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MBoemo / DNAscent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.
https://www.boemogroup.org/
GNU General Public License v3.0
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DNAScent region thresholding #15

Closed john-alexander closed 3 years ago

john-alexander commented 3 years ago

Dear Michael,

Tried having a play with --threshold and --p and ran into the following errors.

 /data/scratch/DBC/UBCN/BCRBIOIN/SHARED/software/DNAscent/v2.0.2/DNAscent/bin//DNAscent regions -d ./output_DNAscent/barcode04.detect -o ./output_DNAscent/barcode04.thres2.regions --threshold 0.99
Estimating analogue incorporation...
[===================================] 100%   17997/17997   0hr 0min 0sec  
Done.
Estimated fraction of analogue substitution in analogue-positive regions: -nan
Setting Z-score threshold...
Done.===============================] 100%   17997/17997   0hr 0min 0sec  
terminate called after throwing an instance of 'NegativeLog'
  what():  Negative value passed to natural log function.
Aborted (core dumped)
/data/scratch/DBC/UBCN/BCRBIOIN/SHARED/software/DNAscent/v2.0.2/DNAscent/bin//DNAscent regions -d ./output_DNAscent/barcode04.detect -o ./output_DNAscent/barcode04.thres2.regions -p 0.01        
Setting Z-score threshold...
Done.===============================] 100%   17997/17997   0hr 0min 0sec  
terminate called after throwing an instance of 'NegativeLog'
  what():  Negative value passed to natural log function.
Aborted (core dumped)
MBoemo commented 3 years ago

This should now be fixed in commit 74b5b7a, just pull from master and recompile. Closing for now, but let me know if there are any further issues.