTCATCCATTCTCCCTCTATCCCTCCCTTCATCAGATCGGAAGAGCGTCGTGTA
/usr/local/gridengine/default/spool/makoshark/job_scripts/225677: line 12: 30062 Aborted (core dumped)
========================
This sequence looks like this:
========================
@DD7DT8Q1:4:1101:20988:58254#ACACAA/1
GATGAAGGGAGGGATAGAGGGAGAATGGATGAAGGGAGAGTGGATGGATGGATGGGTGTAGGGTGGATGTGTGGAGGGCAGGTCGGAAGAGCACACGCCT
+DD7DT8Q1:4:1101:20988:58254#ACACAA/1
c\_b`[ddd`ddd`_`dXddZQcccf^^TeYTTV[cT]`^`a`_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
========================
I don't see the problem with this sequence, but anyway gsnap doesn't accept it. Does anyone know what the problem might be?
Thanks in advance,
Irina
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