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Old 06-24-2015, 02:38 PM   #1
LucasH
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Location: Nebraska

Join Date: Jun 2015
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Default Trouble with iCORN step of PAGIT

Hello,

I am trying to run iCORN as part of the PAGIT package and am having difficulty working with it. It may be that my file structure is different than what it expects, but it can't find the *.fasta.?.ref.fa or *.fasta.?.qry.fa files it is supposed to create after each iteration.

The resulting mapping folder populates with the ins, del and snp files, but the next iteration of the fasta file is created as an empty file (28 bytes, only a name, no content) and can't be used for downstream processing.

Has anyone run into something similar to this? Or, does anyone have any suggestions on how I should proceed to fix this? Thanks!
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Old 08-26-2015, 03:27 AM   #2
mtswain
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Location: Aberystwyth

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Default

It could be easiest to try the updated version of ICORN (ICORN2), downloadable from here with updated instructions:

http://icorn.sourceforge.net/
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