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UnboundLocalError: local variable 'hit' referenced before assignment when using '--fasta_db' #58

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Alenap26 opened this issue Jul 15, 2019 · 3 comments

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@Alenap26
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Hi,
I'm trying to use my personal db:
amptk taxonomy -f miseq.lulu.otus.fa -i miseq.lulu.otu_table.txt -m miseq.mapping_file.txt --fasta_db silva18S.fa -o miseq

I also tried (like: #55 ):
amptk taxonomy -f miseq.lulu.otus.fa -i miseq.lulu.otu_table.txt -m miseq.mapping_file.txt --fasta_db db_18S/silva18S.fa -o miseq -u usearch9

but I have the same error:
`
Traceback (most recent call last):
File "/Users/Alessandro/anaconda3/bin/amptk", line 735, in
main()
File "/Users/Alessandro/anaconda3/bin/amptk", line 726, in main
mod.main(arguments)
File "/Users/Alessandro/anaconda3/lib/python3.7/site-packages/amptk/assign_taxonomy.py", line 320, in main
bestClassify = amptklib.bestclassifier(utaxDict, sintaxDict, otuList)
File "/Users/Alessandro/anaconda3/lib/python3.7/site-packages/amptk/amptklib.py", line 1494, in bestclassifier
BestClassify[otu] = hit
UnboundLocalError: local variable 'hit' referenced before assignment
'

@Alenap26
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I'm looking for to use db SILVA 18S, I saw that's an open issue : #44
Is not possibile to use the db in fasta format as I have tried ?

@nextgenusfs
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If you use only the global alignment search it should be okay (any fasta should work), ie —method usearch.

@Alenap26
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Ok thanks

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