Problem with NextDenovo

[nextomics]

Problem with NextDenovo

[moold]

Hi,
Could you check this file:
/public1/home/windz/software/NextDenovo/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align00/nextDenovo.sh.e to see what is the error?

[WeipengMO]

It seems like an issue with Minimap2 to me.

hostname
+ hostname
cd /public1/home/windz/software/NextDenovo/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align00
+ cd /public1/home/windz/software/NextDenovo/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align00
time /public1/home/windz/software/NextDenovo/bin/minimap2-hack --dual=yes -x ava-ont -t 8 /public1/home/windz/software/NextDenovo/test_data/../01_rundir/01.raw_align/input.seed.001.2bit /public1/home/windz/software/NextDenovo/test_data/../01_rundir/01.raw_align/input.part.001.2bit > input.seed.001.2bit.0.ovl;
+ /public1/home/windz/software/NextDenovo/bin/minimap2-hack --dual=yes -x ava-ont -t 8 /public1/home/windz/software/NextDenovo/test_data/../01_rundir/01.raw_align/input.seed.001.2bit /public1/home/windz/software/NextDenovo/test_data/../01_rundir/01.raw_align/input.part.001.2bit
[M::mm_idx_gen::0.023*0.29] collected minimizers
[M::mm_idx_gen::0.024*0.49] sorted minimizers
[M::main::0.024*0.49] loaded/built the index for 0 target sequence(s)
[M::mm_mapopt_update::0.024*0.49] mid_occ = 1
[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 0
[M::mm_idx_stat::0.024*0.49] distinct minimizers: 0 (-nan% are singletons); average occurrences: -nan; average spacing: -nan
/public1/home/windz/software/NextDenovo/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align00/nextDenovo.sh: line 5:  2150 Segmentation fault               core（dump）/public1/home/windz/software/NextDenovo/bin/minimap2-hack --dual=yes -x ava-ont -t 8 /public1/home/windz/software/NextDenovo/test_data/../01_rundir/01.raw_align/input.seed.001.2bit /public1/home/windz/software/NextDenovo/test_data/../01_rundir/01.raw_align/input.part.001.2bit > input.seed.001.2bit.0.ovl

[moold]

see log: loaded/built the index for 0 target sequence(s)

It seems the input file is empty, please check your input reads file.