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Description
Hi,
I got the following error while running bcftools v1.16, v1.15.1, v1.11, trying to genotype a list of given alleles with bcftools mpileup and bcftools call.
*** Error in `/home/zhangh5/work/software/bcftools-1.16/bin/bcftools': corrupted size vs. prev_size: 0x0000000001bc38f0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f474)[0x7f4b8ce47474]
/lib64/libc.so.6(+0x84f24)[0x7f4b8ce4cf24]
/lib64/libc.so.6(realloc+0x1d2)[0x7f4b8ce4de12]
/home/zhangh5/work/software/bcftools-1.16/bin/bcftools(hts_realloc_or_die+0xba)[0x4e9c8a]
/home/zhangh5/work/software/bcftools-1.16/bin/bcftools(mcall+0x105)[0x473d55]
/home/zhangh5/work/software/bcftools-1.16/bin/bcftools(main_vcfcall+0x1d19)[0x4708d9]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7f4b8cdea555]
/home/zhangh5/work/software/bcftools-1.16/bin/bcftools[0x40f3c0]
======= Memory map: ========
00400000-005fc000 r-xp 00000000 00:2b 8940094858 /juno/work/iacobuzc/haochen/software/bcftools-1.16/bin/bcftools
007fc000-007fd000 r--p 001fc000 00:2b 8940094858 /juno/work/iacobuzc/haochen/software/bcftools-1.16/bin/bcftools
007fd000-00806000 rw-p 001fd000 00:2b 8940094858 /juno/work/iacobuzc/haochen/software/bcftools-1.16/bin/bcftools
00806000-00807000 rw-p 00000000 00:00 0
01af3000-01cac000 rw-p 00000000 00:00 0 [heap]
7f4b84000000-7f4b84021000 rw-p 00000000 00:00 0
7f4b84021000-7f4b88000000 ---p 00000000 00:00 0
7f4b893be000-7f4b893d3000 r-xp 00000000 08:02 82 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4b893d3000-7f4b895d2000 ---p 00015000 08:02 82 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4b895d2000-7f4b895d3000 r--p 00014000 08:02 82 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4b895d3000-7f4b895d4000 rw-p 00015000 08:02 82 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f4b895d4000-7f4b895d6000 r-xp 00000000 08:02 3424 /usr/lib64/libfreebl3.so
7f4b895d6000-7f4b897d5000 ---p 00002000 08:02 3424 /usr/lib64/libfreebl3.so
7f4b897d5000-7f4b897d6000 r--p 00001000 08:02 3424 /usr/lib64/libfreebl3.so
7f4b897d6000-7f4b897d7000 rw-p 00002000 08:02 3424 /usr/lib64/libfreebl3.so
7f4b897d7000-7f4b89837000 r-xp 00000000 08:02 3555 /usr/lib64/libpcre.so.1.2.0
7f4b89837000-7f4b89a37000 ---p 00060000 08:02 3555 /usr/lib64/libpcre.so.1.2.0
7f4b89a37000-7f4b89a38000 r--p 00060000 08:02 3555 /usr/lib64/libpcre.so.1.2.0
7f4b89a38000-7f4b89a39000 rw-p 00061000 08:02 3555 /usr/lib64/libpcre.so.1.2.0
7f4b89a39000-7f4b89a41000 r-xp 00000000 08:02 3452 /usr/lib64/libcrypt-2.17.so
7f4b89a41000-7f4b89c40000 ---p 00008000 08:02 3452 /usr/lib64/libcrypt-2.17.so
7f4b89c40000-7f4b89c41000 r--p 00007000 08:02 3452 /usr/lib64/libcrypt-2.17.so
7f4b89c41000-7f4b89c42000 rw-p 00008000 08:02 3452 /usr/lib64/libcrypt-2.17.so
7f4b89c42000-7f4b89c70000 rw-p 00000000 00:00 0
7f4b89c70000-7f4b89c94000 r-xp 00000000 08:02 3565 /usr/lib64/libselinux.so.1
7f4b89c94000-7f4b89e93000 ---p 00024000 08:02 3565 /usr/lib64/libselinux.so.1
7f4b89e93000-7f4b89e94000 r--p 00023000 08:02 3565 /usr/lib64/libselinux.so.1
7f4b89e94000-7f4b89e95000 rw-p 00024000 08:02 3565 /usr/lib64/libselinux.so.1
7f4b89e95000-7f4b89e97000 rw-p 00000000 00:00 0
7f4b89e97000-7f4b89eb3000 r-xp 00000000 08:02 72025 /usr/lib64/libsasl2.so.3.0.0
7f4b89eb3000-7f4b8a0b2000 ---p 0001c000 08:02 72025 /usr/lib64/libsasl2.so.3.0.0
7f4b8a0b2000-7f4b8a0b3000 r--p 0001b000 08:02 72025 /usr/lib64/libsasl2.so.3.0.0
7f4b8a0b3000-7f4b8a0b4000 rw-p 0001c000 08:02 72025 /usr/lib64/libsasl2.so.3.0.0
7f4b8a0b4000-7f4b8a0ca000 r-xp 00000000 08:02 3476 /usr/lib64/libresolv-2.17.so
7f4b8a0ca000-7f4b8a2ca000 ---p 00016000 08:02 3476 /usr/lib64/libresolv-2.17.so
7f4b8a2ca000-7f4b8a2cb000 r--p 00016000 08:02 3476 /usr/lib64/libresolv-2.17.so
7f4b8a2cb000-7f4b8a2cc000 rw-p 00017000 08:02 3476 /usr/lib64/libresolv-2.17.so
7f4b8a2cc000-7f4b8a2ce000 rw-p 00000000 00:00 0
7f4b8a2ce000-7f4b8a2d1000 r-xp 00000000 08:02 3995 /usr/lib64/libkeyutils.so.1.5
7f4b8a2d1000-7f4b8a4d0000 ---p 00003000 08:02 3995 /usr/lib64/libkeyutils.so.1.5
7f4b8a4d0000-7f4b8a4d1000 r--p 00002000 08:02 3995 /usr/lib64/libkeyutils.so.1.5
7f4b8a4d1000-7f4b8a4d2000 rw-p 00003000 08:02 3995 /usr/lib64/libkeyutils.so.1.5
7f4b8a4d2000-7f4b8a4e0000 r-xp 00000000 08:02 29044 /usr/lib64/libkrb5support.so.0.1
7f4b8a4e0000-7f4b8a6e0000 ---p 0000e000 08:02 29044 /usr/lib64/libkrb5support.so.0.1
7f4b8a6e0000-7f4b8a6e1000 r--p 0000e000 08:02 29044 /usr/lib64/libkrb5support.so.0.1
7f4b8a6e1000-7f4b8a6e2000 rw-p 0000f000 08:02 29044 /usr/lib64/libkrb5support.so.0.1
7f4b8a6e2000-7f4b8a6e9000 r-xp 00000000 08:02 3478 /usr/lib64/librt-2.17.so
7f4b8a6e9000-7f4b8a8e8000 ---p 00007000 08:02 3478 /usr/lib64/librt-2.17.so
7f4b8a8e8000-7f4b8a8e9000 r--p 00006000 08:02 3478 /usr/lib64/librt-2.17.so
7f4b8a8e9000-7f4b8a8ea000 rw-p 00007000 08:02 3478 /usr/lib64/librt-2.17.so
7f4b8a8ea000-7f4b8a951000 r-xp 00000000 08:02 29053 /usr/lib64/libssl.so.1.0.2k
7f4b8a951000-7f4b8ab51000 ---p 00067000 08:02 29053 /usr/lib64/libssl.so.1.0.2k
7f4b8ab51000-7f4b8ab55000 r--p 00067000 08:02 29053 /usr/lib64/libssl.so.1.0.2k
7f4b8ab55000-7f4b8ab5c000 rw-p 0006b000 08:02 29053 /usr/lib64/libssl.so.1.0.2k
7f4b8ab5c000-7f4b8abae000 r-xp 00000000 08:02 164729 /usr/lib64/libldap-2.4.so.2.10.7
7f4b8abae000-7f4b8adae000 ---p 00052000 08:02 164729 /usr/lib64/libldap-2.4.so.2.10.7
7f4b8adae000-7f4b8adb0000 r--p 00052000 08:02 164729 /usr/lib64/libldap-2.4.so.2.10.7
7f4b8adb0000-7f4b8adb1000 rw-p 00054000 08:02 164729 /usr/lib64/libldap-2.4.so.2.10.7
7f4b8adb1000-7f4b8adbf000 r-xp 00000000 08:02 164727 /usr/lib64/liblber-2.4.so.2.10.7
I am attaching a test case: https://mskcc.box.com/s/k9lm1qfh6o9qyej7uglgwb6k0iahgnrj, which includes:
- input BAM file
- input alleles file
It does not include the reference genome which ishg19-b37in this case.
My command was:
${BCFTOOLS_EXEC} mpileup \
-Ou \
-R ${CANDIDATE_ALLELE} \
-f ${REF_GENOME} \
--annotate FORMAT/AD,FORMAT/DP,INFO/AD \
--max-depth 100000 \
--max-idepth 100000 \
${SC_BAM} | \
${BCFTOOLS_EXEC} call \
--keep-alts \
-C alleles \
-T ${CANDIDATE_ALLELE} \
--multiallelic-caller \
-Ou | \
${BCFTOOLS_EXEC} norm \
-Oz \
-o ${SC_MPILEUP_VCF} \
--multiallelics - && \
tabix ${SC_MPILEUP_VCF}
I tested this on a few other cases and could not replicate the error, which means the error could be specific to my input, but I have not figured out why. I would appreciate any help!
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