GoogleCodeExporter
commented
8 years ago Plz, will somebody help me outOriginal comment by mirzagol...@gmail.com on 21 Aug 2015 at 7:13
Open GoogleCodeExporter opened 8 years ago
GoogleCodeExporter
commented
8 years ago Plz, will somebody help me outOriginal comment by mirzagol...@gmail.com on 21 Aug 2015 at 7:13
GoogleCodeExporter
commented
8 years ago Original comment by Mr.Matth...@gmail.com on 21 Aug 2015 at 7:42
GoogleCodeExporter
commented
8 years ago Hi,
This isn't an error I've seen before, but it could be input sequence related.
Do all your sequences conform to this:
https://code.google.com/p/interproscan/wiki/InputFormat
"InterProScan 5 supports unaligned sequences only. Sequences should contain
only valid IUPAC amino acid or nucleic acid characters. In addition gap ('-'),
period ('.'), asterix or underscore symbols are not allowed and should produce
warnings..."
If you still have problems then is it a certain sequence/small selection of
sequences causing this? If you are happy to share, you can send us a test input
so we can see if we have the same problem.
Thanks,
MattOriginal comment by Mr.Matth...@gmail.com on 21 Aug 2015 at 8:14
GoogleCodeExporter
commented
8 years ago
Hi,
thanks for replying.
I suspected the same and have spent 3-4 days trying to figure it out. I
converted all my sequences to fasta format using the tool
"http://www.ebi.ac.uk/Tools/services/rest/emboss_seqret/result/emboss_seqret"
to make sure.
I am attaching a set of my sequences. Kindly let me know the problem.Original comment by mirzagol...@gmail.com on 21 Aug 2015 at 8:26
Attachments:
GoogleCodeExporter
commented
8 years ago I've tried your xaa.txt fasta files with the 64-bit released and it works fine.
Have you changed any of the entries in the properties file? Binaries? Are you
able to identify which sequence is the problem?
The stack trace suggests PRINTS - do the other member databases work as
expected (i.e. using -appl with either just PRINTS or everything except PRINTS)?
SimonOriginal comment by s...@ebi.ac.uk on 21 Aug 2015 at 10:02
GoogleCodeExporter
commented
8 years ago I am new to linux based system/ softwares.
I have downloaded and installed it exactly according to the commands given on
https://code.google.com/p/interproscan/wiki/ and checked (md5), the
installation was successful. I haven't made any changes 'coz I don't really
know how to.
Can u please elaborate your comment-
"he stack trace suggests PRINTS - do the other member databases work as
expected (i.e. using -appl with either just PRINTS or everything except
PRINTS)?"
What would you suggest?
Original comment by mirzagol...@gmail.com on 21 Aug 2015 at 10:14
GoogleCodeExporter
commented
8 years ago If the file is running successfully in your system, this means that the seq
format is ok. What command did you use to run my file? What command line would
you suggest me to execute the job?Original comment by mirzagol...@gmail.com on 21 Aug 2015 at 10:17
GoogleCodeExporter
commented
8 years ago The file certainly looked correctly formatted. Try running just PRINTS:
./interproscan.sh -i xaa.fa -o xaa-1.tsv -appl PRINTS -f tsv
or everything else:
./interproscan.sh -i xaa.fa -o xaa-1.tsv -appl
ProDom,Hamap,SMART,ProSiteProfiles,ProSitePatterns,SUPERFAMILY,Gene3D,PIRSF,Pfam
-f tsvOriginal comment by s...@ebi.ac.uk on 21 Aug 2015 at 10:38
GoogleCodeExporter
commented
8 years ago thank you, I'll try these and let you know the results.Original comment by mirzagol...@gmail.com on 21 Aug 2015 at 11:36
GoogleCodeExporter
commented
8 years ago
The second command worked, thank you so much. But,
I have a question, when this Interproscan is standalone, why it needs net
connectivity? Is continuous net connectivity mandatory?
The net connectivity was lost and I got these msgs-
The pre-calculated match lookup service has been configured in the
interproscan.properties file.
precalculated match lookup service url : http://www.ebi.ac.uk/interpro/match-lookup
precalculated match lookup service proxy host : proxy port : 3128
Unfortunately the web service has failed. Check the configuration of this
service
in the interproscan.properties file and, if necessary, set the following
property to look like this:
precalculated.match.lookup.service.url=
If the problem persists, check if this is a firewall or proxy issue. If it is a
proxy issue, then setting
the following property in the interproscan.properties file should work:
precalculated.match.lookup.service.proxy.host=
precalculated.match.lookup.service.proxy.port=
If this still does not work please inform the InterPro team of this error
by sending an email to:
interhelp@ebi.ac.uk
In the meantime, the analysis will continue to run locally.Original comment by mirzagol...@gmail.com on 22 Aug 2015 at 4:36
GoogleCodeExporter
commented
8 years ago 2nd Que,
-appl PRINTS didn't work, will it effect my outcome?Original comment by mirzagol...@gmail.com on 22 Aug 2015 at 4:42
GoogleCodeExporter
commented
8 years ago and can you suggest possible reason & solution for failure of "PRINTS"
In the prints folder within bin, I can see only one fingerPRINTScan executable
file.Original comment by mirzagol...@gmail.com on 22 Aug 2015 at 5:08
GoogleCodeExporter
commented
8 years ago How can I get the output in svg format using the above command line
./interproscan.sh -i xaa.fa -o xaa-1.tsv -appl
ProDom,Hamap,SMART,ProSiteProfiles,ProSitePatterns,SUPERFAMILY,Gene3D,PIRSF,Pfam
-f tsv
I used
./interproscan.sh -i xab-1.fa -o xab-1.svg.tar.gz -appl
ProDom,Hamap,SMART,ProSiteProfiles,ProSitePatterns,SUPERFAMILY,Gene3D,PIRSF,Pfam
-f svg
it gave
"You must indicate a single output format excluding HTML and SVG using the -f
option if you wish to set an explicit output file name"
Original comment by mirzagol...@gmail.com on 24 Aug 2015 at 7:44
GoogleCodeExporter
commented
8 years ago We're unable to reproduce the problem with prints here. I've just re-built the
fingerPRINTScan binary (attached 64-bit version). Could you please try this?
Either
mv bin/prints/fingerPRINTScan bin/prints/fingerPRINTScan.old
cp <attached file> bin/prints/fingerPRINTScan
or
cp <attached file> bin/prints/fingerPRINTScan.test
edit interproscan.properties and set:
binary.fingerprintscan.path=bin/prints/fingerPRINTScan.test
Regards,
SimonOriginal comment by s...@ebi.ac.uk on 24 Aug 2015 at 10:29
Attachments:
GoogleCodeExporter
commented
8 years ago Regarding SVG output - you can do this:
-f svg -b xab-1
and that will output the tar archive xab-1.svg.tar.gzOriginal comment by s...@ebi.ac.uk on 24 Aug 2015 at 10:57
GoogleCodeExporter
commented
8 years ago Hi,
Simon's replied to most of your other points already, here's #10 and #11:
Comment #10: As part of an InterPro data release we pre-calculate the matches
for the known sequences in the database. Therefore if you search InterProScan
with a known sequence then to improve performance we don't re-calculate
everything from scratch, we just return the matches from the lookup service
http://www.ebi.ac.uk/interpro/match-lookup
It's a service shared by many InterProScan users and there was a temporary
technical issue over the weekend where this service failed, apologies for that.
It seems OK now though.
There is an option of installing your own lookup service as described
https://github.com/ebi-pf-team/interproscan/wiki/LocalLookupService
Or you can use the -dp option to disable the service (so everything is
calculated from scratch). See usage instructions:
https://github.com/ebi-pf-team/interproscan/wiki/HowToRun
And for your point #11 - you can run InterProScan without the PRINTS analysis,
but by turning it off you won't get any PRINTS matches. Simon's suggestions may
help...
Also please note that Google code website is shutting down soon and the content
will be read-only from tomorrow. Therefore the InterProScan documentation is
moving to GitHub: https://github.com/ebi-pf-team/interproscan/wiki
Thanks,
MattOriginal comment by Mr.Matth...@gmail.com on 24 Aug 2015 at 12:18
Original issue reported on code.google.com by
mirzagol...@gmail.comon 19 Aug 2015 at 9:40Attachments: