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Old 08-08-2012, 06:41 AM   #11
ZFHans
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Location: Leiden

Join Date: Jun 2009
Posts: 10
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Hi LSC,

As it turned out it was my mistake all along. I'm using quake corrected Illumina reads as SR input. The fasta headers of these reads contain spaces, and that was causing problems in convertNAV.py I corrected this by removing the spaces from the headers and now the novocraft native output format is understood by convertNAV.py The script now continues to correct_nonredundant.py but gives then the following error:
Traceback (most recent call last):
File "/usr/local/LSC_0.2/bin/correct_nonredundant.py", line 280, in <module>
n_rep = int(NSR.split('_')[1])
IndexError: list index out of range
This is probably still some problem of too many fields
Could you indicate how the headers of the input files should look like (both the LR and SR)

Many thanks in advance,

Hans
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