Failed to generate iontorrent data

[biocyberman]

Server:

$ uname -a
Linux workstation 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

dwgsim version: 0.1.12 (git checkout dwgsim.0.1.12)

This ran fine:

dwgsim -e 0.02 -1 150 -N 10000 -B -f $(cat floworder.txt) hcv_gt3.fasta hcv.dwgsim But this failed: dwgsim -e 0.02 -1 150 -c 2 -N 10000 -B -f $(cat floworder.txt) hcv_gt3.fasta hcv.dwgsim

[dwgsim_core] Updating error rate for end 1
[dwgsim_core] 0*** Error in `/usr/bin/dwgsim': corrupted size vs. prev_size: 0x00000000021453f0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fd485db17e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x83781)[0x7fd485dbd781]
/lib/x86_64-linux-gnu/libc.so.6(+0x85ba9)[0x7fd485dbfba9]
/lib/x86_64-linux-gnu/libc.so.6(realloc+0x22f)[0x7fd485dbe8ef]
/usr/bin/dwgsim[0x408c11]
/usr/bin/dwgsim[0x402bcb]
/usr/bin/dwgsim[0x401147]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fd485d5a830]
/usr/bin/dwgsim[0x401409]
======= Memory map: ========
00400000-00413000 r-xp 00000000 00:29 2400509182                         /usr/dwgsim/dwgsim
00612000-00613000 r--p 00012000 00:29 2400509182                         /usr/dwgsim/dwgsim
00613000-00614000 rw-p 00013000 00:29 2400509182                         /usr/dwgsim/dwgsim
02145000-02166000 rw-p 00000000 00:00 0                                  [heap]
7fd480000000-7fd480021000 rw-p 00000000 00:00 0 
7fd480021000-7fd484000000 ---p 00000000 00:00 0 
7fd485b24000-7fd485b3a000 r-xp 00000000 fc:01 262171                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7fd485b3a000-7fd485d39000 ---p 00016000 fc:01 262171                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7fd485d39000-7fd485d3a000 rw-p 00015000 fc:01 262171                     /lib/x86_64-linux-gnu/libgcc_s.so.1
7fd485d3a000-7fd485efa000 r-xp 00000000 fc:01 262419                     /lib/x86_64-linux-gnu/libc-2.23.so
7fd485efa000-7fd4860fa000 ---p 001c0000 fc:01 262419                     /lib/x86_64-linux-gnu/libc-2.23.so
7fd4860fa000-7fd4860fe000 r--p 001c0000 fc:01 262419                     /lib/x86_64-linux-gnu/libc-2.23.so
7fd4860fe000-7fd486100000 rw-p 001c4000 fc:01 262419                     /lib/x86_64-linux-gnu/libc-2.23.so
7fd486100000-7fd486104000 rw-p 00000000 00:00 0 
7fd486104000-7fd48611c000 r-xp 00000000 fc:01 262370                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7fd48611c000-7fd48631b000 ---p 00018000 fc:01 262370                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7fd48631b000-7fd48631c000 r--p 00017000 fc:01 262370                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7fd48631c000-7fd48631d000 rw-p 00018000 fc:01 262370                     /lib/x86_64-linux-gnu/libpthread-2.23.so
7fd48631d000-7fd486321000 rw-p 00000000 00:00 0 
7fd486321000-7fd486429000 r-xp 00000000 fc:01 262413                     /lib/x86_64-linux-gnu/libm-2.23.so
7fd486429000-7fd486628000 ---p 00108000 fc:01 262413                     /lib/x86_64-linux-gnu/libm-2.23.so
7fd486628000-7fd486629000 r--p 00107000 fc:01 262413                     /lib/x86_64-linux-gnu/libm-2.23.so
7fd486629000-7fd48662a000 rw-p 00108000 fc:01 262413                     /lib/x86_64-linux-gnu/libm-2.23.so
7fd48662a000-7fd486650000 r-xp 00000000 fc:01 262347                     /lib/x86_64-linux-gnu/ld-2.23.so
7fd48681c000-7fd486820000 rw-p 00000000 00:00 0 
7fd48684c000-7fd48684f000 rw-p 00000000 00:00 0 
7fd48684f000-7fd486850000 r--p 00025000 fc:01 262347                     /lib/x86_64-linux-gnu/ld-2.23.so
7fd486850000-7fd486851000 rw-p 00026000 fc:01 262347                     /lib/x86_64-linux-gnu/ld-2.23.so
7fd486851000-7fd486852000 rw-p 00000000 00:00 0 
7ffe6824e000-7ffe68270000 rw-p 00000000 00:00 0                          [stack]
7ffe683c5000-7ffe683c7000 r--p 00000000 00:00 0                          [vvar]
7ffe683c7000-7ffe683c9000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
[1]    19168 abort (core dumped)  /usr/bin/dwgsim -e 0.02 -1 150 -c 2 -N 10000 -B -f  hcv_gt3.fasta 

Attached is floworder data and reference genome sequence.

floworder.txt

hcv_gt3.fasta.txt

[nh13]

I can reproduce, but don't have time to get my mac updated to install valgrind to check. Can you take a shot?

[nh13]

Closing as now follow up