SOAPdenovo-127mer contig Segmentation fault

[Shaun Jackman]

I first ran sparse_pregraph like so:

SOAPdenovo-127mer sparse_pregraph -s hsapiens.config -K127 -z5000000000 -R -o hsapiens -p32

It completed successfully.

Total number of marks in file markOnEdge: 1103907620

Time spent on building preArcs: 6234s.

Overall time spent on constructing lightgraph: 370m.

I then ran contig, and it segfaults immediately:

SOAPdenovo-127mer contig -g hsapiens -R -p32

Version 2.04: released on July 13th, 2012

Compile Jun  3 2016 23:46:00

********************

Contig

********************

Parameters: contig -g hsapiens -R -p 32 

There are 5962126 kmer(s) in vertex file.

There are 17647475 edge(s) in edge file.

make: *** [Makefile:25: hsapiens.contig] Segmentation fault (core dumped)

Any suggestions as to what's going on here? I'm going to try pregraph next rather than sparse_pregraph. See below for the config file.

Thanks,

Shaun

$ cat hsapiens.config 

max_rd_len=250

[LIB]

avg_ins=400

asm_flags=3

rank=1

pair_num_cutoff=3

map_len=32

p=pe400.fa.gz

[LIB]

avg_ins=6000

reverse_seq=1

asm_flags=2

rank=2

pair_num_cutoff=5

map_len=35

p=mp6k.fa.gz