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decodebiology / interproscan

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Feature request: report query sequences with no-hits in output #15

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Ran standalone interproscan on multi-fasta amino acid file.
2. Job was terminated by computer cluster due to time constraints.
3. From tsv output it is impossible to tell which query sequences tried and 
failed. Query sequence do not appear in tsv file in same order as in fasta file.

Please consider adding an option where query sequences whose search completed 
and resulted in no-hits are reported as such. 

Thank you!

Original issue reported on code.google.com by son...@gmail.com on 15 Feb 2013 at 1:57

GoogleCodeExporter commented 9 years ago 
Dear Sonia,
Thank you very much for using InterProScan 5.

You wrote the job was terminated. Could you please confirm that it was the 
final result writing job? That's a bit unfortunate, because the final result 
writing step is the last step in the pipeline after all sequences have been 
analysed.

It is true query sequences with no hits won't show up in the TSV output file, 
but you will find all of them inside the XML file regardless whether they do 
have matches or not. We will discuss your point internally.
From having a quick look into the code they should be in the same order as in 
the input file, but that's not for sure because the software is quite complex.

I am sorry to say that but I think you need to re-run the analysis by switching 
on the TSV and the XML output formats.

As the cluster functionality is quite new in InterProScan 5 we are interest in 
which cluster you are using plus the version and I would also like to let you 
know that we are working towards to support SGE as well.

Kind Regards,
Maxim

Original comment by Maxim.Sc...@gmail.com on 19 Feb 2013 at 11:15

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 May 2014 at 9:11

GoogleCodeExporter commented 9 years ago

Original comment by Maxim.Sc...@gmail.com on 15 May 2014 at 9:13