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Error correction of PE reads failed. Check pe.cor.log. #337

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mictadlo opened this issue Jan 14, 2024 · 0 comments
Open

Error correction of PE reads failed. Check pe.cor.log. #337

mictadlo opened this issue Jan 14, 2024 · 0 comments

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@mictadlo
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mictadlo commented Jan 14, 2024

Hi,
I got an error:

  1. Average PE read length -nan
    Illegal division by zero at -e line 1.
  2. Error correction of PE reads failed. Check pe.cor.log.
    However, I get pe.cor.log No such file or directory
  3. cat quorum.err
    [2024/01/08 07:41:31] Loading mer database
    [2024/01/08 07:48:30] Loading contaminant sequences
    [2024/01/08 07:48:30] Computing Poisson cutoff
    [2024/01/08 07:50:35] distinct mers:0 total mers:0 estimated coverage:-nan
    [2024/01/08 07:50:35] lambda:-nan collision_prob:0.00333333 poisson_threshold:0.0001
    [2024/01/08 07:50:35] Using cutoff of 0
    Cutoff computation failed. Pass it explicitly with -p switch.
> cat masurca.o6087258 
Verifying PATHS...
jellyfish OK
runCA OK
createSuperReadsForDirectory.perl OK
nucmer OK
mega_reads_assemble_cluster2.sh OK
creating script file for the actions...done.
execute assemble.sh to run assembly
[Mon Jan  8 07:28:00 Australia 2024] Processing pe library reads
[Mon Jan  8 07:28:00 Australia 2024] Average PE read length -nan
Illegal division by zero at -e line 1.
[Mon Jan  8 07:28:00 Australia 2024] Using kmer size of for the graph
[Mon Jan  8 07:28:00 Australia 2024] MIN_Q_CHAR: 64
[Mon Jan  8 07:28:01 Australia 2024] Creating mer database for Quorum
[Mon Jan  8 07:41:31 Australia 2024] Error correct PE
[Mon Jan  8 07:50:37 Australia 2024] Error correction of PE reads failed. Check pe.cor.log.

What did I do wrong?

Best wishes,

Michal

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