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ryanlayer / giggle

Interval data structure
MIT License
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Segfault when trying to index #56

Open amathelier opened 4 years ago

amathelier commented 4 years ago

Hi Ryan,

I am trying to index ~3,500 bed files using giggle. They all have been sorted using giggle/scripts/sort_bed "tmp/*.bed" bgzip_sort 4. But typing giggle index -i "bgzip_sort/*.gz" -o giggle_index raises a segfault. I have recompiled giggle to enable debugging with gdb and get the following information:

$ gdb --args ../../bin/giggle/bin/giggle index -i "bgzip_sort/*.gz" -o giggle_index -f

GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-119.el7 Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: http://www.gnu.org/software/gdb/bugs/... Reading symbols from /storage/mathelierarea/processed/anthoma/Projects/UniBind2.0/bin/giggle/bin/giggle...done. (gdb) run Starting program: /storage/mathelierarea/processed/anthoma/Projects/UniBind2.0/results/20201006_giggle/../../bin/giggle/bin/giggle index -i bgzip_sort/*.gz -o giggle_index -f [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1".

Program received signal SIGSEGV, Segmentation fault. 0x000000000041007b in hash_list_add (hashl=0x0, index=0, data=0x7fffffffaa90, data_size=24) at lists.c:280 280 khash_t(hashl) hash = (khash_t(hashl))(hashl->hash); Missing separate debuginfos, use: debuginfo-install cyrus-sasl-lib-2.1.26-23.el7.x86_64 glibc-2.17-307.el7.1.x86_64 keyutils-libs-1.5.8-3.el7.x86_64 krb5-libs-1.15.1-46.el7.x86_64 libcom_err-1.42.9-17.el7.x86_64 libcurl-7.29.0-57.el7_8.1.x86_64 libidn-1.28-4.el7.x86_64 libselinux-2.5-15.el7.x86_64 libssh2-1.8.0-3.el7.x86_64 nspr-4.21.0-1.el7.x86_64 nss-3.44.0-7.el7_7.x86_64 nss-softokn-freebl-3.44.0-8.el7_7.x86_64 nss-util-3.44.0-4.el7_7.x86_64 openldap-2.4.44-21.el7_6.x86_64 openssl-libs-1.0.2k-19.el7.x86_64 pcre-8.32-17.el7.x86_64

Thanks for your help.

fei0810 commented 3 years ago

I had the same problem

ryanlayer commented 3 years ago

Have you raised your ulimit?

On Thu, Mar 25, 2021 at 5:07 AM Fei Zhao @.***> wrote:

I had the same problem

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