no Corrected reads created

[lborcard]

Dear Canu team,

We had contacted you last year regarding the assembly of amplicon and you had kindly answered. Our test with amplicon of size>1000 showed promising results. We now tested we new data of amplicon ~400bp and the output is more erratic but mostly empty. We are getting this error message for certain samples while do produce a contig file:

  -- Finished on Thu Mar 21 14:54:37 2024 (one second) with 486.595 GB free disk space
  ----------------------------------------
  -- Found 1 read correction output files.
  -- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
  -- Found 1 read correction output files.
  -- Finished stage 'cor-generateCorrectedReadsCheck', reset canuIteration.
  --
  -- Loading corrected reads into corStore and seqStore.
  ----------------------------------------
  -- Starting command on Thu Mar 21 14:54:37 2024 with 486.595 GB free disk space

      cd correction
      /usr/local/bin/loadCorrectedReads \
        -S ../barcode07.seqStore \
        -C ./barcode07.corStore \
        -L ./2-correction/corjob.files \
      >  ./barcode07.loadCorrectedReads.log \
      2> ./barcode07.loadCorrectedReads.err

  -- Finished on Thu Mar 21 14:54:37 2024 (like a bat out of hell) with 486.591 GB free disk space
  ----------------------------------------
  --
  -- No corrected reads generated; correctReads output saved.
  --
  -- Purging overlaps used for correction.
  -- Finished stage 'cor-loadCorrectedReads', reset canuIteration.
  ----------------------------------------
  -- Starting command on Thu Mar 21 14:54:37 2024 with 486.598 GB free disk space

      cd .
      /usr/local/bin/sqStoreDumpFASTQ \
        -corrected \
        -S ./barcode07.seqStore \
        -o ./barcode07.correctedReads.gz \
        -fasta \
        -nolibname \
      > barcode07.correctedReads.fasta.err 2>&1

  -- Finished on Thu Mar 21 14:54:37 2024 (in the blink of an eye) with 486.597 GB free disk space
  ----------------------------------------
  --
  -- Corrected reads saved in 'barcode07.correctedReads.fasta.gz'.
  -- Finished stage 'cor-dumpCorrectedReads', reset canuIteration.
  --
  -- Trimming skipped; no corrected reads exist in barcode07.seqStore.
  --
  -- Unitigging skipped; no corrected reads to assemble.
  --
  -- Bye.

canu v2.2

canu \
    -p barcode05 \
    -nanopore \
    genomeSize=1000 \
    'maxInputCoverage=100' 'minReadLength=150' 'minOverlapLength=50' contigFilter='3 0 1.0 0.8 0' 'stopOnLowCoverage = 0' 'corMhapSensitivity=high'  \
    maxThreads=12 \
    barcode05.trimmed.fastq.gz

gzip *.fasta

System: Centos, ran within nextflow.

thanks for the help

[lborcard]

Just to complete my question, these are amplicons with 50K+ reads .

[skoren]

There was an issue in v2.2 correcting reads less than 500bp, see https://github.com/marbl/canu/issues/2182. You can either use the latest tip of canu or wait for a release of v2.3 which should be done in the next couple of weeks.

[lborcard]

Thank you very much, I will update it then. Thanks for the work.

[lborcard]

Question answered

[lborcard]

I have tried to find a way to use the dev branch but the github docs say that it is not possible to compile from the github version and I really need to use the current updates how could I implement the newest changes? @skoren

[gringer]

The docs say that it is not possible to compile from downloaded .zip source code, but it should work if the repository is cloned; have you tried that?

[skoren]

Yes, @gringer is correct. You can checkout and compile the latest unreleased code following the instructions here: https://github.com/marbl/canu?tab=readme-ov-file#install. Starting with git clone.

[lborcard]

Ok I managed to compile from the repo into a singularity container (ubuntu), but now I am getting this error

  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:

Any idea if it's something on my end?

thanks a lot for the support,

[skoren]

Can you open a new issue and post the command you're using and the full canu output, including the report file it generates?

[lborcard]

Alright, I opened a new issue, thanks for the support!