ERROR : Failed to find the number of jobs in 'unitigging/0-mercounts/meryl-count.sh'. 2.3dev

[lborcard]

Dear Canu Team,

I have recently compiled a more recent version of Canu (-- canu snapshot v2.3-development +162 changes (r10433 c61ebbb) to assemble small amplicons and it seems that the software works (in a singularity container) but it throws an error after this command:

initial command:
canu \
    -p barcode10 \
    -nanopore \
    genomeSize=1000 \
    'readSamplingCoverage=100' 'minReadLength=300' 'minOverlapLength=100' contigFilter='2 0 1.0 0.5 0' 'stopOnLowCoverage=0' 'corMhapSensitivity=high'  \
    maxThreads=12 \
    barcode10.trimmed.fastq.gz


Last successful command before the error:
     cd .
      /usr/local/bin/sqStoreDumpFASTQ \
        -trimmed \
        -S ./barcode10.seqStore \
        -o ./barcode10.trimmedReads.gz \
        -fasta \
        -trimmed -normal -nolibname \
      > ./barcode10.trimmedReads.fasta.err 2>&1

error

-- Starting command on Mon Jun 10 09:38:12 2024 with 3453.153 GB free disk space

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

-- Finished on Mon Jun 10 09:38:12 2024 (furiously fast) with 3453.153 GB free disk space
----------------------------------------
--  segments   memory batches
--  -------- -------- -------
--
--  For 0 reads with 0 bases, limit to 0 batches.
--  Will count kmers using  jobs, each using  GB and 4 threads.
--
-- Finished stage 'merylConfigure', reset canuIteration.

ABORT:
ABORT: canu snapshot v2.3-development +162 changes (r10433 c61ebbb7a5f90abb9c034650e2fd95642138de31)
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 'unitigging/0-mercounts/meryl-count.sh'.
ABORT:

best regards,

Loïc

[skoren]

Sorry for not getting back to you earlier. The log indicates there are no input reads (-- For 0 reads with 0 bases, limit to 0 batches.). Is the trimmed file empty? Can you post the full canu report for this run?

[brianwalenz]

I'm with Serge here. The original command had stopOnLowCoverage=0 which will disable the low coverage check causing the failure - instead of a graceful exit - when all reads were trimmed out.