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thegenemyers / DALIGNER

Find all significant local alignments between reads
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Error in HPC.daligner (I think): No such file or directory #72

Closed pb-cdunn closed 6 years ago

pb-cdunn commented 6 years ago 
HPC.daligner comp ../0-rawreads/raw_reads.db| bash -vex
# Daligner jobs (1)
daligner -A -k20 -h50 -e0.85 ../0-rawreads/raw_reads comp && mv raw_reads.comp ../0-rawreads
+ daligner -A -k20 -h50 -e0.85 ../0-rawreads/raw_reads comp
+ mv raw_reads.comp ../0-rawreads
mv: cannot stat `raw_reads.comp': No such file or directory

The file is named raw_reads.comp.las.

Here is the output of HPC.daligner:

# Daligner jobs (1)
daligner -A -k20 -h50 -e0.85 ../0-rawreads/raw_reads comp && mv raw_reads.comp ../0-rawreads
# Check initial .las files jobs (1) (optional but recommended)
LAcheck -vS ../0-rawreads/raw_reads comp ../0-rawreads/raw_reads.comp

This error does not occur in our current fork, which is a bit behind, so this is a recent bug.

thegenemyers commented 6 years ago

Yes, you are correct. Corner case that I missed. Fixed now. -- Gene

On 11/6/17, 3:56 PM, Christopher Dunn wrote:

|HPC.daligner comp ../0-rawreads/raw_reads.db| bash -vex

Daligner jobs (1)

daligner -A -k20 -h50 -e0.85 ../0-rawreads/raw_reads comp && mv raw_reads.comp ../0-rawreads

  • daligner -A -k20 -h50 -e0.85 ../0-rawreads/raw_reads comp
  • mv raw_reads.comp ../0-rawreads mv: cannot stat `raw_reads.comp': No such file or directory |

The file is named |raw_reads.comp.las|.

Here is the output of HPC.daligner:

|# Daligner jobs (1) daligner -A -k20 -h50 -e0.85 ../0-rawreads/raw_reads comp && mv raw_reads.comp ../0-rawreads

Check initial .las files jobs (1) (optional but recommended)

LAcheck -vS ../0-rawreads/raw_reads comp ../0-rawreads/raw_reads.comp |

This error does /not/ occur in our current fork, which is a bit behind, so this is a recent bug.

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