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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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How to check random_round results in Nextdenovo v2.3.1 #88

Closed LeoCao-X closed 3 years ago

LeoCao-X commented 3 years ago

Question or Expected behavior In the old version, NextDenovo will save random assembly results in 03.ctg_graph/03.ctg_cns.sh.work directory. But in the newest version, I set random_round=20 in run.cfg but there are just 7 results in 03.ctg_graph/03.ctg_cns.sh.work directory. Is that normal in the newest version? How to check other random assembly results. This is intact run.cfg I use: [General] job_type = local job_prefix = nextDenovo_20200915_V1 task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 20 input_type = raw input_fofn = ./input.fofn workdir = ./20200915_V1_repeat

[correct_option] read_cutoff = 2k seed_cutoff = 26084 blocksize = 3g pa_correction = 6 seed_cutfiles = 8 sort_options = -m 200g -t 10 -k 45 minimap2_options_raw = -x ava-ont -t 10 correction_options = -p 10

[assemble_option] random_round = 20 minimap2_options_cns = -x ava-ont -t 6 -k17 -w17 nextgraph_options = -a 1

Operating system 4.14.65-gentoo

GCC What version of GCC are you using? gcc version 7.3.0 (Gentoo 7.3.0-r3 p1.4) Python What version of Python are you using? Python 3.8.3

NextDenovo What version of NextDenovo are you using? Nextdenovo v2.3.1

Additional context (Optional) Add any other context about the problem here.

moold commented 3 years ago

The new version doest not support random options, because the random results have more errors than the default one, and most of users do not known how to chose result and just select the one with longest N50.

LeoCao-X commented 3 years ago

Thanks so much.