error of running genomecov

[ymwur]

Hi,

I run the genomecov using the commond line as below:

$ bedtools genomecov -ibam Pp-BWAmemNCBI-90Grmdupl.bam -d > coverage.log

The input bam was generation by using BWA-mem for mapping, picard for sorting and duplicate removing.

Bedtools was runnig for several hours, but after analyzing about 2 million sites (out of 1 billion site), it was corrupted.

I get the error message as below:

*** glibc detected *** bedtools: double free or corruption (out): 0x0000000002597fc0 *** ======= Backtrace: ========= /lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7faa43accb96] bedtools[0x479f57] bedtools[0x47a42d] bedtools[0x47b7ba] bedtools[0x47e909] bedtools[0x406bd5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7faa43a6f76d] bedtools[0x40aff9] ======= Memory map: ======== 00400000-00573000 r-xp 00000000 08:02 44317440 /home/joinet/bin/bedtools 00772000-00774000 r--p 00172000 08:02 44317440 /home/joinet/bin/bedtools 00774000-00775000 rw-p 00174000 08:02 44317440 /home/joinet/bin/bedtools 00775000-00776000 rw-p 00000000 00:00 0 01fe1000-0436e000 rw-p 00000000 00:00 0 [heap] 7faa438fa000-7faa439bc000 rw-p 00000000 00:00 0 7faa43a4e000-7faa43c03000 r-xp 00000000 08:02 41943289 /lib/x86_64-linux-gnu/libc-2.15.so 7faa43c03000-7faa43e02000 ---p 001b5000 08:02 41943289 /lib/x86_64-linux-gnu/libc-2.15.so 7faa43e02000-7faa43e06000 r--p 001b4000 08:02 41943289 /lib/x86_64-linux-gnu/libc-2.15.so 7faa43e06000-7faa43e08000 rw-p 001b8000 08:02 41943289 /lib/x86_64-linux-gnu/libc-2.15.so 7faa43e08000-7faa43e0d000 rw-p 00000000 00:00 0 7faa43e0d000-7faa43e22000 r-xp 00000000 08:02 41946637 /lib/x86_64-linux-gnu/libgcc_s.so.1 7faa43e22000-7faa44021000 ---p 00015000 08:02 41946637 /lib/x86_64-linux-gnu/libgcc_s.so.1 7faa44021000-7faa44022000 r--p 00014000 08:02 41946637 /lib/x86_64-linux-gnu/libgcc_s.so.1 7faa44022000-7faa44023000 rw-p 00015000 08:02 41946637 /lib/x86_64-linux-gnu/libgcc_s.so.1 7faa44023000-7faa4411e000 r-xp 00000000 08:02 41943305 /lib/x86_64-linux-gnu/libm-2.15.so 7faa4411e000-7faa4431d000 ---p 000fb000 08:02 41943305 /lib/x86_64-linux-gnu/libm-2.15.so 7faa4431d000-7faa4431e000 r--p 000fa000 08:02 41943305 /lib/x86_64-linux-gnu/libm-2.15.so 7faa4431e000-7faa4431f000 rw-p 000fb000 08:02 41943305 /lib/x86_64-linux-gnu/libm-2.15.so 7faa4431f000-7faa44401000 r-xp 00000000 08:02 16260627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7faa44401000-7faa44600000 ---p 000e2000 08:02 16260627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7faa44600000-7faa44608000 r--p 000e1000 08:02 16260627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7faa44608000-7faa4460a000 rw-p 000e9000 08:02 16260627 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.16 7faa4460a000-7faa4461f000 rw-p 00000000 00:00 0 7faa4461f000-7faa44635000 r-xp 00000000 08:02 41946727 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7faa44635000-7faa44834000 ---p 00016000 08:02 41946727 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7faa44834000-7faa44835000 r--p 00015000 08:02 41946727 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7faa44835000-7faa44836000 rw-p 00016000 08:02 41946727 /lib/x86_64-linux-gnu/libz.so.1.2.3.4 7faa44836000-7faa44858000 r-xp 00000000 08:02 41943317 /lib/x86_64-linux-gnu/ld-2.15.so 7faa44a3c000-7faa44a41000 rw-p 00000000 00:00 0 7faa44a54000-7faa44a58000 rw-p 00000000 00:00 0 7faa44a58000-7faa44a59000 r--p 00022000 08:02 41943317 /lib/x86_64-linux-gnu/ld-2.15.so 7faa44a59000-7faa44a5b000 rw-p 00023000 08:02 41943317 /lib/x86_64-linux-gnu/ld-2.15.so 7fff7dad1000-7fff7daf2000 rw-p 00000000 00:00 0 [stack] 7fff7dbc8000-7fff7dbc9000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] core dumped

What could be the problem?

Thank you,

Chih