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riteshkrishna / mzidentml-lib

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Error at Tandem2mzid #19

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
I generate a .xml created by rTandem a package of R 
when i try to convert it to mzid with this library i get an error that says:
"Error running pipeline, see feedback"

I am running it on a windows xp 
I can run the .xml created by rTandem with peptide shaker so it is ok.

Maybe a problem with library?, the dummy .xml works fine.

Original issue reported on code.google.com by xabier...@gmail.com on 25 Sep 2014 at 2:34

GoogleCodeExporter commented 9 years ago 
Can you post the zipped XML file here and we'll take a look.

The library has only been tested on the output of X!Tandem, so if the format is 
radically different, then it won't be supported.

best wishes
Andy

Original comment by andrewro...@googlemail.com on 25 Sep 2014 at 3:00

GoogleCodeExporter commented 9 years ago 
Here it is.

thx

Original comment by xabier...@gmail.com on 25 Sep 2014 at 8:06

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GoogleCodeExporter commented 9 years ago 
I had added it to web .

2014-09-25 17:00 GMT+02:00 <mzidentml-lib@googlecode.com>:

Original comment by xabier...@gmail.com on 26 Sep 2014 at 9:10

GoogleCodeExporter commented 9 years ago 
Had you receive it??

Original comment by xabier...@gmail.com on 30 Sep 2014 at 8:57

GoogleCodeExporter commented 9 years ago 
Hi Xabier, I have had a quick look at the file, and the format looks basically 
sensible but clearly is causing us some unexpected problems. I have flagged the 
message for Pieter Lukasse to take a look at, since he looks after this part of 
the mzidLibrary. We will try have an answer shortly, but I can't speak for 
Pieter, so I don't know exactly when,
best wishes
Andy

Original comment by andrewro...@googlemail.com on 30 Sep 2014 at 9:02

GoogleCodeExporter commented 9 years ago 
Thx, i'm looking forward to seeing it working.
xabi

Original comment by xabier...@gmail.com on 1 Oct 2014 at 12:18

GoogleCodeExporter commented 9 years ago 
Hi Xabi,

I tested your file, and for the Tandem2mzid conversion it seems to work fine. 
Can you send more details about how you are running the "pipeline" (e.g. what 
are the parameters you are using? Are you using an UI or the command line?)

Best regards,

Pieter.

Original comment by pieterlu...@gmail.com on 3 Oct 2014 at 1:49

GoogleCodeExporter commented 9 years ago 
Hi Xabi,

hereby also the proof the translation worked (see attachment) ;)

Regards,

Pieter

Original comment by pieterlu...@gmail.com on 3 Oct 2014 at 1:55

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GoogleCodeExporter commented 9 years ago 
Hi, i tried it using console, puting this command   ->>>
java -jar "C:\Documents and 
Settings\d728140\Escritorio\tandem2mzid\mzidentml-lib-1.6.10\mzidentml-lib.jar" 
Tandem2mzid "C:\Documents and 
Settings\d728140\Escritorio\tandem2mzid\OutputPrueba.xml" "C:\Documents and 
Settings\d728140\Escritorio\tandem2mzid\OutputPruebaHecho.mzid" 
XtandemPercolator -decoyRegex decoyregex -compress true

Y tried using GUI puting this(look at message photo)

Using that .xml file

Original comment by xabier...@gmail.com on 3 Oct 2014 at 2:25

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GoogleCodeExporter commented 9 years ago 
what command did you used???????  :/

Original comment by xabier...@gmail.com on 3 Oct 2014 at 2:26

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
i used 1.6.10 version, maybe u used a new develop version ??

Original comment by xabier...@gmail.com on 7 Oct 2014 at 12:39

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
Can i get help with this?

Original comment by xabier...@gmail.com on 9 Oct 2014 at 2:52

GoogleCodeExporter commented 9 years ago 
Hi Xabier,
Please be patient, we will try to find a solution as soon as possible, but we 
don't have the resources for solving all problems instantly.
best wishes
Andy

Original comment by andrewro...@googlemail.com on 9 Oct 2014 at 3:00

GoogleCodeExporter commented 9 years ago 
Hi Xabier,

One further follow up on this from my side, the command you have used does not 
look correct. XTandemPercolater is not the Tandem2mzid converter, please check 
the user guide.

An example command would be:

java -jar "mzidentml-lib.jar" Tandem2mzid mydata.xml mydata_tandem.mzid.gz 
-outputFragmentation false -decoyRegex Rev_ -databaseFileFormatID MS:1001348 
-massSpecFileFormatID MS:1001062 -idsStartAtZero false -compress true

best wishes
Andy

Original comment by andrewro...@googlemail.com on 9 Oct 2014 at 3:04

GoogleCodeExporter commented 9 years ago 
thx Andy, looks like its a prob in rTandem file i seent you, couse it says 
there is a problem with "content not allowed in the final section, of the input 
.XML".

Can see in attached image.

xabi

Original comment by xabier...@gmail.com on 10 Oct 2014 at 7:18

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GoogleCodeExporter commented 9 years ago 
hi

Any idea how to solve it?
how do you convert it to mzid?

xabi

Original comment by xabier...@gmail.com on 13 Oct 2014 at 12:06

GoogleCodeExporter commented 9 years ago 
Hi Xabi, 

sorry for the delayed response. I tried your file again with my wrapper 
available at http://galaxy.wur.nl (search for "DB search converter"). See also 
screenshot. Is this helpful or are you really looking for a way to run this via 
command line to integrate it in a local pipeline? (For your information, this 
same website also has an X!Tandem wrapper). See screenshot.

Regards,

Pieter.

Original comment by pieterlu...@gmail.com on 19 Nov 2014 at 3:21

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