Abacus query

[srihari sharma]

Hello Damian,

I have used  iprophet.pep.xml files to create a combined prot.xml. My first question is, is this right or should I need only use interact.pep.xml to create a combined prot.xml?

Also, I have started my run with this iprophet files and the run has been stuck at 40% for a long time. Does this step usually take a while?

Thanks a lot,
Srihari

[Damian]

Hi Srihari,

Abacus takes either iprophet or regular prot.xml files but not a mix.
Your data has to be either all iprophet or all regular prot.xml

As for the sticking at 40% that suggests that it's crashing.

To find out for sure start the program from the Command Prompt by typing: java -jar abacus.jar

When the Abacus crashes, the error logs will be reported in the Command Prompt . If you could email me that output I can figure out what's going on.

Hope this helps,
Damian


srihari sharma wrote:

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[srihari sharma]

Hi Damian,

I tried running abacus through cmd using java -jar abacus.jar, but nothing responded. However I logged into abacus somehow using cmd and tried running(did not use the command give by u). It seems to not update any error when abacus stopped at 40%.

Could you please suggest me as to what I can do over this.

Thanks
Srihari

[Damian]

Hi Srihari,

Based upon your email it doesn't sound like Abacus is freezing, merely taking a long time.
If your data is particularly complex this will also slow it down.

How big are the files you are processing? Also, how many files?
Could you email me a list of the files you are trying to run through Abacus so I can take a look at their names?

Damian

srihari sharma wrote:

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[srihari sharma]

Hi damian,

I was finally able to capture the error msg on cmd. please see the attached files. I am trying to run 20 files.

Thanks a lot,
Srihari Sharma

[Damian]

Okay, this makes more sense.

The error message implies that Abacus read in peptide data it could not find proteins for.
This can happen if the protXML files are in complete or corrupted.

The protXML files are very small compared to the peptide files.
For example interact-C1.pep.xml is 62MB in size yet the interact-C1.prot.xml file is not even 1MB in size.
This is really weird, could you check to make sure the protXML files are correct?

Damian

srihari sharma

December 5, 2013 8:16 PM

srihari sharma

December 5, 2013 12:19 AM

Hi Damian,

I tried running abacus through cmd using java -jar abacus.jar, but nothing responded. However I logged into abacus somehow using cmd and tried running(did not use the command give by u). It seems to not update any error when abacus stopped at 40%.

Could you please suggest me as to what I can do over this.

Thanks
Srihari

On Wednesday, December 4, 2013 11:07:41 AM UTC+10, dfermin wrote:

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Damian

December 3, 2013 8:07 PM

Hi Srihari,

Abacus takes either iprophet or regular prot.xml files but not a mix.
Your data has to be either all iprophet or all regular prot.xml

As for the sticking at 40% that suggests that it's crashing.

To find out for sure start the program from the Command Prompt by typing: java -jar abacus.jar

When the Abacus crashes, the error logs will be reported in the Command Prompt . If you could email me that output I can figure out what's going on.

Hope this helps,
Damian


srihari sharma wrote:

srihari sharma

December 2, 2013 9:00 PM

Hello Damian,

I have used  iprophet.pep.xml files to create a combined prot.xml. My first question is, is this right or should I need only use interact.pep.xml to create a combined prot.xml?

Also, I have started my run with this iprophet files and the run has been stuck at 40% for a long time. Does this step usually take a while?

Thanks a lot,
Srihari

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You received this message because you are subscribed to the Google Groups "Abacus Support" group.

[srihari sharma]

Hello Damian,

Thanks a lot for your reply. I will go back to my original files and rerun them and then will try Abacus. Will tell you how it goes.

Thanks a lot for your time.

kind regards,
Srihari Sharma