Hi
I'd like to use bwa alignment tool for aligning SOLiD color space reads (SREK)onto reference sequences (human miRNAs).
After converting the csfasta und qual files to fastq by using solid2fastq that was provided in the bwa-software, I have run bwa aln but got a segmentation fault. The fastq files contains 15'643'846 reads. When I use gdb, I got the following output:
[SREK] gdb /apps/bi/bwa-0.5.7/bwa
GNU gdb Red Hat Linux (6.3.0.0-1.153.el4_6.2rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...Using host libthread_db library "/lib64/tls/libthread_db.so.1".
(gdb) run aln -n 2 -c /data/hum_miRNA2DNA.fa 6A1_T.single.fastq.gz > test.sai
Starting program: /apps/bi/bwa-0.5.7/bwa aln -n 2 -c /data/hum_miRNA2DNA.fa 6A1_T.single.fastq.gz > test.sai
[Thread debugging using libthread_db enabled]
[New Thread 182894247456 (LWP 30893)]
[bwa_aln_core] calculate SA coordinate... 5.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.55 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 4.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 6.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_aln_core] calculate SA coordinate...
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 182894247456 (LWP 30893)]
0x00000000004038f6 in bwt_cal_width (rbwt=0x532a20, len=0, str=0x532ec0 "", width=0x0) at bwtaln.c:76
76 bwtaln.c: No such file or directory.
in bwtaln.c
(gdb)
Source code from bwtaln.c :
####################
// width must be filled as zero
static int bwt_cal_width(const bwt_t *rbwt, int len, const ubyte_t *str, bwt_width_t *width)
{
bwtint_t k, l, ok, ol;
int i, bid;
bid = 0;
k = 0; l = rbwt->seq_len;
for (i = 0; i < len; ++i) {
ubyte_t c = str[i];
if (c < 4) {
bwt_2occ(rbwt, k - 1, l, c, &ok, &ol);
k = rbwt->L2[c] + ok + 1;
l = rbwt->L2[c] + ol;
}
if (k > l || c > 3) { // then restart
k = 0;
l = rbwt->seq_len;
++bid;
}
width[i].w = l - k + 1;
width[i].bid = bid;
}
width[len].w = 0;
width[len].bid = ++bid; // ###### line 76 #####
return bid;
}
I have no clue how to solve the problem.
Any help is greatly appreciated!
Many thanks!
I'd like to use bwa alignment tool for aligning SOLiD color space reads (SREK)onto reference sequences (human miRNAs).
After converting the csfasta und qual files to fastq by using solid2fastq that was provided in the bwa-software, I have run bwa aln but got a segmentation fault. The fastq files contains 15'643'846 reads. When I use gdb, I got the following output:
[SREK] gdb /apps/bi/bwa-0.5.7/bwa
GNU gdb Red Hat Linux (6.3.0.0-1.153.el4_6.2rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu"...Using host libthread_db library "/lib64/tls/libthread_db.so.1".
(gdb) run aln -n 2 -c /data/hum_miRNA2DNA.fa 6A1_T.single.fastq.gz > test.sai
Starting program: /apps/bi/bwa-0.5.7/bwa aln -n 2 -c /data/hum_miRNA2DNA.fa 6A1_T.single.fastq.gz > test.sai
[Thread debugging using libthread_db enabled]
[New Thread 182894247456 (LWP 30893)]
[bwa_aln_core] calculate SA coordinate... 5.42 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.55 sec
[bwa_aln_core] write to the disk... 0.02 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.83 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 4.93 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.62 sec
[bwa_aln_core] write to the disk... 0.04 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 6.11 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1572864 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 5.84 sec
[bwa_aln_core] write to the disk... 0.03 sec
[bwa_aln_core] 1835008 sequences have been processed.
[bwa_aln_core] calculate SA coordinate...
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 182894247456 (LWP 30893)]
0x00000000004038f6 in bwt_cal_width (rbwt=0x532a20, len=0, str=0x532ec0 "", width=0x0) at bwtaln.c:76
76 bwtaln.c: No such file or directory.
in bwtaln.c
(gdb)
Source code from bwtaln.c :
####################
// width must be filled as zero
static int bwt_cal_width(const bwt_t *rbwt, int len, const ubyte_t *str, bwt_width_t *width)
{
bwtint_t k, l, ok, ol;
int i, bid;
bid = 0;
k = 0; l = rbwt->seq_len;
for (i = 0; i < len; ++i) {
ubyte_t c = str[i];
if (c < 4) {
bwt_2occ(rbwt, k - 1, l, c, &ok, &ol);
k = rbwt->L2[c] + ok + 1;
l = rbwt->L2[c] + ol;
}
if (k > l || c > 3) { // then restart
k = 0;
l = rbwt->seq_len;
++bid;
}
width[i].w = l - k + 1;
width[i].bid = bid;
}
width[len].w = 0;
width[len].bid = ++bid; // ###### line 76 #####
return bid;
}
I have no clue how to solve the problem.
Any help is greatly appreciated!
Many thanks!
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