Abacus freezes at 70%

[maik_mu...@hotmail.com]

Dear User Support,

when trying to use Abacus with 6x pep.xml and the corresponding 6x prot.xml, as well as the combined prot.xml file, Abacus stops at 70%, when "creating peptide usage table".

We already tried to freshly interact all the files, but it still doesn't run through.

Can you give us a hint what might be wrong?

Thanks a lot in advance,

abacus_user

[Damian]

Hi

Sorry to here you are having issues.
I need a little more info to help debug this.

Could you please run Abacus in the Windows CommandPrompt ?
To do this, start the Windows command prompt, go to the folder that contains Abacus and execute the command: java -jar abacus.jar

Then proceed as you normally do keeping the windows command prompt window open.
When Abacus crashes at the "creating peptide usage table" the error message will appear in the windows command prompt.

Also, can you tell me the names of the xml files you are given Abacus along with their file sizes.
Finally what are the specs of your computer? ie: Operating system? 32-bit? How much ram?

Thanks,
Damian

--
You received this message because you are subscribed to the Google Groups "Abacus Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to abacus-suppor...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[kswea...@systemsbiology.org]

I believe I have found the solution, so I wanted to post it here. I have been able to reproduce the problem of the program freezing at 30% when there is not an interact.prot.xml file for each input interact.pep.xml. Likewise, I can reproduce the problem of the program freezing at 70% if the individual interact.pep.xml files are not present.

I commonly search my data separately with XTandem and Comet. I run PeptideProphet separately on each batch of files. I then combine my comet.interact.pep.xml file with my tandem.interact.pep.xml file into a single interact.iproph.pep.xml file, and then run ProteinProphet on that file. In order to run Abacus, I needed to run ProteinProphet and produce a comet.interact.prot.xml and a tandem.interact.prot.xml file.

I had to read the paper and the tutorial a couple of times to fully grasp this. In summary, here is how you need to set up your data in order to run Abacus.

Any number of <filename>.pep.xml search engine output files are input into the TPP (InteractParser-->RefreshParser-->PeptideProphetParser) and produce a single Experiment.interact.pep.xml file.

Each Experiment.interact.pep.xml must be run through ProteinProphet to produce a Experiment.interact.prot.xml file. 

If there are multiple Experiment.interact.pep.xml files (for example, combining different search engines in iProphet or combining different biological replicates), then you must run Experiment-1.interact.pep.xml, Experiment-2.interact.pep.xml...Experiment-n.interact.pep.xml through ProteinProphet together and generate a combined COMBINED.interact.prot.xml.

All of the interact.pep.xml and interact.prot.xml files must be in the directory where Abacus is run.

[dfermin]

Thanks for posting this.

Damian

[Vidya Venkatraman]

I have a follow-up question on using multiple search engine data.

I have a dataset with 3 biologically different MS runs. I am using comet and xtandem as my search engines. Ultimately i would like to know the protein and peptide spectral counts for each of my 3 biologically different MS runs.

What i have tried so far is to:

1) Run each of the 3 MS run * 2 search engines through peptideprophet->Merge the multiple search engine results for each biological sample using iprophet->then run proteinprophet on each of the 3 iprophet.pep.xml -> followed by a combined proteinprophet run on the 3 iprophet.pep.xmls

In the latest version of Abacus, when i use the peptide report, I get 0 for all charge states so I am not sure this is working correctly.

2) I then tried running each of the 3 MS run * 2 search engines through peptideprophet->Keep the 6 pepxmls separately (without any search engine merging)->then run proteinprophet on the 6 peptide prophet pepxml->followed by a combined peptideprophet run on the 6 peptideprophet pepxmls

This did give me a peptide level report using Abacus but it reports each search engine result separately and ideally i would like sample level peptide spectral counts aggregated from multiple search engines.

Can anyone suggest how i can do this using Abacus?

Thanks

Vidya

[GATTACA]

On Thursday, July 21, 2016 at 2:07:14 PM UTC-4, Vidya Venkatraman wrote:

I have a follow-up question on using multiple search engine data.

I have a dataset with 3 biologically different MS runs. I am using comet and xtandem as my search engines. Ultimately i would like to know the protein and peptide spectral counts for each of my 3 biologically different MS runs.

What i have tried so far is to:

1) Run each of the 3 MS run * 2 search engines through peptideprophet->Merge the multiple search engine results for each biological sample using iprophet->then run proteinprophet on each of the 3 iprophet.pep.xml -> followed by a combined proteinprophet run on the 3 iprophet.pep.xmls

In the latest version of Abacus, when i use the peptide report, I get 0 for all charge states so I am not sure this is working correctly.

Yes it's working correctly. Abacus does not report charge states for iprophet XML files.

 

2) I then tried running each of the 3 MS run * 2 search engines through peptideprophet->Keep the 6 pepxmls separately (without any search engine merging)->then run proteinprophet on the 6 peptide prophet pepxml->followed by a combined peptideprophet run on the 6 peptideprophet pepxmls

This did give me a peptide level report using Abacus but it reports each search engine result separately and ideally i would like sample level peptide spectral counts aggregated from multiple search engines.

Can anyone suggest how i can do this using Abacus?

I would say your best option is to do 1) as you describe above if you want to do this with Abacus. Personally I would generate 6 pepXML files, 6 protXML files and 2 combined protXML files (one for each search engine) for your data. Then run Abacus on each set of search engine results, so in the end you'd have 2 Abacus results (one for comet and one for xtandem). Then use a different tool to reconcile the overlap and distinct features of each output.