Error in line 856, line 568 and line 8

[anacatalan]

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.

[moold]

As the log says, your system do not have psutil module, so try to install it first by pip install psutil

[DaniPaulo]

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?