Segfault (signal 11) when running GDiet with modified -Z and -W parameters

[wanglinqi123]

Hi, thank you for developing this great tool!

I’m testing GDiet using long sequencing reads (184GB) with hs37d5.fa (3GB) as the reference. My goal is to evaluate the impact of different diet pattern settings, so I modified the -Z and -W parameters while keeping the rest of the parameters similar to the ONT recommendations.

I ran this on a CentOS-based cluster with 32 CPU and 1TB RAM, but the job failed with "Command terminated by signal 11 (core dumped)".
Here’s the command I used:

GDiet-LongReads/GDiet -t 32 \
--MD -ax map-ont -Z 101 -W 3 -i 0.2 -k 15 -w 10 -N 1 -r 1300 --vt_dis=1000 --vt_nb_loc=3 --vt_df1=0.007 --vt_df2=0.007 --max_min_gap=4000 --vt_f=0.04 -s 35000 --vt_cov 0.3 --sort=merge --frag=no -F200,1 --secondary=yes -a \
hs37d5.fa \
HG002_Cyclone_Batch4_Raw.30X.fastq

However, the command runs fine with the recommended -Z 10 -W 2 on the same data and environment.

Could you help with this issue?