moold
commented
1 month ago It seems the input file input.fofn is incorrect, assuming the read file is ont.fastq.gz, try the following command to generate input.fofn:
ls ont.fastq.gz > input.fofn
Closed franztastic closed 1 month ago
moold
commented
1 month ago It seems the input file input.fofn is incorrect, assuming the read file is ont.fastq.gz, try the following command to generate input.fofn:
ls ont.fastq.gz > input.fofn
franztastic
commented
1 month ago Thank you very much, it solved it! I thought that naming my ont.fastq.gz input.fofn would work! THANK YOU FOR YOUR QUICK RESPONSE !!
Hi everyone, first of all, thanks for your help and providing such an useful tool!
Describe the bug When trying to use NextDenovo with my data, less than 1 second after starting to run it, it stops.
Error message bioinfo@mola2:~/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo$ cat pid1973801.log.info [1973801 INFO] 2024-05-06 19:01:23 NextDenovo start... [1973801 INFO] 2024-05-06 19:01:23 version:2.5.2 logfile:pid1973801.log.info [1973801 WARNING] 2024-05-06 19:01:23 Re-write workdir [1973801 INFO] 2024-05-06 19:01:23 mkdir: /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir [1973801 INFO] 2024-05-06 19:01:23 mkdir: /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align [1973801 INFO] 2024-05-06 19:01:23 mkdir: /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/02.cns_align [1973801 INFO] 2024-05-06 19:01:23 mkdir: /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/03.ctg_graph [1973801 INFO] 2024-05-06 19:01:28 Total jobs: 1 [1973801 INFO] 2024-05-06 19:01:28 Submitted jobID:[1974259] jobCmd:[/home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle. [1974259 CRITICAL] 2024-05-06 19:01:28 Command '/bin/bash /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 1, error info: . [1973801 ERROR] 2024-05-06 19:01:34 db_stat failed: please check the following logs: [1973801 ERROR] 2024-05-06 19:01:34 /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e
nextDenovo.sh.e
hostname
Genome characteristics genome size: 2.4g
Config file bioinfo@mola2:~/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo$ cat run.cfg [General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 2 input_type = raw read_type = ont input_fofn = input.fofn workdir = rundir
[correct_option] read_cutoff = 1k genome_size = 2.4g pa_correction = 2 sort_options = -m 20g -t 2 minimap2_options_raw = -x ava-ont -t 8 correction_options = -p 15
[assemble_option] minimap2_options_cns = -x ava-ont t 8 nextgraph_options = -a 1
Operating system Which operating system and version are you using? Distributor ID: Ubuntu Description: Ubuntu 22.04.4 LTS Release: 22.04 Codename: jammy
GCC What version of GCC are you using? gcc version 12.3.0 (Ubuntu 12.3.0-1ubuntu1~22.04)
Python What version of Python are you using? Python 3.10.12
NextDenovo What version of NextDenovo are you using? nextDenovo 2.5.2
To Reproduce (Optional) just /ont/NextDenovo/nextDenovo run.cfg
Comments
I've tried to reinstall the tool, give permisions to the folder... I don't why this is looking for this "@d84e39c8-130c-4159-bfa9-5393ad703a1a" path...
Thank you very much, i'm sure it's something quite silly...
Laura