Error in line 856, line 568 and line 8
anacatalan opened this issue · comments
Describe the bug
I am trying to run nextDenovo from our slurm cluster.
Error message
Traceback (most recent call last):
File "/dss/dsslegfs02/pn73se/pn73se-dss-0000/spack/opt/linux-sles15-skylake_avx512/nextdenovo/2.4.0-gcc-8.4.0-54uzind/bin/nextDenovo", line 856, in
main(args)
File "/dss/dsslegfs02/pn73se/pn73se-dss-0000/spack/opt/linux-sles15-skylake_avx512/nextdenovo/2.4.0-gcc-8.4.0-54uzind/bin/nextDenovo", line 568, in main
from task_control import Task, Run
File "/dss/dsslegfs02/pn73se/pn73se-dss-0000/spack/opt/linux-sles15-skylake_avx512/nextdenovo/2.4.0-gcc-8.4.0-54uzind/lib/task_control.py", line 8, in
import psutil
ModuleNotFoundError: No module named 'psutil'
Genome characteristics
Genome size: 759mb. No information on repeats and heterozygosity
Input data
I need to get this info first
Config file
Config file for LaNoc
#[General]
job_type = slurm
job_prefix = nextDenovo_LaNoc
task = all
rewrite = yes
deltmp = yes
parallel_jobs = 20
input_type = raw
read_type = ont # clr, ont, hifi
input_fofn = input_LaNoc.fofn
workdir = 01_rundir
usetempdir= temp
cluster_options= auto
nodelist= biohpc_gen_highmem
#[correct_option]
read_cutoff = 1k
genome_size = 760m # estimated genome size
sort_options = -m 100g -t 30
minimap2_options_raw = -t 8
pa_correction = 3
correction_options = -p 15
#[assemble_option]
minimap2_options_cns = -t 8
nextgraph_options = -a 1
Operating system
I am using slurm
You can use the command lsb_release -a to get it. --> no I can't
GCC
What version of GCC are you using?
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib64/gcc/x86_64-suse-linux/7/lto-wrapper
OFFLOAD_TARGET_NAMES=hsa:nvptx-none
Target: x86_64-suse-linux
Configured with: ../configure --prefix=/usr --infodir=/usr/share/info --mandir=/usr/share/man --libdir=/usr/lib64 --libexecdir=/usr/lib64 --enable-languages=c,c++,objc,fortran,obj-c++,ada,go --enable-offload-targets=hsa,nvptx-none=/usr/nvptx-none, --without-cuda-driver --enable-checking=release --disable-werror --with-gxx-include-dir=/usr/include/c++/7 --enable-ssp --disable-libssp --disable-libvtv --disable-libcc1 --disable-plugin --with-bugurl=https://bugs.opensuse.org/ --with-pkgversion='SUSE Linux' --with-slibdir=/lib64 --with-system-zlib --enable-libstdcxx-allocator=new --disable-libstdcxx-pch --enable-version-specific-runtime-libs --with-gcc-major-version-only --enable-linker-build-id --enable-linux-futex --enable-gnu-indirect-function --program-suffix=-7 --without-system-libunwind --enable-multilib --with-arch-32=x86-64 --with-tune=generic --build=x86_64-suse-linux --host=x86_64-suse-linux
Thread model: posix
gcc version 7.5.0 (SUSE Linux)
Python
Python 3.7.10
NextDenovo
nextdenovo/2.4.0
To Reproduce (Optional)
Steps to reproduce the behavior. Providing a minimal test dataset on which we can reproduce the behavior will generally lead to quicker turnaround time!
Additional context (Optional)
Add any other context about the problem here.
As the log says, your system do not have psutil module, so try to install it first by pip install psutil
Hi @anacatalan,
I'm also trying to figure out how to run NextDenovo in a HPC environment using SLURM.
Would you be able to share your script.slurm.sh with me?