db_stat failed
alexvasilikop opened this issue · comments
Describe the bug
Hello, running nextdenovo on my PacBio HiFi dataset using the following configuration file
gives the following error message:
nextDenovo Rotaria_rotatoria.inputHiFi.conf --log Rotaria_rotatoria.inputHiFi.conf.log
[17184 INFO] 2022-12-15 10:00:59 NextDenovo start...
[17184 INFO] 2022-12-15 10:00:59 version:v2.5.0 logfile:pid17184.Rotaria_rotatoria.inputHiFi.conf.log
[17184 WARNING] 2022-12-15 10:00:59 Re-write workdir
[17184 WARNING] 2022-12-15 10:00:59 Change task "all" to "assemble", becasue the input_type is "corrected"
[17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir
[17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align
[17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/02.cns_align
[17184 INFO] 2022-12-15 10:00:59 skip mkdir: /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/03.ctg_graph
[17184 INFO] 2022-12-15 10:01:04 Total jobs: 1
[17184 INFO] 2022-12-15 10:01:04 Submitted jobID:[17185] jobCmd:[/mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle.
[17185 CRITICAL] 2022-12-15 10:01:04 Command '/bin/sh /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 1, error info: .
Traceback (most recent call last):
File "/mnt/sdc1/Alex/software/NextDenovo/nextDenovo", line 850, in
main(args)
File "/mnt/sdc1/Alex/software/NextDenovo/nextDenovo", line 594, in main
task.run.start()
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 347, in start
self._start()
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 371, in _start
self.submit(job)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 255, in submit
_, stdout, _ = self.run(job.cmd)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/task_control.py", line 291, in run
log.critical("Command '%s' returned non-zero exit status %d, error info: %s." % (cmd, p.returncode, stderr))
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1219, in critical
self._log(CRITICAL, msg, args, **kwargs)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1293, in _log
self.handle(record)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1303, in handle
self.callHandlers(record)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 1343, in callHandlers
hdlr.handle(record)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/logging/init.py", line 766, in handle
self.emit(record)
File "/home/lege/anaconda3/envs/nextomics/lib/python2.7/site-packages/paralleltask/kit.py", line 42, in emit
raise Exception(record.msg)
Exception: Command '/bin/sh /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh > /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.o 2> /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e' returned non-zero exit status 1, error info: .
[17184 ERROR] 2022-12-15 10:01:10 db_stat failed: please check the following logs:
[17184 ERROR] 2022-12-15 10:01:10 /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e
Content of nextDenovo.sh.e:
hostname
hostname
cd /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1
cd /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/01.db_stat.sh.work/db_stat1
time /mnt/sdc1/Alex/software/NextDenovo/bin/seq_stat -f 10k -g 180m -d 30 -a -o /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/input.reads.stat /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.inputHiFi.fofn
time /mnt/sdc1/Alex/software/NextDenovo/bin/seq_stat -f 10k -g 180m -d 30 -a -o /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.all_reads.workdir/01.raw_align/input.reads.stat /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.inputHiFi.fofn
Error! /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/02.FILTLONG/Rotaria_rotatoria.PacBio_HiFi.m64279e_221025_110133.fastq.gz does not exist!Command exited with non-zero status 1
0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 1932maxresident)k
0inputs+0outputs (0major+80minor)pagefaults 0swaps
Genome characteristics
The genome size should be aroung 180-200Mb (haploid) although we are not sure
Input data
The input length distribution is the following
Types Count (#) Length (bp)
N10 6415 14208
N20 13658 13204
N30 21350 12547
N40 29407 12028
N50 37786 11589
N60 46465 11210
N70 55425 10875
N80 64655 10562
N90 74151 10270
Types Count (#) Bases (bp) Depth (X)
Raw 83911 989053808 4.95
Filtered 0 0 0.00
Clean 83911 989053808 4.95
Config file
[General]
job_type = local
job_prefix = nextDenovo
task = all
rewrite = yes
deltmp = yes
rerun = 3
parallel_jobs = 10
input_type = raw
input_fofn = Rotaria_rotatoria.inputHiFi.10000.90.fofn
workdir = /mnt/sdc1/Alex/Rotaria_rotatoria_assembly/03.NextDenovo/Rotaria_rotatoria.ND.10000.90.workdir
[correct_option]
read_cutoff = 10k
seed_cutoff = 10001
seed_depth = 45
read_type=hifi
genome_size = 200M # estimated genome size
blocksize = 1g
pa_correction = 10
seed_cutfiles = 2
sort_options = -m 5g -t 2 -k 40
minimap2_options_raw = -x ava-hifi -t 2
correction_options = -p 15
[assemble_option]
random_round = 10
minimap2_options_cns = -x ava-hifi -t 2 -k17 -w17
nextgraph_options = -a 1
Operating system
Distributor ID: Ubuntu
Description: Ubuntu 18.10
Release: 18.10
Codename: cosmic
GCC
gcc version 8.3.0 (Ubuntu 8.3.0-6ubuntu1~18.10.1)
Python
Python 2.7.15
NextDenovo
nextDenovo v2.5.0
Any help would be appreciated thanks
Alex
Input reads file was in a different path so issue closed