Closed JWDebler closed 1 year ago
Looks like the problem was that I was running our of RAM. I played with the config settings a little adjusting the number of parallel tasks and now it seems fine. Cheers.
can you help me to solve this problem?thank you very much!
run.cfg:[General] job_type = local # local, slurm, sge, pbs, lsf job_prefix = nextDenovo task = all # all, correct, assemble rewrite = yes # yes/no rerun = 3 deltmp = yes parallel_jobs = 15 # number of tasks used to run in parallel input_type = raw # raw, corrected read_type = ont # clr, ont, hifi input_fofn = ./input.fofn workdir = ./01_rundir
[correct_option]
read_cutoff = 1k
seed_cutoff = 23576
genome_size = 487.15m # estimated genome size
sort_options = -m 20g -t 15
minimap2_options_raw = -x ava-ont -t 10
pa_correction = 3 # number of corrected tasks used to run in parallel, each corrected task requires ~TOTAL_INPUT_BASES/4 bytes of memory usage.
correction_options = -p 15 -dbuf
[assemble_option] minimap2_options_cns = -x ava-ont -t 8 -k 17 -w 17 nextgraph_options = -a 1
my Linux RAM total 128672 used 64326 free 25876 shared 23027 buff/cache 38469 available 40090
[460027 CRITICAL] 2024-06-20 01:55:44 Command '/bin/bash /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh > /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh.o 2> /data5/fulongwen/opt/biosoft/NextDenovo/dataLDh/01_rundir/01.raw_align/02.raw_align.sh.work/raw_align05/nextDenovo.sh.e' returned non-zero exit status 137, error info: .
Traceback (most recent call last):
File "/data5/fulongwen/opt/biosoft/NextDenovo/nextDenovo", line 857, in
Running our of RAM, so just reduce the value of parallel_jobs
and rerun.
Running our of RAM, so just reduce the value of
parallel_jobs
and rerun.
I lowered the value of the parallel_jobs to 5 and I still have the same problem nextDenovo.sh.e is hostname
real 0m51.342s user 0m59.960s sys 0m22.921s
You can run these failed tasks manually using command: sh nextDenovo.sh
After you manually run all failed tasks, you can continue to run the main task. if this doesn't work, you need change a computer with more RAM.
Describe the bug I'm running the latest version 2.5.2.
This might be a strange conda problem.
Somehow
python
runs 3.9.13, but the full path to it runs 3.11.3Error message This python error prints after every instance of the CRITICAL message in the main logfile:
Here's the main logfile, as you can see there are several [CRITICAL] messages, yet the assembly still finishes.
Genome characteristics
42 mb homozygous fungal genome
Input data
Q20 Nanopore raw data, filtered to remove <1000 bp reads and keeping only the 90% best reads (filtlong). 286,834 reads, 3,668,039,649 bases
Config file
Operating system Ubuntu 18.04.6 LTS
GCC gcc version 7.5.0 (Ubuntu 7.5.0-3ubuntu1~18.04)
Python Python 3.9.13 / 3.11.3 (not sure which is used)
NextDenovo nextDenovo 2.5.2