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drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
https://drivenbyentropy.github.io/
GNU General Public License v3.0
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AptaTRACE does not complete #1

Closed CentauriAlex closed 6 years ago

CentauriAlex commented 6 years ago

Hi,

Having run the v0.4 I am unable to get the AptaTRACE function to complete, please see attached log file.

Thanks. log_2017-08-21_08-33-11.txt

drivenbyentropy commented 6 years ago

Thank you reporting this. I think this was caused due to an unchecked condition when dealing with missing data between selection cycles in AptaTRACE. I have updated the current release with a fix (see 6619bb203fff199d5f2ef47a468f6b072a976f2e, v.0.4.1). Please download this version and let me know if it fixes the issue.

Thanks!

CentauriAlex commented 6 years ago

Hi,

I have downloaded the v0.4.1 and re-run the AptaTRACE, which gets a bit further but gives a different error. Please see attached log file.

Thanks

log_2017-08-22_07-32-09.txt

drivenbyentropy commented 6 years ago

I believe this is caused when AptaTRACE encounters a sequence which only occurs in a negative or counter selection. I have added this case to the code base (see aa02c4b7e8cbf7333f6aa908367d4ca71fdd746e). Please try again with v.0.4.2 and let me know if it works now.

Thanks

CentauriAlex commented 6 years ago

Hi,

That appears to have fixed it!

Many Thanks

drivenbyentropy commented 6 years ago

Great. Thanks again for reporting this bug.