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vibansal / HapCUT2

software tools for haplotype assembly from sequence data
BSD 2-Clause "Simplified" License
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double free or corruption (out) #121

Open tiffuhu opened 2 years ago

tiffuhu commented 2 years ago

After running extractHAIRS and LinkedFragments.py successfully, I have been running HAPCUT2 that gives the "double free or corruption (out)" error. Both the haplotype block file and the phased VCF are output successfully and have results within the files, but I am still getting the error. Is this something that is cause for concern? I have provided the readout below.

[2021:11:30 01:22:52] OUTPUTTING PRUNED HAPLOTYPE ASSEMBLY TO FILE haplotype
[2021:11:30 01:22:52] N50 haplotype length is 5.04 kilobases
[2021:11:30 01:22:52] OUTPUTTING PHASED VCF TO FILE haplotype.phased.VCF
*** Error in /home/ec2-user/software/hapcut2/build/HAPCUT2': double free or corruption (out): 0x0000000002170c90 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x814f9)[0x7fa94e8744f9]
/home/ec2-user/software/hapcut2/build/HAPCUT2[0x40c734]
/home/ec2-user/software/hapcut2/build/HAPCUT2[0x40d1c0]
/home/ec2-user/software/hapcut2/build/HAPCUT2[0x401003]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x7fa94e815445]
/home/ec2-user/software/hapcut2/build/HAPCUT2[0x40107e]
======= Memory map: ========
00400000-00413000 r-xp 00000000 ca:01 6031725                            /home/ec2-user/software/hapcut2/build/HAPCUT2
00613000-00614000 rw-p 00013000 ca:01 6031725                            /home/ec2-user/software/hapcut2/build/HAPCUT2
00614000-00628000 rw-p 00000000 00:00 0
01e62000-02189000 rw-p 00000000 00:00 0                                  [heap]
7fa948000000-7fa948021000 rw-p 00000000 00:00 0
7fa948021000-7fa94c000000 ---p 00000000 00:00 0
7fa94dd75000-7fa94dd8b000 r-xp 00000000 ca:01 2389                       /lib64/libgcc_s-7-20170915.so.1
7fa94dd8b000-7fa94df8a000 ---p 00016000 ca:01 2389                       /lib64/libgcc_s-7-20170915.so.1
7fa94df8a000-7fa94df8b000 rw-p 00015000 ca:01 2389                       /lib64/libgcc_s-7-20170915.so.1
7fa94df8b000-7fa94dfa2000 r-xp 00000000 ca:01 2469                       /lib64/libpthread-2.17.so
7fa94dfa2000-7fa94e1a1000 ---p 00017000 ca:01 2469                       /lib64/libpthread-2.17.so
7fa94e1a1000-7fa94e1a2000 r--p 00016000 ca:01 2469                       /lib64/libpthread-2.17.so
7fa94e1a2000-7fa94e1a3000 rw-p 00017000 ca:01 2469                       /lib64/libpthread-2.17.so
7fa94e1a3000-7fa94e1a7000 rw-p 00000000 00:00 0
7fa94e1a7000-7fa94e1bc000 r-xp 00000000 ca:01 2590                       /lib64/libz.so.1.2.8
7fa94e1bc000-7fa94e3bb000 ---p 00015000 ca:01 2590                       /lib64/libz.so.1.2.8
7fa94e3bb000-7fa94e3bc000 r--p 00014000 ca:01 2590                       /lib64/libz.so.1.2.8
7fa94e3bc000-7fa94e3bd000 rw-p 00015000 ca:01 2590                       /lib64/libz.so.1.2.8
7fa94e3bd000-7fa94e3cd000 r-xp 00000000 ca:01 2681                       /lib64/libbz2.so.1.0.6
7fa94e3cd000-7fa94e5cc000 ---p 00010000 ca:01 2681                       /lib64/libbz2.so.1.0.6
7fa94e5cc000-7fa94e5ce000 rw-p 0000f000 ca:01 2681                       /lib64/libbz2.so.1.0.6
7fa94e5ce000-7fa94e5f2000 r-xp 00000000 ca:01 2690                       /usr/lib64/liblzma.so.5.2.2
7fa94e5f2000-7fa94e7f2000 ---p 00024000 ca:01 2690                       /usr/lib64/liblzma.so.5.2.2
7fa94e7f2000-7fa94e7f3000 rw-p 00024000 ca:01 2690                       /usr/lib64/liblzma.so.5.2.2
7fa94e7f3000-7fa94e9b5000 r-xp 00000000 ca:01 2443                       /lib64/libc-2.17.so
7fa94e9b5000-7fa94ebb5000 ---p 001c2000 ca:01 2443                       /lib64/libc-2.17.so
7fa94ebb5000-7fa94ebb9000 r--p 001c2000 ca:01 2443                       /lib64/libc-2.17.so
7fa94ebb9000-7fa94ebbb000 rw-p 001c6000 ca:01 2443                       /lib64/libc-2.17.so
7fa94ebbb000-7fa94ebc0000 rw-p 00000000 00:00 0
7fa94ebc0000-7fa94eca3000 r-xp 00000000 ca:01 9589                       /usr/local/lib/libhts.so.1.14-8-gf1ac6bb
7fa94eca3000-7fa94eea3000 ---p 000e3000 ca:01 9589                       /usr/local/lib/libhts.so.1.14-8-gf1ac6bb
7fa94eea3000-7fa94eea5000 rw-p 000e3000 ca:01 9589                       /usr/local/lib/libhts.so.1.14-8-gf1ac6bb
7fa94eea5000-7fa94eea6000 rw-p 00000000 00:00 0
7fa94eea6000-7fa94efa7000 r-xp 00000000 ca:01 2451                       /lib64/libm-2.17.so
7fa94efa7000-7fa94f1a6000 ---p 00101000 ca:01 2451                       /lib64/libm-2.17.so
7fa94f1a6000-7fa94f1a7000 r--p 00100000 ca:01 2451                       /lib64/libm-2.17.so
7fa94f1a7000-7fa94f1a8000 rw-p 00101000 ca:01 2451                       /lib64/libm-2.17.so
7fa94f1a8000-7fa94f1ca000 r-xp 00000000 ca:01 2436                       /lib64/ld-2.17.so
7fa94f331000-7fa94f3b9000 rw-p 00000000 00:00 0
7fa94f3c7000-7fa94f3c9000 rw-p 00000000 00:00 0
7fa94f3c9000-7fa94f3ca000 r--p 00021000 ca:01 2436                       /lib64/ld-2.17.so
7fa94f3ca000-7fa94f3cb000 rw-p 00022000 ca:01 2436                       /lib64/ld-2.17.so
7fa94f3cb000-7fa94f3cc000 rw-p 00000000 00:00 0
7ffed6f8d000-7ffed7554000 rw-p 00000000 00:00 0                          [stack]
7ffed7574000-7ffed7577000 r--p 00000000 00:00 0                          [vvar]
7ffed7577000-7ffed7579000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted
vibansal commented 2 years ago

This looks like an error in freeing the memory at the end of the program. The output should not be affected. If possible, could you run the code using gdb and share the output. This will help figure out the problematic line(s) in the code. Thanks.