Segmentation fault (core dumped) during bwa mem mapping
Hi,
I ran bwa mem with trimmed fastq files (ERR2593198) but I saw following error:
bwa mem CHO-PICR.fasta ../2.ngsShort/trimmed_ERR2593198_1.fastq ../2.ngsShort/trimmed_ERR2593198_2.fastq
>[M::bwa_idx_load_from_disk] read 0 ALT contigs
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:../downloads/bwa-0.7.17/bwa mem CHO-PICR.fasta ../2.ngsShort/trimmed_ERR2593198_1.fastq ../2.ngsShort/trimmed_ERR2593198_2.fastq
[M::process] read 92156 sequences (10000179 bp)...
Segmentation fault (core dumped)
To figure out what's happening, I ran gdb and the report was like this:
bwa mem CHO-PICR.fasta ../2.ngsShort/trimmed_ERR2593198_1.fastq ../2.ngsShort/trimmed_ERR2593198_2.fastq
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[New Thread 0x7ffff7c2a700 (LWP 18232)]
[New Thread 0x7ffff7429700 (LWP 18233)]
[M::process] read 92156 sequences (10000179 bp)...
[New Thread 0x7ffff6052700 (LWP 18234)]
Thread 4 "bwa" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ffff6052700 (LWP 18234)]
bwt_2occ4 (bwt=bwt@entry=0x5555555ad6e0, k=18446744073709551615, l=18446744073709551615,
cntk=cntk@entry=0x7ffff6051a70, cntl=cntl@entry=0x7ffff6051a90) at bwt.c:203
203 memcpy(cntk, p, 4 * sizeof(bwtint_t));
------------------------------------------------
(gdb) bt
#0 bwt_2occ4 (bwt=bwt@entry=0x5555555ad6e0, k=18446744073709551615, l=18446744073709551615,
cntk=cntk@entry=0x7ffff6051a70, cntl=cntl@entry=0x7ffff6051a90) at bwt.c:203
#1 0x000055555557a56b in bwt_extend (bwt=bwt@entry=0x5555555ad6e0,
ik=ik@entry=0x7ffff6051b50, ok=ok@entry=0x7ffff6051ba0, is_back=is_back@entry=0)
at bwt.c:266
#2 0x000055555557a843 in bwt_smem1a (bwt=bwt@entry=0x5555555ad6e0, len=len@entry=96,
q=q@entry=0x7ffff0013900 "\001\003\001", x=x@entry=0, min_intv=min_intv@entry=1,
max_intv=max_intv@entry=0, mem=0x7ffff1e1afd8, tmpvec=0x7ffff1e1aff0) at bwt.c:310
#3 0x000055555557adf6 in bwt_smem1 (bwt=bwt@entry=0x5555555ad6e0, len=len@entry=96,
q=q@entry=0x7ffff0013900 "\001\003\001", x=x@entry=0, min_intv=min_intv@entry=1,
mem=mem@entry=0x7ffff1e1afd8, tmpvec=0x7ffff1e1aff0) at bwt.c:355
#4 0x00005555555819fd in mem_collect_intv (a=0x7ffff1e1afc0,
seq=0x7ffff0013900 "\001\003\001", len=96, bwt=0x5555555ad6e0, opt=0x5555555ad3b0)
at bwamem.c:123
#5 mem_chain (opt=opt@entry=0x5555555ad3b0, bwt=0x5555555ad6e0, bns=bns@entry=0x5555555adb50,
len=len@entry=96, seq=seq@entry=0x7ffff0013900 "\001\003\001", buf=0x7ffff1e1afc0)
at bwamem.c:264
#6 0x000055555558fac4 in mem_align1_core (opt=0x5555555ad3b0, bwt=<optimized out>,
bns=0x5555555adb50, pac=0x5555555add90 "", l_seq=96, seq=0x7ffff0013900 "\001\003\001",
buf=0x7ffff1e1afc0) at bwamem.c:1060
#7 0x000055555558fe56 in worker1 (data=0x7ffff7c29cb0, i=<optimized out>, tid=<optimized out>)
at bwamem.c:1181
#8 0x00005555555766ca in ktf_worker (data=0x7ffff7c29bf0) at kthread.c:42
#9 0x00007ffff7e33609 in start_thread (arg=<optimized out>) at pthread_create.c:477
#10 0x00007ffff7d4f293 in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95
Can anyone please help me how to fix this error?
Thank you.
1 answer
The two standard points to check first:
a) google the error message, gives https://github.com/lh3/bwa/issues/181 which suggests a corrupted index. Try to make a short subset of the fastq files (like head -n 40 for each) and run bwa mem manually. This tells you whether the index is ok.
b) check if you have enough memory
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