Loading python3/3.7.4
  Loading requirement: intel-mkl/2019.3.199

Found perl:
   /bin/perl
   This is perl 5, version 26, subversion 3 (v5.26.3) built for x86_64-linux-thread-multi

Found java:
   /bin/java
   openjdk version "1.8.0_242"

Found canu:
   /apps/canu/2.0/bin/canu
   Canu 2.0

-- Canu 2.0
--
-- Detected Java(TM) Runtime Environment '1.8.0_242' (from 'java') with -d64 support.
-- Detected gnuplot version '5.2 patchlevel 4   ' (from 'gnuplot') and image format 'png'.
-- Detected 96 CPUs and 189 gigabytes of memory.
-- Detecting PBSPro resources.
--
-- Found 2875 hosts with  48 cores and  192 GB memory under PBSPro control.
-- Found 153 hosts with  48 cores and  203 GB memory under PBSPro control.
-- Found  49 hosts with  48 cores and 1536 GB memory under PBSPro control.
-- Found 160 hosts with  48 cores and  383 GB memory under PBSPro control.
-- Found   1 host  with  48 cores and 1503 GB memory under PBSPro control.
--
--                         (tag)Threads
--                (tag)Memory         |
--        (tag)             |         |  algorithm
--        -------  ----------  --------  -----------------------------
-- Grid:  meryl     12.000 GB    4 CPUs  (k-mer counting)
-- Grid:  hap        8.000 GB    4 CPUs  (read-to-haplotype assignment)
-- Grid:  cormhap    6.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  obtmhap    6.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  utgmhap    6.000 GB   16 CPUs  (overlap detection with mhap)
-- Grid:  cor        8.000 GB    4 CPUs  (read correction)
-- Grid:  ovb        4.000 GB    1 CPU   (overlap store bucketizer)
-- Grid:  ovs        8.000 GB    1 CPU   (overlap store sorting)
-- Grid:  red       16.000 GB    4 CPUs  (read error detection)
-- Grid:  oea        8.000 GB    1 CPU   (overlap error adjustment)
-- Grid:  bat       16.000 GB    4 CPUs  (contig construction with bogart)
-- Grid:  cns        -.--- GB    4 CPUs  (consensus)
-- Grid:  gfa       16.000 GB    4 CPUs  (GFA alignment and processing)
...
----------------------------------------
-- Starting command on Tue Jun  9 09:44:08 2020 with 4913847.217 GB free disk space

    cd correction/0-mercounts
    ./meryl-configure.sh \
    > ./meryl-configure.err 2>&1

-- Finished on Tue Jun  9 09:44:09 2020 (one second) with 4913847.217 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--
--  For 1572 reads with 16809400 bases, limit to 1 batch.
--  Will count kmers using  jobs, each using  GB and 4 threads.
--
-- Report changed.
-- Finished stage 'merylConfigure', reset canuIteration.

ABORT:
ABORT: Canu 2.0
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:   failed to find the number of jobs in 'correction/0-mercounts/meryl-count.sh'.
ABORT:

if [ $jobid -gt  ]; then
  echo Error: Only  jobs, you asked for $jobid.
  exit 1
fi

canu \
    -d canu_out4 \
    -p rdna \
    overlapper=mhap \
    utgReAlign=true \
    genomeSize=84k \
    useGrid=true \
    gridEngineSubmitCommand="${CANU_BASE}/Linux-amd64/bin/jobwrapper.sh -j oe" \
    gridEngine=pbspro \
    gridEngineResourceOption="-lncpus=THREADS,mem=MEMORY" \
    gridEngineNameToJobIDCommand="qstat -f |grep -F -B 1 WAIT_TAG | grep Id: | cut -c 9-" \
    stageDirectory=\$PBS_JOBFS \
    gridEngineStageOption="-ljobfs=10GB" \
    gridEngineArrayMaxJobs=500 \
    gridOptionsExecutive="-lwalltime=4:00:00" \
    gridOptions="-q normal -lwd -P a00 -lstorage=tmp/a00" \
    -nanopore-raw 20samples.fastq 2> canu.log