Canu failed when I ran on the HPC

[WengangXbio]

Hi developer, I came across an issue when I tried to run Canu on the server. Error reported as follow. Any suggestions? Looking forward to hearing back from you, many thanks! Wengang

---

Include the canu command used, or at least tell us what options you've set.

canu \
-p asm -d YLcattle \
genomeSize=3g \
-pacbio-hifi PB-hifi.fastq.gz \
-nanopore ONT-UL.fastq.gz

Include the output of canu -version if it isn't in any outputs. It's reported at the start of the logging, and just before any crash report.

-- canu 2.2

Include what system you're running on. MacOS, Linux, or other? In a virtual machine? On a grid?

LSB Version:
Distributor ID: CentOS
Description: CentOS Linux release 7.9.2009 (Core)
Release: 7.9.2009
Codename: Core

Error reported as follow:

-- canu 2.2
--
-- CITATIONS
--
-- For assemblies of PacBio HiFi reads:
--   Nurk S, Walenz BP, Rhiea A, Vollger MR, Logsdon GA, Grothe R, Miga KH, Eichler EE, Phillippy AM, Koren S.
--   HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.
--   biorXiv. 2020.
--   https://doi.org/10.1101/2020.03.14.992248
-- 
-- Read and contig alignments during correction and consensus use:
--   Šošic M, Šikic M.
--   Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance.
--   Bioinformatics. 2017 May 1;33(9):1394-1395.
--   http://doi.org/10.1093/bioinformatics/btw753
-- 
-- Overlaps are generated using:
--   Berlin K, et al.
--   Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
--   Nat Biotechnol. 2015 Jun;33(6):623-30.
--   http://doi.org/10.1038/nbt.3238
-- 
--   Myers EW, et al.
--   A Whole-Genome Assembly of Drosophila.
--   Science. 2000 Mar 24;287(5461):2196-204.
--   http://doi.org/10.1126/science.287.5461.2196
-- 
-- Contig consensus sequences are generated using an algorithm derived from pbdagcon:
--   Chin CS, et al.
--   Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
--   Nat Methods. 2013 Jun;10(6):563-9
--   http://doi.org/10.1038/nmeth.2474
-- 
-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '22.0.1-internal' (from '/share/home/yzwl_zhangwg/.conda/envs/canu/lib/jvm/bin/java') without -d64 support.
-- Detected gnuplot version '5.4 patchlevel 8   ' (from 'gnuplot') and image format 'png'.
--
-- Detected 48 CPUs and 376 gigabytes of memory on the local machine.
--
-- Detected Slurm with 'sinfo' binary in /opt/skyformai/bin/sinfo.
flag provided but not defined: -exact
Argument "sinfo" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 141, <F> line 5.
Argument "value" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 139, <F> line 8.
Argument "on" isn't numeric in division (/) at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 140, <F> line 8.
Argument "--partition" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 141, <F> line 8.
Argument "value" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 139, <F> line 9.
Argument "on" isn't numeric in division (/) at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 140, <F> line 9.
Argument "--nodes" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 141, <F> line 9.
Argument "help" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 139, <F> line 10.
Argument "false)" isn't numeric in division (/) at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 140, <F> line 10.
Argument "--help," isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 141, <F> line 10.
Argument "the" isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 139, <F> line 11.
Argument "(default:" isn't numeric in division (/) at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 140, <F> line 11.
Argument "--version," isn't numeric in int at /share/home/yzwl_zhangwg/.conda/envs/canu/bin/../lib/site_perl/canu/Grid_Slurm.pm line 141, <F> line 11.
-- 
-- Slurm support detected.  Resources available:

ABORT:
ABORT: canu 2.2
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:
ABORT:   invalid useGrid (1) and gridEngine (SLURM); found no execution hosts - is grid available from this host?.
ABORT:
Job 10887760 stderr output:

---

[skoren]

It looks like you have slurm binaries but not all of it is correctly configured. This meant canu detected slurm but failed running the info command. You can disable grid support and run completely on a single node by adding useGrid=false.

[skoren]

Idle, partially installed but non-working slurm.