[interhelp #33970] "-f tsv -iprlookup" - tabular output does not include IPR entries

[GoogleCodeExporter]

What steps will reproduce the problem?
1. interproscan-5.8-49.0/interproscan.sh -i test -f tsv -goterms -iprlookup -pa 
--disable-precalc

What is the expected output? What do you see instead?
I would like to see the InterPro entries matching the found Pfam, Superfamily, 
etc entries. Instead I only get the Pfam IDs. This is NOT the case, when 
writing XML output. 

What version of the product are you using? On what operating system?
5.8-49.0 on Debian Wheezy 64 bit

Please provide any additional information below.
Find attached the used input "test", and the corresponding output in TSV and 
XML format.

Your help will be much appreciated!
Cheers and a happy new year!

Original issue reported on code.google.com by asis.hal...@gmail.com on 6 Jan 2015 at 2:50

Attachments:

• test.zip

[GoogleCodeExporter]

Original comment by Mr.Matth...@gmail.com on 6 Jan 2015 at 4:06

• Changed title: _[interhelp #33970] "-f tsv -iprlookup" - tabular output does not include IPR entries _

[GoogleCodeExporter]

Hi,

Thank you for the email! I tried your input file here and it worked as expected 
- the TSV did contain the IPR entries for me! So I'll have to ask some more 
questions...

You are not specifying the output file name with your command (-o or -b or -d). 
That is OK, so it will use the default filename. The first time you ran with 
"-f tsv" it would default to test.tsv and the first time you ran with "-f xml" 
it would default to test.xml. If running again and test.tsv already exists then 
it would use test_1.tsv or test_2.tsv etc instead. So if you ran multiple 
similar commands, it's worth confirming you are looking at the output file 
produced with the iprlookup option, as it could be in test_1.tsv or similar? 

So _number can sometimes cause confusion, otherwise I'm not sure how this 
happened!

I assume you installed it as described here?
https://code.google.com/p/interproscan/wiki/HowToDownload

And there weren't any errors reported during the installation process? Or when 
running your test file? And the test.tsv you emailed was the output from 
InterProScan, you didn't process it afterwards in any way?

Do you only see this behaviour with this test file, or do others like the 
test_proteins.fasta we provide work OK?

If you have any other information that may help reproduce this then that would 
be useful!

Thanks,

Matthew
InterPro team

Original comment by Mr.Matth...@gmail.com on 8 Jan 2015 at 12:21

[GoogleCodeExporter]

Dear Matthew,

after our cluster has been updated by the system administrators the problem 
disappeared. Since today I cannot reproduce the error. I inquired whether they 
could investigate which now updated libraries could have caused the problem. 
Unfortunately the system administrators replied with "As long as it works now, 
we prefer to focus our time on more pressing tasks." 
I apologize for having raised this issue and now being unable to provide 
further information.

Keep up the good work and have a prosperous happy new year!
Cheers!

Original comment by asis.hal...@gmail.com on 9 Jan 2015 at 8:29

[GoogleCodeExporter]

Hi,

Thanks for the update, glad it works now anyway! A happy new year to you too!

Regards, 

Matthew

Original comment by Mr.Matth...@gmail.com on 9 Jan 2015 at 10:55

[GoogleCodeExporter]

Original comment by Mr.Matth...@gmail.com on 9 Jan 2015 at 10:58

• Changed state: Done