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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

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db_stat failed, @d84e39c8-130c-4159-bfa9-5393ad703a1a does not exist!

franztastic opened this issue · comments

commented

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

  • hostname
    cd /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1
  • cd /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/01.db_stat.sh.work/db_stat1
    ( time /opt/NextDenovo/bin/seq_stat -f 1k -g 2.4g -d 45 -o /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/input.reads.stat /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/input.fofn )
  • /opt/NextDenovo/bin/seq_stat -f 1k -g 2.4g -d 45 -o /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/rundir/01.raw_align/input.reads.stat /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/input.fofn
    Error! /home/bioinfo/Raja_radula_WGA/both_runs/duplex_assembly/NextDeNovo/@d84e39c8-130c-4159-bfa9-5393ad703a1a does not exist!
    real 0m0,017s
    user 0m0,001s
    sys 0m0,000s

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

commented

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

commented

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 !!