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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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NextDenovo assemble has no result file #26

Closed ruanyingfei closed 4 years ago

ruanyingfei commented 4 years ago

My problem is that my process runs out, but there are no final assembled result,There ais only 01_rundir/02.cns_align/01.get_cns.sh.work/get_cns0/cns.fasta.

my run.cfg is: [General] job_type = local job_prefix = nextDenovo task = all rewrite = yes # yes/no input_type = raw input_fofn = ./input.fofn workdir = ./nb_assmble

[correct_option] read_cuoff = 1k seed_cutoff = 32k blocksize = 1g pa_raw_align = 2 pa_correction = 2 seed_cutfiles = 2 sort_options = -m 1g -t 2 -k 50 minimap2_options = -x ava-pb -t 8 correction_options = -p 15

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

The final content of the report file: [INFO] 2019-11-07 10:18:43,231 remove temporary result: /share/microlab/student/ruanyingfei/biosoft/NextDenovo/test_data/nb_assmble/01.raw_align/02.raw_align.sh.work/raw_align18/input.seed.002.2bit.18.ovl [INFO] 2019-11-07 10:18:43,352 sort_align done [INFO] 2019-11-07 10:18:43,387 analysis tasks done [INFO] 2019-11-07 10:18:43,544 total jobs: 2 [INFO] 2019-11-07 10:18:43,545 Throw jobID:[4798] jobCmd:[/share/microlab/student/ruanyingfei/biosoft/NextDenovo/test_data/nb_assmble/02.cns_align/01.get_cns.sh.work/get_cns0/nextDenovo.sh] in the local_cycle. [INFO] 2019-11-07 10:18:44,079 Throw jobID:[4821] jobCmd:[/share/microlab/student/ruanyingfei/biosoft/NextDenovo/test_data/nb_assmble/02.cns_align/01.get_cns.sh.work/get_cns1/nextDenovo.sh] in the local_cycle.

Looking forward to your valuable advice, thank you very much!!!

moold commented 4 years ago

How about your genome size and input data size?

ruanyingfei commented 4 years ago

my genome size is 27M and input data size is 9.1G.

moold commented 4 years ago

Could you paste the seq_stat result to here?

moold commented 4 years ago

BTW, do you use the latest version of NextDenovo?

ruanyingfei commented 4 years ago

Thank you very much! I've solved this problem, and I didn't get results before because the software I downloaded wasn't the latest version, and there was no nextgraph in its NextDenovo/bin directory, so there was no final assembly result.Thank you again!