Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

bcftools corrupted size vs. prev_size error #1790

Closed
haochenz96 opened this issue Sep 13, 2022 · 1 comment
Closed

bcftools corrupted size vs. prev_size error #1790

haochenz96 opened this issue Sep 13, 2022 · 1 comment

Comments

@haochenz96
Copy link

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 is hg19-b37 in 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!
@haochenz96 haochenz96 mentioned this issue Sep 13, 2022
Closed
@pd3 pd3 closed this as completed in 99f3988 Sep 20, 2022
@pd3
Copy link
Member

pd3 commented Sep 20, 2022

Hopefully this is now fixed by 99f3988, please try it out

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@pd3 @haochenz96