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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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Running error assembling Pacbio data #28

Closed Dichromatism closed 4 years ago

Dichromatism commented 4 years ago

Hello! I am trying to use NextDenovo these days and found it's okay using Ont data. But when I was trying to assemble Pacbio data some errors appeared and I cannot figure out. There were Errors in the ./02.cns_align/02.cns_align.sh.work/cns_align*/nextDenovo.sh.e which showed [ERROR] failed to find seq file type or empty file. I wrote

 [correct_option]
read_cutoff = 1k
seed_cutoff = 1057
blocksize = 3g
pa_correction = 20
seed_cutfiles = 20
sort_options = -m 20g -t 10 -k 20
minimap2_options_raw = -x ava-pb -H -t 8
correction_options = -p 15

[assemble_option]
random_round = 20
minimap2_options_cns = -x ava-pb -H -t 8 -k17 -w17
nextgraph_options = -a 1

in my run.cfg when the errors come out. I need help, thanks!

moold commented 4 years ago

I guess the input file of some tasks: ./02.cns_align/02.cns_align.sh.work/cns_align*/nextDenovo.sh is empty, and try to increase the value of -k in sort_options = -m 20g -t 10 -k 20. 20 is too small, recommend >= 40.