#!/bin/bash
#SBATCH --job-name=strain4-canu-maxcov  		
#SBATCH --partition=hugemem				
#SBATCH -o output_%j.txt				
#SBATCH -e errors_%j.txt				


cp Strain04-from1804.fastq.gz $SCRATCH

## Move to work directory
cd $SCRATCH

## Loading and running canu module
module load canu
canu -p strain4-canu-maxcov -d strain4-canu-maxcov genomeSize=4.8m corOutCoverage=999 -nanopore-raw Strain04-from1804.fastq.gz

**Error output**

-- CONFIGURE CANU
--
-- Detected Java(TM) Runtime Environment '1.8.0_65' (from '/local/genome/packages/java/jdk1.8.0_65/bin/java').
-- Detected gnuplot version '5.0 patchlevel 6' (from 'gnuplot') and image format 'svg'.
-- Detected 80 CPUs and 1010 gigabytes of memory.
-- Detected Slurm with 'sinfo' binary in /local/genome/packages/slurm/15.08.5/bin/sinfo.
-- Detected Slurm with 'MaxArraySize' limited to 99999 jobs.
-- 
-- Found   1 host  with  12 cores and   31 GB memory under Slurm control.
-- Found   2 hosts with  80 cores and 1009 GB memory under Slurm control.
-- Found  18 hosts with   8 cores and   15 GB memory under Slurm control.
-- Found   7 hosts with  32 cores and  189 GB memory under Slurm control.
-- Found   3 hosts with   4 cores and    3 GB memory under Slurm control.
-- Found   1 host  with   6 cores and   14 GB memory under Slurm control.
-- Found   1 host  with  48 cores and  189 GB memory under Slurm control.
-- Found   2 hosts with  12 cores and   62 GB memory under Slurm control.
--
--                     (tag)Threads
--            (tag)Memory         |
--        (tag)         |         |  algorithm
--        -------  ------  --------  -----------------------------
-- Grid:  meryl      8 GB    4 CPUs  (k-mer counting)
-- Grid:  cormhap    6 GB    4 CPUs  (overlap detection with mhap)
-- Grid:  obtovl     4 GB    4 CPUs  (overlap detection)
-- Grid:  utgovl     4 GB    4 CPUs  (overlap detection)
-- Grid:  ovb        2 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs        8 GB    1 CPU   (overlap store sorting)
-- Grid:  red        3 GB    4 CPUs  (read error detection)
-- Grid:  oea        4 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat       16 GB    4 CPUs  (contig construction)
-- Grid:  gfa        8 GB    4 CPUs  (GFA alignment and processing)
--
-- In 'strain4-canu-maxcov.gkpStore', found Nanopore reads:
--   Raw:        332249
--   Corrected:  216721
--   Trimmed:    196452
--
-- Generating assembly 'strain4-canu-maxcov' in '/mnt/SCRATCH/rmeisal/strain4-canu-maxcov'
--
-- Parameters:
--
--  genomeSize        4800000
--
--  Overlap Generation Limits:
--    corOvlErrorRate 0.3200 ( 32.00%)
--    obtOvlErrorRate 0.1440 ( 14.40%)
--    utgOvlErrorRate 0.1440 ( 14.40%)
--
--  Overlap Processing Limits:
--    corErrorRate    0.5000 ( 50.00%)
--    obtErrorRate    0.1440 ( 14.40%)
--    utgErrorRate    0.1440 ( 14.40%)
--    cnsErrorRate    0.1920 ( 19.20%)
--
--
-- BEGIN ASSEMBLY
--
--
-- Running jobs.  First attempt out of 2.
--

CRASH:
CRASH: Canu 1.7
CRASH: Please panic, this is abnormal.
ABORT:
CRASH:   Failed to submit batch jobs.
CRASH:
CRASH: Failed at /mnt/various/local/genome/packages/canu/1.7/Linux-amd64/bin/../lib/site_perl/canu/Execution.pm line 1101.
CRASH: 	canu::Execution::submitOrRunParallelJob("strain4-canu-maxcov", "red", "unitigging/3-overlapErrorAdjustment", "red", 1, 2, 3, 4, ...) called at /mnt/various/local/genome/packages/canu/1.7/Linux-amd64/bin/../lib/site_perl/canu/OverlapErrorAdjustment.pm line 351
CRASH: 	canu::OverlapErrorAdjustment::readErrorDetectionCheck("strain4-canu-maxcov") called at /local/genome/packages/canu/1.7/bin/canu line 685
CRASH: 
CRASH: Last 50 lines of the relevant log file (unitigging/3-overlapErrorAdjustment/red.jobSubmit-01.out):
CRASH:
CRASH:

sbatch: error: Batch job submission failed: Pathname of a file, directory or other parameter too long