Deleted:Segmentation fault (core dumped) during bwa mem mapping
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16 months ago
chansik ▴ 10


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/".

[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.

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