Galaxy wrapping of SearchGUI-1.23.3 and PeptideShaker-0.35.6

[Pratik Jagtap]

Hello Everyone,

Sorry for the long silence.

A) Marc and Harald - Both Candace and myself have tested SearchGUI and PeptideShaker and we think that the versions SearchGUI-1.23.3 and PeptideShaker-0.35.6 can be Galaxy-wrapped and placed in galaxy-toolshed so that we can start using them within GalaxyP. (Candace - please add any inputs if you have any).

Here are results with two small datasets that I searched with a Human UniProt - subset microbial database and a subset 3-frame translated cDNA EnSEMBL database.

	ProteinPilot	MS-GF+	MS-GF+, X!tandem, Myrimatch, Comet
CONTROL
Spectra	5405	4824	8098
Peptides	2826	2187	2680
Proteins	1002	525	563
LESION
Spectra	6145	5840	9341
Peptides	3183	2541	3046
Proteins	988	713	735
All identifications at 1% FDR

We are still facing problems searching with large databases - but believe that we can try this on a larger memory system and see if we can get these results.

In my opinion, we are ready for installation of SearchGUI-PeptideShaker for standard searches.

B) Ira or Bjoern - will it be possible to use the latest versions of SearchGUI ( 1.23.3 ) and PeptideShaker ( 0.35.6 ) and wrap them for Galaxy and place them in galaxy toolshed? We will greatly appreciate it.

C) Once in toolshed, MSI developers will install it on new galaxyp so that we can all test it.

Thanks and Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Tue, Nov 25, 2014 at 12:09 PM, harald.barsnes <harald....@gmail.com> wrote:

 

Hi Pratik,

 

It would again seem like you have problems with the connection to the database dropping in between SearchGUI and PeptideShaker. I'm not really sure why this is happening. Could you try loading the search results manually in PeptideShaker? Simply start PeptideShaker and choose New Project, load the zip file as the identification files and try loading the data. This should give as a bit more details on what the problem is.

 

Best regards,

Harald

 

 

On Tuesday, November 25, 2014 4:55:10 PM UTC+1, Pratik Jagtap wrote:

Hello Harald,

Sorry for taking time to get back to you. I was not well last week and hence the delay.

I tried searches with MS-GF+, X!tandem and Myrimatch against a large target-decoy database after increasing the allocated memory to 16 GB on SearchGUI and PeptideShaker and here is the message I got (example of MyriMatch). I am going to try searches with smaller subset databases to see how it works.

Tue Nov 25 09:16:06 CST 2014        Processing tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf with MyriMatch.

Process #0 (UMN201557439) is starting.

MyriMatch 2.2.140 (2014-4-4)

FreiCore 1.6.230 (2014-4-7)

ProteoWizard MSData 3.0.5941 (2014-3-20)

ProteoWizard Proteome 3.0.4080 (2012-11-7)

Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari

Licensed under the Apache License, Version 2.0

Could not find the default configuration file (hard-coded defaults in use).

Reading "C:\Users\pjagtap\DATA\Databases\Human_UniProt_06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.fasta"

Read 9760648 proteins; 65.6576 seconds elapsed.

Reading spectra from file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf"

Read 331 spectra with 74309 peaks; 0.163324 seconds elapsed.

Preparing 331 spectra.

Trimming spectra with less than 7 peaks.

Trimmed 4 spectra for being too sparse.

Preprocessing 327 spectra.

Finished preprocessing its spectra; 0.0329603 seconds elapsed.

Trimming spectra with less than 7 peaks.

Trimming spectra with precursors too small or large: 0 - 10000

Trimmed 0 spectra.

Finished preparing spectra; 0.0330231 seconds elapsed.

Mean original (filtered) peak count: 227 (88)

Min/max original (filtered) peak count: 7 (7) / 1060 (100)

Original (filtered) peak count at 1st/2nd/3rd quartiles: 115 (98), 226 (98), 315 (99)

Filtered out 61.2335% of peaks.

Monoisotopic mass precursor hypotheses: 1308

Average mass precursor hypotheses: 0

Min. effective peptide mass is 684.85

Max. effective peptide mass is 4832.76

Min. effective peptide length is 6

Max. effective peptide length is 30

Commencing database search on 327 spectra.

Searched 329352 of 9760648 proteins; 16501 per second, 00:00:19 elapsed, 00:09:32 remaining.

Searched 658449 of 9760648 proteins; 16494 per second, 00:00:39 elapsed, 00:09:12 remaining.

Searched 992451 of 9760648 proteins; 16574 per second, 00:00:59 elapsed, 00:08:49 remaining.

Searched 1327906 of 9760648 proteins; 16632 per second, 00:01:19 elapsed, 00:08:27 remaining.

Searched 1664228 of 9760648 proteins; 16676 per second, 00:01:39 elapsed, 00:08:06 remaining.

Searched 2000586 of 9760648 proteins; 16705 per second, 00:01:59 elapsed, 00:07:45 remaining.

Searched 2338319 of 9760648 proteins; 16736 per second, 00:02:19 elapsed, 00:07:24 remaining.

Searched 2506847 of 9760648 proteins; 16741 per second, 00:02:29 elapsed, 00:07:13 remaining.

Searched 2843571 of 9760648 proteins; 16755 per second, 00:02:49 elapsed, 00:06:53 remaining.

Searched 3181400 of 9760648 proteins; 16773 per second, 00:03:09 elapsed, 00:06:32 remaining.

Searched 3518651 of 9760648 proteins; 16784 per second, 00:03:29 elapsed, 00:06:12 remaining.

Searched 3854861 of 9760648 proteins; 16788 per second, 00:03:49 elapsed, 00:05:52 remaining.

Searched 4023003 of 9760648 proteins; 16789 per second, 00:03:59 elapsed, 00:05:42 remaining.

Searched 4359938 of 9760648 proteins; 16793 per second, 00:04:19 elapsed, 00:05:22 remaining.

Searched 4527528 of 9760648 proteins; 16791 per second, 00:04:29 elapsed, 00:05:12 remaining.

Searched 4864665 of 9760648 proteins; 16796 per second, 00:04:49 elapsed, 00:04:51 remaining.

Searched 5200021 of 9760648 proteins; 16794 per second, 00:05:09 elapsed, 00:04:32 remaining.

Searched 5369595 of 9760648 proteins; 16799 per second, 00:05:19 elapsed, 00:04:21 remaining.

Searched 5700341 of 9760648 proteins; 16786 per second, 00:05:39 elapsed, 00:04:02 remaining.

Searched 6037671 of 9760648 proteins; 16789 per second, 00:05:59 elapsed, 00:03:42 remaining.

Searched 6206091 of 9760648 proteins; 16790 per second, 00:06:09 elapsed, 00:03:32 remaining.

Searched 6534539 of 9760648 proteins; 16771 per second, 00:06:29 elapsed, 00:03:12 remaining.

Searched 6867766 of 9760648 proteins; 16766 per second, 00:06:49 elapsed, 00:02:53 remaining.

Searched 7032862 of 9760648 proteins; 16760 per second, 00:06:59 elapsed, 00:02:43 remaining.

Searched 7365703 of 9760648 proteins; 16755 per second, 00:07:19 elapsed, 00:02:23 remaining.

Searched 7699359 of 9760648 proteins; 16752 per second, 00:07:39 elapsed, 00:02:03 remaining.

Searched 7868334 of 9760648 proteins; 16754 per second, 00:07:49 elapsed, 00:01:53 remaining.

Searched 8037315 of 9760648 proteins; 16757 per second, 00:07:59 elapsed, 00:01:43 remaining.

Searched 8206030 of 9760648 proteins; 16759 per second, 00:08:09 elapsed, 00:01:33 remaining.

Searched 8540595 of 9760648 proteins; 16760 per second, 00:08:29 elapsed, 00:01:13 remaining.

Searched 8847716 of 9760648 proteins; 16706 per second, 00:08:49 elapsed, 00:00:55 remaining.

Searched 9006065 of 9760648 proteins; 16690 per second, 00:08:59 elapsed, 00:00:45 remaining.

Searched 9170331 of 9760648 proteins; 16684 per second, 00:09:09 elapsed, 00:00:35 remaining.

Searched 9336019 of 9760648 proteins; 16682 per second, 00:09:19 elapsed, 00:00:25 remaining.

Searched 9670888 of 9760648 proteins; 16684 per second, 00:09:39 elapsed, 00:00:05 remaining.

Finished database search; 586.301 seconds elapsed.

Overall stats: 9760648 proteins; 357285325 peptides; 474713452 variants; 29018772 comparisons

Writing search results to file "tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf.myrimatch.mzid".

Finished file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr1.mgf"; 586.728 seconds elapsed.

Tue Nov 25 09:26:59 CST 2014        MyriMatch Process Finished.

Tue Nov 25 09:26:59 CST 2014        Processing tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf with MyriMatch.

Process #0 (UMN201557439) is starting.

MyriMatch 2.2.140 (2014-4-4)

FreiCore 1.6.230 (2014-4-7)

ProteoWizard MSData 3.0.5941 (2014-3-20)

ProteoWizard Proteome 3.0.4080 (2012-11-7)

Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari

Licensed under the Apache License, Version 2.0

Could not find the default configuration file (hard-coded defaults in use).

Reading "C:\Users\pjagtap\DATA\Databases\Human_UniProt_06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.fasta"

Read 9760648 proteins; 0.0326305 seconds elapsed.

Reading spectra from file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf"

Read 3187 spectra with 533722 peaks; 0.782982 seconds elapsed.

Preparing 3187 spectra.

Trimming spectra with less than 7 peaks.

Trimmed 11 spectra for being too sparse.

Preprocessing 3176 spectra.

Finished preprocessing its spectra; 0.249652 seconds elapsed.

Trimming spectra with less than 7 peaks.

Trimming spectra with precursors too small or large: 0 - 10000

Trimmed 1 spectra.

Finished preparing spectra; 0.249828 seconds elapsed.

Mean original (filtered) peak count: 168 (88)

Min/max original (filtered) peak count: 7 (7) / 822 (100)

Original (filtered) peak count at 1st/2nd/3rd quartiles: 107 (93), 162 (98), 217 (99)

Filtered out 47.619% of peaks.

Monoisotopic mass precursor hypotheses: 12700

Average mass precursor hypotheses: 0

Min. effective peptide mass is 686.918

Max. effective peptide mass is 6056.36

Min. effective peptide length is 6

Max. effective peptide length is 30

Commencing database search on 3175 spectra.

Searched 104820 of 9760648 proteins; 10475 per second, 00:00:10 elapsed, 00:15:22 remaining.

Searched 210707 of 9760648 proteins; 10527 per second, 00:00:20 elapsed, 00:15:07 remaining.

Searched 315744 of 9760648 proteins; 10516 per second, 00:00:30 elapsed, 00:14:58 remaining.

Searched 420089 of 9760648 proteins; 10492 per second, 00:00:40 elapsed, 00:14:50 remaining.

Searched 524743 of 9760648 proteins; 10487 per second, 00:00:50 elapsed, 00:14:41 remaining.

Searched 629167 of 9760648 proteins; 10479 per second, 00:01:00 elapsed, 00:14:31 remaining.

Searched 733416 of 9760648 proteins; 10469 per second, 00:01:10 elapsed, 00:14:22 remaining.

Searched 942949 of 9760648 proteins; 10470 per second, 00:01:30 elapsed, 00:14:02 remaining.

Searched 1047220 of 9760648 proteins; 10465 per second, 00:01:40 elapsed, 00:13:53 remaining.

Searched 1151898 of 9760648 proteins; 10464 per second, 00:01:50 elapsed, 00:13:43 remaining.

Searched 1361210 of 9760648 proteins; 10464 per second, 00:02:10 elapsed, 00:13:23 remaining.

Searched 1465655 of 9760648 proteins; 10462 per second, 00:02:20 elapsed, 00:13:13 remaining.

Searched 1570118 of 9760648 proteins; 10460 per second, 00:02:30 elapsed, 00:13:03 remaining.

Searched 1775631 of 9760648 proteins; 10438 per second, 00:02:50 elapsed, 00:12:45 remaining.

Searched 1873174 of 9760648 proteins; 10400 per second, 00:03:00 elapsed, 00:12:38 remaining.

Searched 1972204 of 9760648 proteins; 10373 per second, 00:03:10 elapsed, 00:12:31 remaining.

Searched 2175875 of 9760648 proteins; 10356 per second, 00:03:30 elapsed, 00:12:12 remaining.

Searched 2278310 of 9760648 proteins; 10351 per second, 00:03:40 elapsed, 00:12:03 remaining.

Searched 2456104 of 9760648 proteins; 10230 per second, 00:04:00 elapsed, 00:11:54 remaining.

Searched 2547871 of 9760648 proteins; 10187 per second, 00:04:10 elapsed, 00:11:48 remaining.

Searched 2644671 of 9760648 proteins; 10167 per second, 00:04:20 elapsed, 00:11:40 remaining.

Searched 2744342 of 9760648 proteins; 10159 per second, 00:04:30 elapsed, 00:11:31 remaining.

Searched 2845401 of 9760648 proteins; 10157 per second, 00:04:40 elapsed, 00:11:21 remaining.

Searched 2942510 of 9760648 proteins; 10142 per second, 00:04:50 elapsed, 00:11:12 remaining.

Searched 3037071 of 9760648 proteins; 10119 per second, 00:05:00 elapsed, 00:11:04 remaining.

Searched 3135665 of 9760648 proteins; 10110 per second, 00:05:10 elapsed, 00:10:55 remaining.

Searched 3234727 of 9760648 proteins; 10104 per second, 00:05:20 elapsed, 00:10:46 remaining.

Searched 3436026 of 9760648 proteins; 10101 per second, 00:05:40 elapsed, 00:10:26 remaining.

Searched 3535834 of 9760648 proteins; 10098 per second, 00:05:50 elapsed, 00:10:16 remaining.

Searched 3634191 of 9760648 proteins; 10090 per second, 00:06:00 elapsed, 00:10:07 remaining.

Searched 3734563 of 9760648 proteins; 10089 per second, 00:06:10 elapsed, 00:09:57 remaining.

Searched 3936091 of 9760648 proteins; 10088 per second, 00:06:30 elapsed, 00:09:37 remaining.

Searched 4137453 of 9760648 proteins; 10087 per second, 00:06:50 elapsed, 00:09:17 remaining.

Searched 4238377 of 9760648 proteins; 10087 per second, 00:07:00 elapsed, 00:09:07 remaining.

Searched 4440593 of 9760648 proteins; 10088 per second, 00:07:20 elapsed, 00:08:47 remaining.

Searched 4541123 of 9760648 proteins; 10087 per second, 00:07:30 elapsed, 00:08:37 remaining.

Searched 4643630 of 9760648 proteins; 10090 per second, 00:07:40 elapsed, 00:08:27 remaining.

Searched 4743238 of 9760648 proteins; 10087 per second, 00:07:50 elapsed, 00:08:17 remaining.

Searched 4845707 of 9760648 proteins; 10091 per second, 00:08:00 elapsed, 00:08:07 remaining.

Searched 4947470 of 9760648 proteins; 10092 per second, 00:08:10 elapsed, 00:07:57 remaining.

Searched 5049742 of 9760648 proteins; 10095 per second, 00:08:20 elapsed, 00:07:47 remaining.

Searched 5149600 of 9760648 proteins; 10093 per second, 00:08:30 elapsed, 00:07:37 remaining.

Searched 5250979 of 9760648 proteins; 10093 per second, 00:08:40 elapsed, 00:07:27 remaining.

Searched 5350770 of 9760648 proteins; 10091 per second, 00:08:50 elapsed, 00:07:17 remaining.

Searched 5449967 of 9760648 proteins; 10088 per second, 00:09:00 elapsed, 00:07:07 remaining.

Searched 5550203 of 9760648 proteins; 10087 per second, 00:09:10 elapsed, 00:06:57 remaining.

Searched 5652335 of 9760648 proteins; 10089 per second, 00:09:20 elapsed, 00:06:47 remaining.

Searched 5752948 of 9760648 proteins; 10088 per second, 00:09:30 elapsed, 00:06:37 remaining.

Searched 5853553 of 9760648 proteins; 10088 per second, 00:09:40 elapsed, 00:06:27 remaining.

Searched 6049176 of 9760648 proteins; 10077 per second, 00:10:00 elapsed, 00:06:08 remaining.

Searched 6246496 of 9760648 proteins; 10070 per second, 00:10:20 elapsed, 00:05:49 remaining.

Searched 6348688 of 9760648 proteins; 10073 per second, 00:10:30 elapsed, 00:05:39 remaining.

Searched 6448754 of 9760648 proteins; 10071 per second, 00:10:40 elapsed, 00:05:29 remaining.

Searched 6542126 of 9760648 proteins; 10060 per second, 00:10:50 elapsed, 00:05:20 remaining.

Searched 6642884 of 9760648 proteins; 10060 per second, 00:11:00 elapsed, 00:05:10 remaining.

Searched 6744540 of 9760648 proteins; 10062 per second, 00:11:10 elapsed, 00:05:00 remaining.

Searched 6846478 of 9760648 proteins; 10064 per second, 00:11:20 elapsed, 00:04:50 remaining.

Searched 6943808 of 9760648 proteins; 10059 per second, 00:11:30 elapsed, 00:04:40 remaining.

Searched 7044300 of 9760648 proteins; 10059 per second, 00:11:40 elapsed, 00:04:30 remaining.

Searched 7143783 of 9760648 proteins; 10057 per second, 00:11:50 elapsed, 00:04:20 remaining.

Searched 7245438 of 9760648 proteins; 10058 per second, 00:12:00 elapsed, 00:04:10 remaining.

Searched 7344949 of 9760648 proteins; 10057 per second, 00:12:10 elapsed, 00:04:00 remaining.

Searched 7445738 of 9760648 proteins; 10057 per second, 00:12:20 elapsed, 00:03:50 remaining.

Searched 7541682 of 9760648 proteins; 10051 per second, 00:12:30 elapsed, 00:03:41 remaining.

Searched 7642014 of 9760648 proteins; 10051 per second, 00:12:40 elapsed, 00:03:31 remaining.

Searched 7743809 of 9760648 proteins; 10052 per second, 00:12:50 elapsed, 00:03:21 remaining.

Searched 7939027 of 9760648 proteins; 10045 per second, 00:13:10 elapsed, 00:03:01 remaining.

Searched 8029553 of 9760648 proteins; 10032 per second, 00:13:20 elapsed, 00:02:53 remaining.

Searched 8129810 of 9760648 proteins; 10032 per second, 00:13:30 elapsed, 00:02:43 remaining.

Searched 8228268 of 9760648 proteins; 10030 per second, 00:13:40 elapsed, 00:02:33 remaining.

Searched 8422734 of 9760648 proteins; 10022 per second, 00:14:00 elapsed, 00:02:13 remaining.

Searched 8521681 of 9760648 proteins; 10021 per second, 00:14:10 elapsed, 00:02:04 remaining.

Searched 8621841 of 9760648 proteins; 10021 per second, 00:14:20 elapsed, 00:01:54 remaining.

Searched 8820558 of 9760648 proteins; 10019 per second, 00:14:40 elapsed, 00:01:34 remaining.

Searched 8919186 of 9760648 proteins; 10017 per second, 00:14:50 elapsed, 00:01:24 remaining.

Searched 9017653 of 9760648 proteins; 10015 per second, 00:15:00 elapsed, 00:01:14 remaining.

Searched 9203528 of 9760648 proteins; 9999 per second, 00:15:20 elapsed, 00:00:56 remaining.

Searched 9301167 of 9760648 proteins; 9996 per second, 00:15:30 elapsed, 00:00:46 remaining.

Searched 9497002 of 9760648 proteins; 9992 per second, 00:15:50 elapsed, 00:00:26 remaining.

Searched 9594362 of 9760648 proteins; 9989 per second, 00:16:00 elapsed, 00:00:17 remaining.

Searched 9693199 of 9760648 proteins; 9988 per second, 00:16:10 elapsed, 00:00:07 remaining.

Finished database search; 977.919 seconds elapsed.

Overall stats: 9760648 proteins; 357285325 peptides; 474195809 variants; 610251975 comparisons

Writing search results to file "tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf.myrimatch.mzid".

Finished file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf"; 981.208 seconds elapsed.

Tue Nov 25 09:43:21 CST 2014        MyriMatch Process Finished.

Tue Nov 25 09:43:21 CST 2014        Zipping output files.

Tue Nov 25 09:43:22 CST 2014        Processing identification files with PeptideShaker.

Tue Nov 25 09:47:03 CST 2014        PeptideShaker processing canceled. See the PeptideShaker log for details.

Tue Nov 25 09:47:04 CST 2014        Search Canceled!

Tue Nov 25 09:47:04 CST 2014        The search or post-processing did not finish properly!

PeptideShaker Log:

Tue Nov 25 09:43:23 CST 2014: PeptideShaker version 0.35.4.

Memory given to the Java virtual machine: 15270936576.

Total amount of memory in the Java virtual machine: 129499136.

Free memory: 105176432.

Java version: 1.7.0_71.

java.sql.SQLNonTransientConnectionException: No current connection.

at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.Util.noCurrentConnection(Unknown Source)

at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)

at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)

at org.apache.derby.impl.jdbc.EmbedConnection.createStatement(Unknown Source)

at com.compomics.util.db.ObjectsDB.retrieveObjectSynchronized(ObjectsDB.java:723)

at com.compomics.util.db.ObjectsDB.retrieveObject(ObjectsDB.java:677)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.getNode(ProteinTreeComponentsFactory.java:227)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getNodeSynchronized(ProteinTree.java:1428)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getNode(ProteinTree.java:1407)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getProteinMapping(ProteinTree.java:1008)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.getProteinMapping(ProteinTree.java:934)

at com.compomics.util.experiment.biology.Peptide.getParentProteins(Peptide.java:341)

at com.compomics.util.experiment.biology.Peptide.getParentProteins(Peptide.java:281)

at com.compomics.util.experiment.biology.Peptide.getParentProteins(Peptide.java:317)

at eu.isas.peptideshaker.protein_inference.PeptideMapper.mapPeptide(PeptideMapper.java:244)

at eu.isas.peptideshaker.protein_inference.PeptideMapper.access$200(PeptideMapper.java:27)

at eu.isas.peptideshaker.protein_inference.PeptideMapper$PeptideListMapperRunnable.run(PeptideMapper.java:294)

at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)

at java.util.concurrent.FutureTask.run(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)

at java.lang.Thread.run(Unknown Source)

Caused by: java.sql.SQLException: No current connection.

at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)

... 25 more

java.sql.SQLNonTransientConnectionException: No current connection.

at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.Util.noCurrentConnection(Unknown Source)

at org.apache.derby.impl.jdbc.EmbedConnection.checkIfClosed(Unknown Source)

at org.apache.derby.impl.jdbc.EmbedConnection.getMetaData(Unknown Source)

at com.compomics.util.db.ObjectsDB.hasTable(ObjectsDB.java:220)

at com.compomics.util.db.ObjectsDB.saveLongKeys(ObjectsDB.java:1074)

at com.compomics.util.db.ObjectsDB.close(ObjectsDB.java:1104)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTreeComponentsFactory.close(ProteinTreeComponentsFactory.java:149)

at com.compomics.util.experiment.identification.protein_inference.proteintree.ProteinTree.close(ProteinTree.java:1466)

at com.compomics.util.experiment.identification.SequenceFactory.closeFile(SequenceFactory.java:844)

at com.compomics.util.experiment.identification.SequenceFactory.clearFactory(SequenceFactory.java:138)

at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:531)

at eu.isas.peptideshaker.fileimport.FileImporter.importFiles(FileImporter.java:158)

at eu.isas.peptideshaker.PeptideShaker.importFiles(PeptideShaker.java:229)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:649)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:162)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:937)

Caused by: java.sql.SQLException: No current connection.

at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)

at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)

... 19 more

Tue Nov 25 09:47:29 CST 2014: PeptideShaker version 0.35.4.

Memory given to the Java virtual machine: 15270936576.

Total amount of memory in the Java virtual machine: 129499136.

Free memory: 114446856.

Java version: 1.7.0_71.

1714 script command tokens

(C) 2009 Jmol Development

Jmol Version: 12.0.43  2011-05-03 14:21

java.vendor: Oracle Corporation

java.version: 1.7.0_71

os.name: Windows 7

memory: 37.3/129.5

processors available: 8

useCommandThread: false

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Thu, Nov 20, 2014 at 8:24 AM, Pratik Jagtap <pja...@umn.edu> wrote:

Thanks Harald,

I will give it a try once I am back in the office. 

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

On Wed, Nov 19, 2014 at 10:14 PM, harald.barsnes <harald....@gmail.com> wrote:

 

Hi Pratik,

 

Generally, the more memory you give PeptideShaker (and I assume the same is true for MS-GF+) the quicker it will go, as this makes it possible to keep all the information in memory and thus reduces the need to read/write to the disk. So the more memory you can give these tools the better.

 

We run most of our heavier searches using 60 GB of memory. But most searches should run fine with a lot less memory.

 

And as you mention, the search settings used also has an impact. Both on the speed and the memory required. The number of variable modifications is usually the setting that has the biggest impact. But this may differ between the search engines.

 

Best regards,

Harald

 

 

On Thursday, November 20, 2014 3:15:48 AM UTC+1, Pratik Jagtap wrote:

Thanks Harald,

> For bigger databases or larger spectrum files we'd strongly recommend providing a lot more memory. As > Marc already mentioned you can edit the memory settings at tool startup via "Settings and Help" -> 

> "Settings" -> "Java Settings" in PeptideShaker, or via "Edit" -> "Java Settings" in both SearchGUI and 

> PeptideShaker.

How much more should I go? 8 GB ? 16 GB? Or should I try different settings?

> Our tools should simply take longer in low memory settings, but as you can see MS-GF+ will simply stop > working.

i will contact Sangtae and see whether he can help.

I will also try Myrimatch, X!tandem and other search algorithms.

I am going a step at a time - and I very much appreciate your inputs and changes. I am hoping once we have a working version for both Candace and myself - we will request Ira or Bjoern to galaxy-wrap the tool.

Thanks,

Pratik

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[Marc Vaudel]

Dear Pratik,

That is very good news, how many spectra are in your dataset? I am a bit puzzled by the fact that with 40% less identified spectra and roughly the same number of peptides ProteinPilot identifies twice the number of proteins. Are we really looking at the same thing here in terms of FDR and ambiguity groups?

It seems very reasonable to use these versions in Galaxy. They are stable and no functional bug was reported on them. On the development side we have been mainly working on the GUI and on reducing our memory consumption. There will be a new release by the end of the year but in terms of results, nothing will differ from these. Did you manage to wrap both tools separately btw?

Best regards,

Marc

[Pratik Jagtap]

Hello Marc,

> Are we really looking at the same thing here in terms of FDR and ambiguity groups?

I should correct myself  - the numbers that I have for PeptideShaker are from the default output of PSMs, peptides and proteins from PeptideShaker (which I assume are at 1% FDR). For ProteinPilot, I had those numbers from their single summary sheet (1% global FDR). If both are indeed 1% global FDR - I am also surprised by the protein group numbers.

> Did you manage to wrap both tools separately btw?

I am requesting Ira or Bjoern if they can wrap the tools.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Björn Grüning]

Hi,

Am 12.12.2014 um 12:54 schrieb Pratik Jagtap:
> Hello Marc,
>
>> Are we really looking at the same thing here in terms of FDR and
> ambiguity groups?
>
> I should correct myself - the numbers that I have for PeptideShaker are
> from the default output of PSMs, peptides and proteins from PeptideShaker
> (which I assume are at 1% FDR). For ProteinPilot, I had those numbers from
> their single summary sheet (1% global FDR). If both are indeed 1% global
> FDR - I am also surprised by the protein group numbers.
>
>> Did you manage to wrap both tools separately btw?
>
> I am requesting Ira or Bjoern if they can wrap the tools.

Not yet, I will work on this during the weekend and the next week.

Thanks for all the updates and the hard work!
Bjoern

>>> *ProteinPilot* *MS-GF+* *MS-GF+, X!tandem, Myrimatch, Comet*
>>> *CONTROL* Spectra 5405 4824 8098 Peptides 2826 2187 2680
>>> Proteins 1002 525 563 *LESION* Spectra 6145 5840 9341

>>> Peptides 3183 2541 3046 Proteins 988 713 735
>>>
>>>

>>> *All identifications at 1% FDR*

>>>>> patient4_control_CA_Fr2.mgf.myrimatch.mzid".

>>>>> Finished file "C:\Users\pjagtap\DATA\MGF files\tgriffin_koore004_

>>>> <https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu?utm_medium=email&utm_source=footer>
>>>> .
>>>>
>>>
>>>
>>
>

[Pratik Jagtap]

Thanks Bjoern !

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Ira Cooke]

Hi Harald,

That's super helpful. Thanks.

I'm assuming Pratik and Candace would like the wrappers to make use of the new zipped output style. From what I can remember, the idea was for the Galaxy tools to be able to run SearchGUI, and peptideshaker .. and then to be able to download the results for use on the desktop app.

Cheers
Ira


> On 14 Dec 2014, at 12:37 am, Harald Barsnes <Harald....@biomed.uib.no> wrote:
>
>
> Hi Ira,
>
> I had a quick look at the changes in SearchGUI and PeptideShaker compared to the versions currently in the toolshed. Here are the most important changes:
>
> SearchGUI:
> - MyriMatch has been added.
> - Comet has been added.
> - MS Amanda is now supported on Linux and Mac (requires Mono: http://www.mono-project.com).
> - Renamed "no enzyme" to the more understandable "unspecific".
> - The output can now zipped, see "Optional output compression parameters" in the wiki.
>
> For details see http://code.google.com/p/searchgui/wiki/SearchCLI
>
> PeptideShaker:
> - Support for MyriMatch and Comet.
> - Possible to import zipped SearchGUI projects.
> - Zip export from the command line (-zip).
> - Possible to set the number of threads used via -threads.
> - Added a new command line parameter called species_update to the PeptideShakerCLI to control the update of the species and GO mappings.
> - Improved speed and memory usage.
>
> For details see http://code.google.com/p/peptide-shaker/wiki/PeptideShakerCLI
>
> Let me know if you need more information about any of these.
>
> Best regards,
> Harald
>
>
>
>
> Den 2014-12-12 21:09, skrev Ira Cooke:
>> Hi Bjoern/Pratik,
>> I am happy to work on this on Monday, if Bjoern has not already
>> finished it by then ;).
>> Candace, did you use the command-line for your searches, or the GUI
>> version? If you used the command-line it would be very useful to know
>> the commands you used in the new version.
>> I haven't really kept up with changes since last time, but I'm
>> guessing there have been many. If there are any in particular (eg non
>> backwards compatible command-line changes) to be aware of it would be
>> great to get a heads-up about that. The current versions on the
>> toolshed are;
>> SearchGUI 1.19.5
>> PeptideShaker 0.31.4
>> Cheers
>> Ira

>>>>> Phone: 612-624-9275 [1]

>>>>>>>>> Reading "C:UserspjagtapDATADatabasesHuman_UniProt_

>>>> 06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.
>>>>>>>>> fasta"
>>>>>>>>> Read 9760648 proteins; 65.6576 seconds elapsed.

>>>>>>>>> Reading spectra from file "C:UserspjagtapDATAMGF
>>>>>>>>> filestgriffin_koore004_040511_patient4_control_CA_Fr1.mgf"

>>>>>>>>> Finished file "C:UserspjagtapDATAMGF
>>>> filestgriffin_koore004_

>>>>>>>>> 040511_patient4_control_CA_Fr1.mgf"; 586.728 seconds
>>>> elapsed.
>>>>>>>>> Tue Nov 25 09:26:59 CST 2014 MyriMatch Process Finished.
>>>>>>>>> Tue Nov 25 09:26:59 CST 2014 Processing
>>>> tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf
>>>>>>>>> with MyriMatch.
>>>>>>>>> Process #0 (UMN201557439) is starting.
>>>>>>>>> MyriMatch 2.2.140 (2014-4-4)
>>>>>>>>> FreiCore 1.6.230 (2014-4-7)
>>>>>>>>> ProteoWizard MSData 3.0.5941 (2014-3-20)
>>>>>>>>> ProteoWizard Proteome 3.0.4080 (2012-11-7)
>>>>>>>>> Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari
>>>>>>>>> Licensed under the Apache License, Version 2.0
>>>>>>>>> Could not find the default configuration file (hard-coded
>>>> defaults in
>>>>>>>>> use).

>>>>>>>>> Reading "C:UserspjagtapDATADatabasesHuman_UniProt_

>>>> 06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.
>>>>>>>>> fasta"
>>>>>>>>> Read 9760648 proteins; 0.0326305 seconds elapsed.

>>>>>>>>> Reading spectra from file "C:UserspjagtapDATAMGF
>>>>>>>>> filestgriffin_koore004_040511_patient4_control_CA_Fr2.mgf"

>>>>>>>>> Finished file "C:UserspjagtapDATAMGF
>>>> filestgriffin_koore004_

>>>>>>>>> os.name [2]: Windows 7

>>>>>>>>> memory: 37.3/129.5
>>>>>>>>> processors available: 8
>>>>>>>>> useCommandThread: false
>>>>>>>>> Pratik Jagtap,
>>>>>>>>> Managing Director,
>>>>>>>>> Center for Mass Spectrometry and Proteomics,
>>>>>>>>> 43 Gortner Laboratory
>>>>>>>>> 1479 Gortner Avenue
>>>>>>>>> St. Paul, MN 55108
>>>>>>>>> Phone: 612-624-9275
>>>>>>>>> On Thu, Nov 20, 2014 at 8:24 AM, Pratik Jagtap
>>>> <pja...@umn.edu> wrote:
>>>>>>>>> Thanks Harald,
>>>>>>>>> I will give it a try once I am back in the office.
>>>>>>>>> Regards,
>>>>>>>>> Pratik
>>>>>>>>> Pratik Jagtap,
>>>>>>>>> Managing Director,
>>>>>>>>> Center for Mass Spectrometry and Proteomics,
>>>>>>>>> 43 Gortner Laboratory
>>>>>>>>> 1479 Gortner Avenue
>>>>>>>>> St. Paul, MN 55108

>>>>>>>>> Phone: 612-624-9275 [1]

>>>> http://groups.google.com/a/umn.edu/group/galaxyp/ [3].

>>>>>>>> To view this discussion on the web visit
>> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu

>>>> [4]
>> <https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu?utm_medium=email&utm_source=footer
>>>> [5]>
>>>>>>>> .
>> Links:
>> ------
>> [1] tel:612-624-9275
>> [2] http://os.name/
>> [3] http://groups.google.com/a/umn.edu/group/galaxyp/
>> [4]
>> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu
>> [5]
>> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu?utm_medium=email&amp;utm_source=footer

[Pratik Jagtap]

Hello Ira,

> I'm assuming Pratik and Candace would like the wrappers to make use of the new zipped output style. 

That is correct. The idea is to download the zipped file results and later open the .cps file so as to visualize the results.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Marc Vaudel]

Hi Ira, Hi Pratik,

Indeed, the idea between the zipped output is to have one file out, one file in between SeachGUI and PeptideShaker, without path dependency (the mgf, parameters and fasta files can be included in the zip using the -output_data
option). You can hence have two independent wrappers and run multiple PeptideShaker tasks without redoing the search. We also added different packing options in SearchGUI: single zip, grouped by search engine, grouped  by mgf file. That way the user can choose how to organize results for later reuse, making the file history much cleaner.

As Pratik mentioned, the zip file produced by PeptideShaker can be reopened on any computer upon unpacking - there is no need to keep track of additional files. The hard work can thus be done in Galaxy and the results viewed locally. Of course, if you see any way of making your life (or the one of the user) easier, we will be glad to implement it!

Best regards,

Marc

[Björn Grüning]

Hi!

I started to work on this here:
https://bitbucket.org/BjoernGruening/peptideshaker

I splitted our old wrapper into two smalers once that share one macro
file for all options that are necessary in both tools (e.g. "General
parameters"). I updated all requirements and added myrimatch and comet
as search engines.

See my inline comments.

> SearchGUI:
> - MyriMatch has been added.

Done, parameters missing.

> - Comet has been added.

Done, parameters missing.

> - MS Amanda is now supported on Linux and Mac (requires Mono:
> http://www.mono-project.com).

Is there a standalone mono runtime? So that we can install the runtime
together with all the jar files?

> - Renamed "no enzyme" to the more understandable "unspecific".

Haven’t found this.

> - The output can now zipped, see "Optional output compression
> parameters" in the wiki.

What is the name of the resulting zip file?

> For details see http://code.google.com/p/searchgui/wiki/SearchCLI
>
> PeptideShaker:
> - Support for MyriMatch and Comet.
> - Possible to import zipped SearchGUI projects.
> - Zip export from the command line (-zip).
> - Possible to set the number of threads used via -threads.

Done!

> - Added a new command line parameter called species_update to the
> PeptideShakerCLI to control the update of the species and GO mappings.

This will update the local installed mapping DB?

> - Improved speed and memory usage.

Very nice!
Thanks for such a detailed guide, this helped a lot.
@Ira I will be travelling the next 24h. Please feel free to work on it,
I will try to catch up on Tuesday.

Ciao,
Bjoern

>
> For details see
> http://code.google.com/p/peptide-shaker/wiki/PeptideShakerCLI
>
> Let me know if you need more information about any of these.
>
> Best regards,
> Harald
>
>
>
>
> Den 2014-12-12 21:09, skrev Ira Cooke:
>> Hi Bjoern/Pratik,
>>
>> I am happy to work on this on Monday, if Bjoern has not already
>> finished it by then ;).
>>
>> Candace, did you use the command-line for your searches, or the GUI
>> version? If you used the command-line it would be very useful to know
>> the commands you used in the new version.
>>
>> I haven't really kept up with changes since last time, but I'm
>> guessing there have been many. If there are any in particular (eg non
>> backwards compatible command-line changes) to be aware of it would be
>> great to get a heads-up about that. The current versions on the
>> toolshed are;
>>
>> SearchGUI 1.19.5
>> PeptideShaker 0.31.4
>>
>> Cheers
>> Ira
>>

>>>>> Phone: 612-624-9275 [1]

>>>>>>>>> Reading "C:UserspjagtapDATADatabasesHuman_UniProt_

>>>>>>>>>
>>>> 06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.
>>>>>>>>> fasta"
>>>>>>>>> Read 9760648 proteins; 65.6576 seconds elapsed.

>>>>>>>>> Reading spectra from file "C:UserspjagtapDATAMGF
>>>>>>>>> filestgriffin_koore004_040511_patient4_control_CA_Fr1.mgf"

>>>>>>>>> Finished file "C:UserspjagtapDATAMGF
>>>> filestgriffin_koore004_

>>>>>>>>> 040511_patient4_control_CA_Fr1.mgf"; 586.728 seconds
>>>> elapsed.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Tue Nov 25 09:26:59 CST 2014 MyriMatch Process Finished.
>>>>>>>>>
>>>>>>>>> Tue Nov 25 09:26:59 CST 2014 Processing
>>>> tgriffin_koore004_040511_patient4_control_CA_Fr2.mgf
>>>>>>>>> with MyriMatch.
>>>>>>>>>
>>>>>>>>> Process #0 (UMN201557439) is starting.
>>>>>>>>> MyriMatch 2.2.140 (2014-4-4)
>>>>>>>>> FreiCore 1.6.230 (2014-4-7)
>>>>>>>>> ProteoWizard MSData 3.0.5941 (2014-3-20)
>>>>>>>>> ProteoWizard Proteome 3.0.4080 (2012-11-7)
>>>>>>>>> Vanderbilt University (c) 2012, D.Tabb/M.Chambers/S.Dasari
>>>>>>>>> Licensed under the Apache License, Version 2.0
>>>>>>>>>
>>>>>>>>> Could not find the default configuration file (hard-coded
>>>> defaults in
>>>>>>>>> use).

>>>>>>>>> Reading "C:UserspjagtapDATADatabasesHuman_UniProt_

>>>>>>>>>
>>>> 06272014_HOMD_dynamic_12252013_Modified_concatenated_target_decoy.
>>>>>>>>> fasta"
>>>>>>>>> Read 9760648 proteins; 0.0326305 seconds elapsed.

>>>>>>>>> Reading spectra from file "C:UserspjagtapDATAMGF
>>>>>>>>> filestgriffin_koore004_040511_patient4_control_CA_Fr2.mgf"

>>>>>>>>> Finished file "C:UserspjagtapDATAMGF
>>>> filestgriffin_koore004_

>>>>>>>>> os.name [2]: Windows 7

>>>>>>>>> memory: 37.3/129.5
>>>>>>>>> processors available: 8
>>>>>>>>> useCommandThread: false
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Pratik Jagtap,
>>>>>>>>> Managing Director,
>>>>>>>>> Center for Mass Spectrometry and Proteomics,
>>>>>>>>> 43 Gortner Laboratory
>>>>>>>>> 1479 Gortner Avenue
>>>>>>>>> St. Paul, MN 55108
>>>>>>>>> Phone: 612-624-9275
>>>>>>>>>
>>>>>>>>> On Thu, Nov 20, 2014 at 8:24 AM, Pratik Jagtap
>>>> <pja...@umn.edu> wrote:
>>>>>>>>>
>>>>>>>>> Thanks Harald,
>>>>>>>>>
>>>>>>>>> I will give it a try once I am back in the office.
>>>>>>>>>
>>>>>>>>> Regards,
>>>>>>>>>
>>>>>>>>> Pratik
>>>>>>>>>
>>>>>>>>> Pratik Jagtap,
>>>>>>>>> Managing Director,
>>>>>>>>> Center for Mass Spectrometry and Proteomics,
>>>>>>>>> 43 Gortner Laboratory
>>>>>>>>> 1479 Gortner Avenue
>>>>>>>>> St. Paul, MN 55108

>>>>>>>>> Phone: 612-624-9275 [1]

>>>> http://groups.google.com/a/umn.edu/group/galaxyp/ [3].

>>>>>>>> To view this discussion on the web visit
>>>>>>>>
>>>>
>>>
>> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu
>>

[harald.barsnes]

 

Hi Bjoern,

 

I'm not sure if there is a standalone runtime version of Mono. At least I haven't been able to find a way of installing Mono together with the search engines when people download SearchGUI. But I don't have much experience with Mono besides trying to install it on Linux. For my tips on how to install Mono on Linux, please see "MS Amanda in Linux" at http://code.google.com/p/searchgui/#Troubleshooting.

 

The renaming of "no enzyme" to "unspecific" only comes into play when selecting the enzyme for the search. We changed the name for the unspecific cleavage, i.e., cleave everywhere, as "no enzyme" could also be understood as "don't cleave anywhere", i.e., when using peptides or top down.

 

The name of the zip file from SearchGUI will always be "searchgui_out.zip". For details on what to include in the zip file please see "Optional output compression parameters" at http://code.google.com/p/searchgui/wiki/SearchCLI.

 

The species_update parameter in SearchGUI will update the local gene and GO mappings if set to true. Or more specifically, if set to true, a check for new mappings will be done and downloaded if available.

 

If think that should answer all of your questions so far?

 

Best regards,

Harald 

>> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/a235a440-0f56-453b-a1fc-0fc0f6cc1496%40umn.edu?utm_medium=email&amp;utm...

[Ira Cooke]

Hi Bjoern, 

Just to let you know that I’m gradually going through, testing, and adding/fixing things as I find them. 

I’m pushing anything I do straight away to here;

https://bitbucket.org/iracooke/peptideshaker

And when I’ve got something that I’m happy with I’ll send a pull request.

Cheers

Ira

[Björn Grüning]

Thanks Ira!

If you are done we can ask Patrik to test it also and meanwhile
implement some more parameters for the new search engines.

Cheers,
Bjoern

> Hi Bjoern,
>
> Just to let you know that I’m gradually going through, testing, and adding/fixing things as I find them.
>
> I’m pushing anything I do straight away to here;
>

> https://bitbucket.org/iracooke/peptideshaker <https://bitbucket.org/iracooke/peptideshaker>

[Ira Cooke]

Hi Bjoern,

Of course, I’ll let you know when I’m done. There is not much point handing it to Pratik yet though as it’s still quite broken.

When I get it to work properly I will send a pull request.

Cheers
Ira

[Ira Cooke]

Hi Harald and Marc, 

The new zip input and output seems like it will be a huge win when adding these tools to Galaxy.  So far we have things working for SearchGUI … it creates a zip file OK which seems to contain all the necessary info for PeptideShaker. 

Now I would like to be able to adapt the PeptideShaker tool so that it can run (in Galaxy) directly from the SearchGUI zipped outputs.  And of course, I’d also like to use the -zip option in PeptideShaker to produce a zip output that I can download and open in the Desktop app.

I’m a bit stuck on the right way to do this … looking at this page

https://code.google.com/p/peptide-shaker/wiki/PeptideShakerCLI

I see that PeptideShaker has alot of Mandatory parameters … but many of these are things that it should be able to determine on its own if given a SearchGUI zip file right?  Is there any chance you could an option to simply provide a single SearchGUI zip input .. and if so, this would remove the requirement to specify -experiment, -sample, -replicate, -identification_files, -spectrum_files, -id_params.  Not only would this be more convenient, but also more consistent since it would avoid users having to reenter the same data twice (eg as in the case of experiment, sample, replicate and id_params).

As an interim measure I am using the following set of commands to unzip the SearchGUI input and then run PeptideShaker.  (These commands are run in a Galaxy job running directory).

mkdir inputs; 

# This is the SearchGUI input from the previous Galaxy task (dataset_13.dat) copied to inputs/in.zip

cp '/home/vagrant/galaxy-dist/database/files/000/dataset_13.dat' inputs/in.zip; 

unzip inputs/in.zip -d inputs/;

# I found that I needed to remove the in.zip file or it would be recognised as a search result by PeptideShaker

rm inputs/in.zip;

# In SearchGUI the original path to the DB was in the working dir so I need to copy that back to where it should be

cp inputs/data/*.fasta .; 

cwd=`pwd`; (java -Xmx5G -cp $PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -temp_folder `pwd` -experiment 'Galaxy_Experiment_2014121623181418771922' -sample 'Sample_2014121623181418771922' -replicate 1 -spectrum_files $cwd/inputs/data/ -identification_files $cwd/inputs/ -out $cwd/peptide_shaker_output.cps -id_params $cwd/inputs/SearchGUI.parameters -zip $cwd/peptideshaker_out.zip -threads "${GALAXY_SLOTS:-12}" 2>> peptideshaker_stderr) && exit_code_for_galaxy=$?; cat peptideshaker_stderr 2>&1;

Notice that I have -Xmx5G set as part of this command.  It seems like I must be doing something wrong because PeptideShaker starts using memory like crazy.  My search database is only 137Mb, and my mgf only 8.5Mb.  But after running for a about 10 minutes PeptideShaker is using around 3.2Gb of memory.  

So far I have been unable to get it to run to completion.

I was hoping that you could take a look at my SearchGUI results zip file .. and see if you can process it.  Perhaps there is a trick I am missing with regards to setting up the inputs correctly.

My SearchGUI test results file is here.

https://dl.dropboxusercontent.com/u/226794/MassSpec/searchgui_test.zip

Cheers

Ira

On 16 Dec 2014, at 9:52 pm, Björn Grüning <bjoern....@gmail.com> wrote:

[Marc Vaudel]

Hi Ira and thanks for the positive feedback!

Concerning the issue with the mandatory parameter, sorry that the documentation is not optimal but we did not find any better way to explain it: The "-spectrum_files, -id_params" parameters are mandatory unless present in the zip file. i.e. you don't need to unzip the searchgui output, and don't need to provide spectrum files and id parameters files - just provide the searchgui zip file in identification_files and the tool will do the rest. The parameters for the annotation of the projects are mandatory though, as they are project dependent. To sum up, you just need -experiment, -sample, -replicate, -identification_files.

I will look at your files later, is there any simple way for you to access the log file available in the installation folder (resources/PeptideShaker.log)? Could it be that you have some home made headers in your fasta file? If so the tool might have troubles parsing them. You will find more help on database formatting here: https://code.google.com/p/searchgui/wiki/DatabaseHelp

Best regards,

Marc

[harald.barsnes]

 

Hi Ira,

 

I did some testing and it seems like the id parameters still have to be provided separately on the command line. This should however not be the case if included in the SearchGUI zip file. I'll try to fix this and release a new version as soon as possible where you should be able to use command lines like this one:

 

java -Xms128M -Xmx6000M -cp PeptideShaker-0.36.0-beta.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment ProjectName -sample SampleName -replicate 0 -identification_files "...\searchgui_out.zip" -out "...\ps_out_2.cps" -species "Human (Homo sapiens)" -species_type "Vertebrates" -zip "...\PeptideShaker.zip"

 

As Marc says the experiment, sample and replicate number (and if wanted the species details) have to be provided here. But this information is only provided once, as it is not used in SearchGUI.

 

And keep in mind that you have to use the options "-output_option 0" and "-output_data 1" in SearchGUI for the spectrum files and the search parameters to be included in the zip file and later automatically picked up by PeptideShaker.

 

Best regards,

Harald 

[harald.barsnes]

 

Hi again,

 

I've now fixed the problem with the id parameters not being picked up from the SearchGUI zip file.

 

Beta versions for testing are available here:

https://www.dropbox.com/s/q2c9v0l89murp5k/SearchGUI-1.24.0.beta-mac_and_linux.tar.gz?dl=0
https://www.dropbox.com/s/ws2m1v6eb0pesxz/PeptideShaker-0.36.0-beta.zip?dl=0

 

Note that there are lots of other fixes and improvements to these versions:
http://code.google.com/p/peptide-shaker/wiki/ReleaseNotes
http://code.google.com/p/searchgui/wiki/ReleaseNotes

But there should be no changes to the command lines.

[Ira Cooke]

Hi Harald and Marc, 

Thanks for quick response.   I’ll try to address each issue separately. 

1.  Documentation

I just checked the wiki and I can see that you updated the documentation … I think it’s clear now :) .. great!

One little suggestion might be to say somewhere in the wiki that all paths provided as arguments must be absolute paths (in my experience so far this seems to be required).  Maybe this could go under “General” at the bottom.

2.  Running SearchGUI

When I run searchgui I use parameters as suggested to embed all required info.  I think this is correct … but please let me know if not.

-output_option 0 -output_data 1

If you check out the zip file that I provided it should reflect this (i.e. it contains a fasta file and an mgf file)

3. Testing new beta versions of PeptideShaker

Based on your suggestions I am now doing the following 

a. Checked my database … oops … it contained decoys.  I fixed that. Now it only contains Swissprot Mouse sequences (unmodified downloaded direct from uniprot.org).

b. I reran my SearchGUI analysis using the new database .. and the beta jar file provided this morning.

c. I copied my SearchGUI zip file to a test directory and I call it “in.zip”

d. I then run PeptideShaker as follows (using the new beta jar file) (See attached output)

Unfortunately, now I am running into a divide by zero error in the unzip routine.

I’m not really sure where to go from here.  But hopefully it should be easy for you to reproduce this issue by downloading my zip file from here

https://dl.dropboxusercontent.com/u/226794/MassSpec/searchgui_test.zip

And then running PeptideShaker on it.

Thanks so far for all your help and quick responses.  Hopefully we almost have it working.

Cheers

Ira

java -Xmx5G -cp $PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment 'Galaxy_Experiment_2014121623181418771922' -sample 'Sample_2014121623181418771922' -replicate 1  -identification_files '/home/vagrant/test/in.zip' -out '/home/vagrant/test/peptide_shaker_output.cps' -temp_folder '/home/vagrant/test/tmp' -zip '/home/vagrant/test/out.zip'

Path configuration completed.

Wed Dec 17 22:57:42 UTC 2014 Unzipping in.zip.

Wed Dec 17 22:57:42 UTC 2014 An error occurred while creating the PeptideShaker project.

java.lang.ArithmeticException: / by zero

at com.compomics.util.gui.waiting.waitinghandlers.WaitingHandlerCLIImpl.setSecondaryProgressCounter(WaitingHandlerCLIImpl.java:81)

at com.compomics.util.io.compression.ZipUtils.unzip(ZipUtils.java:228)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.createProject(PeptideShakerCLI.java:465)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:162)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:973)

Wed Dec 17 22:57:42 UTC 2014 Project successfully created.

Wed Dec 17 22:57:42 UTC 2014 Saving results.

Wed Dec 17 22:57:42 UTC 2014 An exception occurred while saving the project.

java.lang.NullPointerException

at eu.isas.peptideshaker.utils.CpsParent.saveProject(CpsParent.java:231)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:186)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:973)

Wed Dec 17 22:57:42 UTC 2014 Zipping project.

Wed Dec 17 22:57:42 UTC 2014 PeptideShaker processing failed. See the PeptideShaker log for details.

<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for details.</CompomicsError>

java.lang.NullPointerException

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(PeptideShakerCLI.java:318)

at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:973)

[harald.barsnes]

 

Hi Ira,

 

1) I'm not sure if absolute paths are mandatory, but I added a comment recommending the use of absolute paths to the wiki as suggested.

 

2) The SearchGUI zip file contains all the wanted files, so yes, you are using the zip options correctly.

 

3) It was a bug on our side. Has now been fixed. I've updated the version on Dropbox (same version number though):
https://www.dropbox.com/s/ws2m1v6eb0pesxz/PeptideShaker-0.36.0-beta.zip?dl=0

 

Hopefully you will now be able to process the data in PeptideShaker.

[Ira Cooke]

Hi Harald, 

That’s perfect. Thanks! … It works now :)!  

Regarding memory usage, I’m a bit worried that what I’m seeing is not normal.   During my Peptideshaker run, memory usage went up to around 3.5Gb … this is based off a SearchGUI zip file of around 30Mb. 

I could see that this seems to have to do with creating a hash map from the FASTA file (am I right that this is the major memory contributor?).  I was just wondering why this happens .. and if there are any rules of thumb I could use to figure out expected memory usage for given inputs? And is my experience in line with what you have seen? 

Best wishes

Ira

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[Marc Vaudel]

Hi Ira,

You are right, the first time PeptideShaker is used on a given database, it has to create an index (many hashmaps) and the creation of this index is the main memory demanding task. The memory used by the index creation depends on how much memory you give to the tool: 1GB it will use 1GB, 3GB it will use 3GB and be faster. If the downstream process does not use much memory like in your case, these maps will never get garbage collected and will stay in memory until the end of the process. So as far as I can see, nothing to worry about. A good test would be to try with less memory to see if the tool handles it nicely.

What is more important is to make sure that this index is not recreated every time you run the tool, because it is the most time consuming part. Is there a way for you to have a resources folder for a given wrapper where we could store these indexes between runs? Note that only one connection is allowed to these indexes so we cannot use one for multiple PeptideShaker instances.

Other than that it seems that these new wrappers are a great improvement compared to the previous versions, thank you very much to you two for getting them up and running! Sorry about the divided by zero issue, we still need to validate some bits of code in these new versions.

Best regards,

Marc

To view this discussion on the web visit https://groups.google.com/a/umn.edu/d/msgid/galaxyp/AF08F727-E8E5-4CF7-9364-F96714E999A9%40gmail.com.

[Björn Grüning]

Hi Marc,

> Hi Ira,
>
> You are right, the first time PeptideShaker is used on a given database, it
> has to create an index (many hashmaps) and the creation of this index is
> the main memory demanding task. The memory used by the index creation
> depends on how much memory you give to the tool: 1GB it will use 1GB, 3GB
> it will use 3GB and be faster. If the downstream process does not use much
> memory like in your case, these maps will never get garbage collected and
> will stay in memory until the end of the process. So as far as I can see,
> nothing to worry about. A good test would be to try with less memory to see
> if the tool handles it nicely.

This is good to know. In Galaxy every admin can give a particular tool a
specific amount of memory (depending on the node it is running), slots
and so on. For a HPC environment this means, that we can run
PeptideShaker with 24G or more if we want. This is great!

> What is more important is to make sure that this index is not recreated
> every time you run the tool, because it is the most time consuming part. Is
> there a way for you to have a resources folder for a given wrapper where we
> could store these indexes between runs? Note that only one connection is
> allowed to these indexes so we cannot use one for multiple PeptideShaker
> instances.

Unless we isolate the index-build into a separate tool and store it into
another datatype this will not work.
In Galaxy you can run as many jobs as you want on one input datatype and
multiple PeptideShaker instances needs to work on one input.
What is the expected timeframe for indexing? I would guess Galaxy is
running on big comoputers, do we need to worry about this?

Ciao,
Bjoern

>>> at eu.isas.peptideshaker.cmd.PeptideShakerCLI.call(
>>> PeptideShakerCLI.java:162)
>>> at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(

>> <https://groups.google.com/a/umn.edu/d/msgid/galaxyp/076f1bea-ff85-4d9b-9d77-5a9fc01ba4ef%40umn.edu?utm_medium=email&utm_source=footer>
>> .

>>
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to galaxyp+u...@umn.edu.
>>
>>
>> --
>> You received this message because you are subscribed to the Google Groups
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>> Visit this group at http://groups.google.com/a/umn.edu/group/galaxyp/.
>> To view this discussion on the web visit
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>> .

[Marc Vaudel]

Hi Bjoern,

Yes it is possible to provide the index folder as command line argument just like you provide the temp folder. So having a separate datatype would do the trick, but maybe this is advanced processing and should not be a priority at the moment. The time needed depends on the database size obviously, but also on the number of cores and IO speed. On a standard laptop count ~5 minutes on human swissprot. On your formula 1 computers it will be faster of course, as soon as you have a project running we can inspect that time in the log of the project creation.

Best regards,

Marc

[Björn Grüning]

Hi Marc,

Am 18.12.2014 um 15:11 schrieb Marc Vaudel:
> Hi Bjoern,
>
> Yes it is possible to provide the index folder as command line argument
> just like you provide the temp folder. So having a separate datatype would
> do the trick, but maybe this is advanced processing and should not be a
> priority at the moment.

Yes I think you are right, this is not a priority now. Last question,
would it be possible to have multiple PS running one this index? I
understood from your last mail that this is not possible.

> The time needed depends on the database size
> obviously, but also on the number of cores and IO speed. On a standard
> laptop count ~5 minutes on human swissprot. On your formula 1 computers it
> will be faster of course, as soon as you have a project running we can
> inspect that time in the log of the project creation.

Ok. Thanks,
Bjoern

[Marc Vaudel]

Hi Björn,

Yes, only one instance at a time can use the index in the current setup. The idea was more to reuse it once your import is completed :) But we can work on alternative solutions.

Best regards,

Marc

[Ira Cooke]

Hi Bjoern and Marc,

I agree … let’s not worry about this for now. In the first version of the Galaxy tool we can live with a little inefficiency (the database will need to be reindexed every time) … most Galaxy jobs tend to be run on pretty high end machines with heaps of memory, so hopefully it will be quick.

Bjoern, one thing I was wondering was whether we should define a new datatype for the zip files. As far as I can tell Galaxy only has the type “bgzip” .. and this isn’t really appropriate since it looks like SearchGUI and PeptideShaker both create ZIP files. I’m not sure of all the subtleties … but at the very least these should have extension “zip” rather than “bgzip”. If we defined a type called “searchguizip” (subtype of Binary) .. and another type called “peptideshakerzip”, it would also make workflows easier since galaxy could tell the difference between outputs from SearchGUI versus PeptideShaker?

What do you think? If we add this, I’m thinking that it should just go straight in the PeptideShaker toolshed package because it is completely specialised on these tools.

Cheers
Ira

[Björn Grüning]

Hi Ira,

Am 19.12.2014 um 01:16 schrieb Ira Cooke:
> Hi Bjoern and Marc,
>
> I agree … let’s not worry about this for now. In the first version of the Galaxy tool we can live with a little inefficiency (the database will need to be reindexed every time) … most Galaxy jobs tend to be run on pretty high end machines with heaps of memory, so hopefully it will be quick.
>
> Bjoern, one thing I was wondering was whether we should define a new datatype for the zip files. As far as I can tell Galaxy only has the type “bgzip” .. and this isn’t really appropriate since it looks like SearchGUI and PeptideShaker both create ZIP files. I’m not sure of all the subtleties … but at the very least these should have extension “zip” rather than “bgzip”. If we defined a type called “searchguizip” (subtype of Binary) .. and another type called “peptideshakerzip”, it would also make workflows easier since galaxy could tell the difference between outputs from SearchGUI versus PeptideShaker?
>
> What do you think? If we add this, I’m thinking that it should just go straight in the PeptideShaker toolshed package because it is completely specialised on these tools.

Yes this makes totally sense. Let's subclass it :)
The policy for datatypes is currently not clear, we can also try to add
it to main Galaxy. Part of the ToolShed repo is also ok.

Thanks,
Bjoern

[Ira Cooke]

Cool, for now let’s just add it to the toolshed repo.

[Pratik Jagtap]

Thank you very much Ira, Bjoern, Marc and Harald,

Please let us know when the latest build is in the toolshed and we will have it installed for testing. Hopefully, we can match your enthusiasm and hard work !

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Pratik Jagtap]

Hello Ira and Bjoern,

Is the latest version SearchGUI and PeptideShaker that you worked on in a galaxy toolshed?

Thanks,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Björn Grüning]

Hi Pratik,

not yet. The latest version is here:

https://bitbucket.org/BjoernGruening/peptideshaker

We found a small bug? that we discussed with Marc. If this one is fixed
we are ready to upload to the TTS.

In principle the wrappers are useable, the reports are currently not
working.

Cheers and a few nice days!
Bjoern

[Pratik Jagtap]

Thanks Bjoern,

We will wait for the bug to be taken care of and use the one that you would upload.

Cheers and Happy Holidays !

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Pratik Jagtap]

Hello Bjoern, Ira and Marc,

Wish you a happy new year !

Let us know if there is anything that we can do to take care of the bug before having it deposited in the toolshed for installation.

Thanks and Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Björn Grüning]

Hi Pratik,

the wrappers are mostly working and needs to be tested carefully.
We found two small bugs and as soon as the new release is available we
can all start testing.

Cheers,
Bjoern

[Björn Grüning]

Hi,

congrats to the new peptide shaker paper! I added it as references to
the Galaxy wrapper!

Cheers,
Bjoern

Am 08.01.2015 um 14:34 schrieb Pratik Jagtap:

[Pratik Jagtap]

Congratulations Harald, Marc and Lennart !

http://www.nature.com/nbt/journal/v33/n1/full/nbt.3109.html

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

[Lennart Martens]

Hi Pratik,


Thanks! :D


Cheers,

lnnrt.

> > Phone: 612-624-9275 <tel:612-624-9275>

> >
> > On Tue, Dec 23, 2014 at 8:00 AM, Pratik Jagtap <pja...@umn.edu
> <mailto:pja...@umn.edu>> wrote:
> >
> >> Thanks Bjoern,
> >>
> >> We will wait for the bug to be taken care of and use the one
> that you
> >> would upload.
> >>
> >> Cheers and Happy Holidays !
> >>
> >> Regards,
> >>
> >> Pratik
> >>
> >> Pratik Jagtap,
> >> Managing Director,
> >> Center for Mass Spectrometry and Proteomics,
> >> 43 Gortner Laboratory
> >> 1479 Gortner Avenue
> >> St. Paul, MN 55108

> >> Phone: 612-624-9275 <tel:612-624-9275>

> >>
> >> On Tue, Dec 23, 2014 at 7:55 AM, Björn Grüning

> <bjoern....@gmail.com <mailto:bjoern....@gmail.com>>

> >>>> Phone: 612-624-9275 <tel:612-624-9275>

> >>>>
> >>>> On Fri, Dec 19, 2014 at 1:31 PM, Pratik Jagtap
> <pja...@umn.edu <mailto:pja...@umn.edu>> wrote:
> >>>>
> >>>>> Thank you very much Ira, Bjoern, Marc and Harald,
> >>>>>
> >>>>> Please let us know when the latest build is in the toolshed
> and we will
> >>>>> have it installed for testing. Hopefully, we can match your
> enthusiasm
> >>> and
> >>>>> hard work !
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> Pratik
> >>>>>
> >>>>> Pratik Jagtap,
> >>>>> Managing Director,
> >>>>> Center for Mass Spectrometry and Proteomics,
> >>>>> 43 Gortner Laboratory
> >>>>> 1479 Gortner Avenue
> >>>>> St. Paul, MN 55108

> >>>>> Phone: 612-624-9275 <tel:612-624-9275>

> >>>>>
> >>>>> On Thu, Dec 18, 2014 at 6:40 PM, Ira Cooke
> <irac...@gmail.com <mailto:irac...@gmail.com>> wrote:
> >>>>>
> >>>>>> Cool, for now let’s just add it to the toolshed repo.
> >>>>>>
> >>>>>>> On 19 Dec 2014, at 11:34 am, Björn Grüning <

> >>> bjoern....@gmail.com <mailto:bjoern....@gmail.com>>

> >>> bjoern....@gmail.com <mailto:bjoern....@gmail.com>>

> >>> bjoern....@gmail.com <mailto:bjoern....@gmail.com>

> <irac...@gmail.com <mailto:irac...@gmail.com>>:

> >>>>>> harald....@gmail.com <mailto:harald....@gmail.com>>

> >>>>>>>>>>>>>> from uniprot.org <http://uniprot.org>).

> >>> harald....@gmail.com <mailto:harald....@gmail.com>

> <mailto:gal...@umn.edu>.

> >>>>>>>>>>>>> Visit this group at
> >>>>>> http://groups.google.com/a/umn.edu/group/galaxyp/.
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> >>>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>
> >>>
> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/076f1bea-ff85-4d9b-9d77-5a9fc01ba4ef%40umn.edu
> >>>>>>>>>>>>> <
> >>>>>>>>>>>
> >>>>>>
> >>>
> https://groups.google.com/a/umn.edu/d/msgid/galaxyp/076f1bea-ff85-4d9b-9d77-5a9fc01ba4ef%40umn.edu?utm_medium=email&utm_source=footer
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[Marc Vaudel]

Dear all,

Thank you for your messages and happy new year to all from the team in Bergen!

As Björn mentioned, the last issues for the integration of the tools in Galaxy are being taken care of, and the system will be operational very soon :)

Best regards,

Harald and Marc

[Pratik Jagtap]

Hello Harald and Marc,

Please let us know once the issues for integration into Galaxy are addressed. Keenly looking forward to testing and using this tool within Galaxy.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

CMSP Newsletter (Jan 2015)

[Marc Vaudel]

Dear Pratik,

Thank you very much for your enthusiasm!

We will make a maintenance release later this week and then release next week a new version where, among many new functionalities, the last details for full integration in Galaxy will be sorted out. If we count a couple of week for the integration in the wrappers and testing you should be able to play around with the tools by the end of February :-)

I hope this schedule suits you and does not delay any other project.

Best regards,

Marc

[Pratik Jagtap]

Thanks Marc,

We look forward to a release next week. After wrapping - we will have it installed and have it ready for testing.

Thanks again,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

CMSP Newsletter (Jan 2015)

[Pratik Jagtap]

Hello Marc and Harald,

I have two questions related to PeptideShaker :

a) In one of the release notes, we noticed that there is a beta version of SWATH report that PeptieShaker can generate. Can this export be used as an input (along with pepxml file) for SpectraST? Which software would use this report?

Changes in PeptideShaker 0.25.0 (February 4. 2014)

• NEW FEATURE: Added a simple swath export.

b) Do you know of any tool that can generate a pepxml report from a mzidentml file?

Thanks and Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

CMSP Newsletter (Jan 2015)

[Marc Vaudel]

Dear Pratik,

We implemented the SWATH report for a user who was using it as input in a manufacturer (AB) tool directly, and according to the manufacturer specifications. However, due to the lack of documentation of this export, and the absence of support from the manufacturer, we were never able to get this file in the software... 

Now as far as I heard from users, the best results in DIA are obtained when combining PeptideShaker with Skyline. The best for this would be to use mzIdentML export but the support in Skyline is not ready (you can follow the progress on this thread https://brendanx-uw1.gs.washington.edu/labkey/announcements/home/support/thread.view?rowId=18964 - and eventually post to get us higher in the todolist ;) ).

I would stay away from the pepxml format because it is not well designed to store identification results. As a results the different implementations have different hacks around the format shortcomings, and we might run into compatibility issues there. We are encountering these when taking pepxml as input and would be happy to stay away from these for our output :) However, I see that SpectraST supports simple text input, we can implement such an export very easily. I will contact the developers on this.

Best regards,

Marc

[Pratik Jagtap]

Thanks for your answer.

> However, I see that SpectraST supports simple text input, we can implement such an export very easily. I will contact the developers on this.

This would be great. We would really look forward to this functionality as we are looking at using OpenSWATH workflow within Galaxy.

Regards,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275

CMSP Newsletter (Jan 2015)

[Marc Vaudel]

Dear Pratik,

After digging a bit more in the documentation it seems that there is no alternative to a PeptideProphet-like pepXML file. Would you by any chance have such a file at hand?

I must say I don't get the connection with OpenSWATH? Is there a way to connect both software? Sorry, I am not familiar with these tools :)

Best regards,

Marc

[Marc Vaudel]

Hi Sarah,

Thank you for your quick answer. Do you by any chance plan to implement the conversion from mzIdentML too? If this is not an option note that we could generate TraML files directly if you provide us with the information needed for this. This sounds to me like a much more generic solution and not more work than pepXML.

Best regards,

Marc

2015-02-05 22:07 GMT+01:00 Sarah Parker <spar...@gmail.com>:

Hello Marc,

The pep.xml is needed in the established version we have for building an assay library for openSWATH to read and use to extract and identify peptides from the DIA files. For that workflow, there are already scripts to convert SpectraST library files into the .TraML file format needed for openSWATH analysis. An alternative tool could be built to convert a library other than SpectraST into the right format, it's just that we already have the tools to work with SpectraST so it's a lower hanging fruit. As long as we can convert any search result into the pep.XML format it can be incorporated into spectrast.

Does that help?

Sarah

[Ira Cooke]

Hi All, 

I'm not sure if I'm following exactly, but could idconvert (from proteowizard) be a solution here?  It can do mzid to pepxml conversion.

Cheers

Ira

[Marc Vaudel]

Hi Ira,

That is a good idea, but you might want to test whether the pepxml file generated by idconvert is compatible with SpectraST - ie is the PeptideProphet/iProphet flavor of pepxml, with indexes, charges, PTMs and PEPs annotated accordingly.

Best regards,

Marc

[Gmail]

Hi Marc

Yes totally true. It would likely be a good start and then usually some kind of "fixing" is sure to be required

Cheers

Ira

Sent from my iPhone

[Pratik Jagtap]

This is great news !

Bjoern - once the wrapping is done can you let us / Trevor know about the location of latest wrapper so that it can be installed on GalaxyP for testing?

Thanks a lot ! Looking forward to having latest version of PeptideShaker in Galaxy !

Regards,

Pratik

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt

On Mon, Feb 16, 2015 at 2:43 AM, Marc Vaudel <mva...@gmail.com> wrote:

Hi guys,

The week starts with a good news: we have knocked out all remaining issues for the use of the latest versions in Galaxy. For the record the problems were (1) packaging issues for the follow-up and report command lines, (2) our ensembl annotation working only on desktop computers, and (3) reports crashed when working with databases of unrecognized formats as the one used for testing. You should now be able to create projects on galaxy, download the zip file of your project and open it locally without extra work - you  don't even need to unzip it :)

It would be great if you could test the beta version Björn put in the wrappers this week. If there is no more issue I will proceed with the implementation of a TraML export :)

Best regards,

Marc

2015-02-09 22:21 GMT+01:00 Björn Grüning <bjoern....@gmail.com>:

Hi Candace,

actually we are currently working on fixing some small bugs. If we can
track that down and if Marc will time to fix it we are ready to go and
release the first new version.

We will let you know as soon as possible!
Cheers,
Bjoern

Am 09.02.2015 um 21:05 schrieb Candace Guerrero:

> Hey Guys,
> Hello, I hope all is going well with everyone! I was wondering is there
> were any updates on timelines for PeptideShaker being implemented into
> GalaxyP? I will be presenting at the US HUPO conference (March 15-18th) and
> would like to start using PeptideShakers within some proteogenomic
> workflows. I have some interesting results using ProteinPIlot and would
> love to see what PeptideShaker can do in its place.
> Thanks
> Candace
>
> On Fri, Feb 6, 2015 at 6:14 AM, Pratik Jagtap <pja...@umn.edu> wrote:
>
>> Hello Marc, Harald, Ira and Bjoern,
>>
>> PeptideShaker within GalaxyP will be an important tool and topic for
>> posters, application projects and two workshops this summer. It will be
>> great if the latest version of the PeptideShaker is ready for wrapping so
>> that we can start using this exciting tool.
>>
>> Integration with OpenSWATH workflow can come in during a latter version as
>> we proceed.

>>>>>> *CMSP Newsletter (Jan 2015) <http://z.umn.edu/cmspnewsletter01>*

>>>>>>>> *Changes in PeptideShaker 0.25.0 (February 4. 2014)*
>>>>>>>>
>>>>>>>>    - *NEW FEATURE: Added a simple swath export.*

>>>>>>>>
>>>>>>>>
>>>>>>>> b) Do you know of any tool that can generate a pepxml report from a
>>>>>>>> mzidentml file?
>>>>>>>>
>>>>>>>> Thanks and Regards,
>>>>>>>>
>>>>>>>> Pratik
>>>>>>>>
>>>>>>>> Pratik Jagtap,
>>>>>>>> Managing Director,
>>>>>>>> Center for Mass Spectrometry and Proteomics,
>>>>>>>> 43 Gortner Laboratory
>>>>>>>> 1479 Gortner Avenue
>>>>>>>> St. Paul, MN 55108
>>>>>>>> Phone: 612-624-9275

>>>>>>>> *CMSP Newsletter (Jan 2015) <http://z.umn.edu/cmspnewsletter01>*

>>>>>>>>
>>>>>>>> On Thu, Jan 22, 2015 at 8:59 AM, Pratik Jagtap <pja...@umn.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Thanks Marc,
>>>>>>>>>
>>>>>>>>> We look forward to a release next week. After wrapping - we will
>>>>>>>>> have it installed and have it ready for testing.
>>>>>>>>>
>>>>>>>>> Thanks again,
>>>>>>>>>
>>>>>>>>> Pratik
>>>>>>>>>
>>>>>>>>> Pratik Jagtap,
>>>>>>>>> Managing Director,
>>>>>>>>> Center for Mass Spectrometry and Proteomics,
>>>>>>>>> 43 Gortner Laboratory
>>>>>>>>> 1479 Gortner Avenue
>>>>>>>>> St. Paul, MN 55108
>>>>>>>>> Phone: 612-624-9275

>>>>>>>>> *CMSP Newsletter (Jan 2015) <http://z.umn.edu/cmspnewsletter01>*

>>>>>>>>>>> *CMSP Newsletter (Jan 2015) <http://z.umn.edu/cmspnewsletter01>*

[Björn Grüning]

Hi Pratik,

done is so relative ;)

I have commited the latest changes and they pass our small test example.
Ira ist currently busy with more testing. If you have time and brave
enough you can install them (they will install the latest version of
SG/PS) and try it. We will know more if Ira has tested it a little bit more.

Cheers,
Bjoern

Am 16.02.2015 um 14:40 schrieb Pratik Jagtap:
> This is great news !
>
> Bjoern - once the wrapping is done can you let us / Trevor know about the
> location of latest wrapper so that it can be installed on GalaxyP for
> testing?
>
> Thanks a lot ! Looking forward to having latest version of PeptideShaker in
> Galaxy !
>
> Regards,
>
> Pratik
>
> Pratik Jagtap,
> Managing Director, Center for Mass Spectrometry and Proteomics,
> 43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108
> Phone: 612-624-9275

> *http://z.umn.edu/multiomicsnbt <http://z.umn.edu/multiomicsnbt>*

[Pratik Jagtap]

Thanks Bjoern,

We can test the latest GUI versions and see how they work for small datasets. However, for actual testing within Galaxy - we will wait for Ira's tests and recommendations and install it on Galaxy for its functionality.

Regards,

Pratik

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt