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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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problem:The data from canu's correctedReads had no results with the nextdenovo software. #50

Closed clover163 closed 4 years ago

clover163 commented 4 years ago

Hi, I have a problem about the nextdenovo assemble task. when I used the data from canu's correctedReads to assemble, I couldn,t get any results . run.cfg: [General] job_type = sge job_prefix = *** task =assemble # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 200 input_type = corrected ...... [assemble_option] random_round = 100 minimap2_options_cns = -x ava-pb -t 8 -k17 -w17 nextgraph_options = -a 1

Please give me some advises to solve this problem. Thanks a lot !!!

moold commented 4 years ago

Could you provide the unfinished subtask log and NextDenovo version? BTW, the assembly module of NextDenovo with default parameters is primary designed for reads corrected by NextCorrect (the first module of NextDenovo), and I do not test it with reads corrected with Canu, so the result is uncertain, pls check the quality after getting the assembly result.

clover163 commented 4 years ago

All jobs have been done, but the assembly fasta is empty .Maybe I should try other parameters? NextDenovo version:NextDenovo-v2.2-beta.0

moold commented 4 years ago

Hi, could you try to rename the corrected reads ID with integer (int), and rerun all pipeline?

clover163 commented 4 years ago

enmm, means I should rename reands ID ,and then , run pipeline with "task = all“ ，or just rerun with "task =assemble" ?

moold commented 4 years ago

task =assemble

clover163 commented 4 years ago

Hi, NextDenovo version is NextDenovo-v2.2-beta.0, how can I solve the problem: Unfinished assembly, this is a limited version, currently only supports assembly for genome size < 3500000000 bp, please ask for help.

moold commented 4 years ago

See #31 and #52