Exit code -11

[rec3141]

Hello, I'm running into an error with a few of my samples. I ran gdb -arg on all of them and got the same fault. (I changed to threads=1 to make sure it wasn't a threading issue).

Starting program: /home/rec3141/apps/MEGAHIT-1.2.9-Linux-x86_64-static/bin/megahit_core assemble -s /project/6043541/rec3141/metta/assembly/bbpipe/Plate1-14-10E/megahit_out/tmp/k97/97 -o /project/6043541/rec3141/metta/assembly/bbpipe/Plate1-14-10E/megahit_out/intermediate_contigs/k97 -t 1 --min_standalone 300 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble
INFO  main_assemble.cpp             :  129 - Loading succinct de Bruijn graph: /project/6043541/rec3141/metta/assembly/bbpipe/Plate1-14-10E/megahit_out/tmp/k97/97Done. Time elapsed: 11.664069
INFO  main_assemble.cpp             :  133 - Number of Edges: 282511894; K value: 97
INFO  main_assemble.cpp             :  140 - Number of CPU threads: 1

Program received signal SIGSEGV, Segmentation fault.
0x00000000004c46c0 in sdbg_pruning::RemoveTips(SDBG&, int) [clone ._omp_fn.4] ()

> uname -a
Linux cedar5.cedar.computecanada.ca 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 GNU/Linux

Plate1-14-10E.log

[voutcn]

Hello @rec3141, are you able to compile Megahit by:

git clone https://github.com/voutcn/megahit.git
cd megahit
mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Debug  -DSANITIZER=ON
make -j $(nproc)

and then rerun the last command which incurs segfault.

# under the directory megahit/build
./megahit_core assemble -s /project/6043541/rec3141/metta/assembly/bbpipe/Plate1-14-10E/megahit_out/tmp/k97/97 -o /project/6043541/rec3141/metta/assembly/bbpipe/Plate1-14-10E/megahit_out/intermediate_contigs/k97 -t 1 --min_standalone 300 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2 --bubble_level 2 --max_tip_len -1 --careful_bubble

and copy-paste the error message here?

[gaofangzhou377]

hello, i followed your suggestions above and received the message as follow: INFO main_assemble.cpp : 129 - Loading succinct de Bruijn graph: /mnt/f/zhangmin/temp/megahit/tmp/k21/21FATAL utils/utils.h : 172 - Invalid format. Expect field k, got

what can i do next? by the way, i use ubuntu 18.04 under windows 10 system