The bioBakery help forum

Shortbred error 0 reads in file

Hello,

I get the following error when running shortbred on some of our files:

Traceback (most recent call last):
File “/opt/anaconda/envs/python2/bin/shortbred_quantify.py”, line 588, in
dReadLength = float(args.iAvgReadBP), iWGSReads = iTotalReadCount, strCentCheck=args.strCentroids,dAlnLength=args.dAlnLength,strFile = strInputFile)
File “/opt/anaconda/envs/python2/bin/src/quantify_functions.py”, line 580, in CalculateCounts
sys.stderr.write(“WARNING: 0 Reads found in file:” + strFile )
TypeError: cannot concatenate ‘str’ and ‘list’ objects
(python2) vaccaro1@JOAN9000:~$

The input fasta files clearly have reads in them, so I don’t know why I get this error.

Thanks.

Daniel Barich
Biology Department
Kenyon College