SMIS fails with memory error : core dumped

[lakhujanivijay]

Hi SMIS fails with below error at my end with pacbio sequel data. I am provided it sample-2.contigs.fasta which is the denovo assembly output from canu assembler.

command

date && time smis_pipeline -score 50 -len 2000 -step 200 -contig 3000 -edge 5 sample-2.fq sample-2.contigs.fasta sample-2.scaffolds.fasta

Error

Thu Jul 19 12:08:00 IST 2018
*** buffer overflow detected ***: smis_pipeline terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f9724c667e5]
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f9724d0815c]
/lib/x86_64-linux-gnu/libc.so.6(+0x117160)[0x7f9724d06160]
/lib/x86_64-linux-gnu/libc.so.6(+0x116609)[0x7f9724d05609]
smis_pipeline[0x4012ec]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f9724c0f830]
smis_pipeline[0x402439]
======= Memory map: ========
00400000-00407000 r-xp 00000000 08:01 48903153                           /opt/app/smis/smis_pipeline
00607000-00608000 r--p 00007000 08:01 48903153                           /opt/app/smis/smis_pipeline
00608000-00609000 rw-p 00008000 08:01 48903153                           /opt/app/smis/smis_pipeline
00609000-00685000 rw-p 00000000 00:00 0 
024c4000-024e5000 rw-p 00000000 00:00 0                                  [heap]
7f97249d7000-7f97249ed000 r-xp 00000000 08:01 49811787                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f97249ed000-7f9724bec000 ---p 00016000 08:01 49811787                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9724bec000-7f9724bed000 rw-p 00015000 08:01 49811787                   /lib/x86_64-linux-gnu/libgcc_s.so.1
7f9724bef000-7f9724daf000 r-xp 00000000 08:01 49820527                   /lib/x86_64-linux-gnu/libc-2.23.so
7f9724daf000-7f9724faf000 ---p 001c0000 08:01 49820527                   /lib/x86_64-linux-gnu/libc-2.23.so
7f9724faf000-7f9724fb3000 r--p 001c0000 08:01 49820527                   /lib/x86_64-linux-gnu/libc-2.23.so
7f9724fb3000-7f9724fb5000 rw-p 001c4000 08:01 49820527                   /lib/x86_64-linux-gnu/libc-2.23.so
7f9724fb5000-7f9724fb9000 rw-p 00000000 00:00 0 
7f9724fbf000-7f9724fe5000 r-xp 00000000 08:01 49820525                   /lib/x86_64-linux-gnu/ld-2.23.so
7f97251c5000-7f97251c7000 rw-p 00000000 00:00 0 
7f97251e3000-7f97251e4000 rw-p 00000000 00:00 0 
7f97251e4000-7f97251e5000 r--p 00025000 08:01 49820525                   /lib/x86_64-linux-gnu/ld-2.23.so
7f97251e5000-7f97251e6000 rw-p 00026000 08:01 49820525                   /lib/x86_64-linux-gnu/ld-2.23.so
7f97251e6000-7f97251e8000 rw-p 00000000 00:00 0 
7fff8925c000-7fff8927d000 rw-p 00000000 00:00 0                          [stack]
7fff892a7000-7fff892aa000 r--p 00000000 00:00 0                          [vvar]
7fff892aa000-7fff892ac000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

real	0m0.180s
user	0m0.000s
sys	0m0.004s