Does Shortbred.quantify generate empty results. file?

[Violetta Florova]

I faced up with the event that I don't get results.file  output from all my shortbred.quantify runs. Although the -tmp folders were created.

Does it mean that results files from "no-match" runs weren't generated by default?

If it does - how can I change this settings? Since It would be more convenient for analysing the data after merging all 'results' output files

P.S.

Also I get this notes in my nophup.out files after the run, can it affect on the results?

 File "./shortbred_quantify_test.py", line 526, in <module>

   for seq in SeqIO.parse(streamWGS, strFormat):

 File "/util/academic/biopython/1.70/anaconda-5.0.1/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 611, in parse

   for r in i:

 File "/util/academic/biopython/1.70/anaconda-5.0.1/lib/python2.7/site-packages/Bio/SeqIO/QualityIO.py", line 1033, in FastqPhredIterator

   for title_line, seq_string, quality_string in FastqGeneralIterator(handle):

 File "/util/academic/biopython/1.70/anaconda-5.0.1/lib/python2.7/site-packages/Bio/SeqIO/QualityIO.py", line 918, in FastqGeneralIterator

   raise ValueError("End of file without quality information.")

ValueError: End of file without quality information.

('Using this version of usearch: ', u'v8.0.1623')

Thank you,

 

[Jim Kaminski]

Hi Violetta,

I think this might be due to the extension on the filenames. If these are labeled as fastq files but are fasta files, then the "SeqIO.parse" step will fail to convert them.

I apologize for my late response. Please also let me know if you still have the problem mentioned in your email, "ErrNo 32 during building markers database" on 12/14/2017.

Thank you,

Jim

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