Shortbred error 0 reads in file

Microbial community profiling ShortBRED
1

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

2

I have also encountered this error running shortbred_quantify.py on some .fastq files, where it has previously fully processed others. It also seems to be reporting hits correctly to the intermediate SBhits.txt and wgsfull_results.tab. This sub-forum doesn’t seem to be too active anymore, but will report back if I manage to troubleshoot it myself.

…
Reported 19574 pairwise alignments, 19574 HSPs.
17323 queries aligned.
Processing DIAMOND results…
Tabulating results for each marker…
[‘/XXX_R1.fastq’, ‘/XXX_R2.fastq’]Traceback (most recent call last):
File “/install/software/shortbred/biobakery-shortbred-918294a74d70/shortbred_quantify.py”, line 626, in
dAlnLength=args.dAlnLength,strFile = strInputFile)
File “/install/software/shortbred/biobakery-shortbred-918294a74d70/src/quantify_functions.py”, line 558, in CalculateCounts
sys.stderr.write(“WARNING: 0 Reads found in file:” + strFile )
TypeError: cannot concatenate ‘str’ and ‘list’ objects

3

After some time debugging it seems that the internal calls to convert .fastq to .fasta are not working properly, at least on a subset of my files - possibly a SeqIO deprecation issue?

In any case it was possible at least for me to workaround this by converting the .fastq files to .fasta myself and provide those directly to shortbred_quantify.py - may be an option for anyone else encountering similiar issues.