No assembly file after running NextDenovo
RacheliHadjez opened this issue · comments
RacheliHadjez commented
Hello,
I ran NextDenovo on a 60m sized genome and it ran for a few hours but I did not get an assembly file.
This is the command I used:
#!/bin/bash
#PBS -q huchond
#PBS -o out_Assemble_Nextdenovo_HSA
#PBS -e err_Assemble_Nextdenovo_HSA
#PBS -l nodes=compute-0-60:ppn=250
#PBS -r y
module load Python-3.10.2
module load NextDenovo-2.5.2
nextDenovo /dorotheeh/hadjez/NextDenovo_cfg_HSA.cfg -b -l LOG_HSA_Nextdenovo.txt
What version of GCC are you using?
4.8.5
What version of Python are you using?
3.10.2
What version of NextDenovo are you using?
2.5.2
This is the error file I am getting:
NextDenovoError.txt
Thank you!!!
Hu Jiang commented
As the log says:
[174109 INFO] 2023-06-14 11:56:30 nextDenovo finished
[174109 INFO] 2023-06-14 11:56:30 final assembly file:
[174109 INFO] 2023-06-14 11:56:30 �[35m /dorotheeh/hadjez/NextDenovo_HSA/03.ctg_graph/nd.asm.fasta �[0m
[174109 INFO] 2023-06-14 11:56:30 final stat file:
[174109 INFO] 2023-06-14 11:56:30 �[35m /dorotheeh/hadjez/NextDenovo_HSA/03.ctg_graph/nd.asm.fasta.stat �[0m
[174109 INFO] 2023-06-14 11:56:30 asm stat:
[174109 INFO] 2023-06-14 11:56:30
Type Length (bp) Count (#)
N10 8023315 1
N20 5372645 3
N30 4668152 4
N40 3402517 6
N50 2258397 9
N60 2148079 12
N70 1796393 16
N80 1221106 21
N90 488771 30
Min. 25907 -
Max. 8023315 -
Ave. 787407 -
Total 74803720 95