Loading results into PeptideShaker fails.

[ulrich-eckhard]

Hey Marc and Harald,

i somehow fail to load some data into PeptideShaker (more details below). tried PS 1.7.5 and 1.7.4, both the same result. It was a rather open search of a QC sample, so with variable dm@K and variable cm@Cys on top of all the other variable ones we typically have (dm/acet/pyro@Nter, Ox@Met). Results are from comet. I also had to add dm4 - 12C(2) 2H(4) [Unimod 199] as we used "deuterated formaldehyde" but "light" sodium cyanoborohydride, giving us +4.

can you have a quick look into that, or have a quick idea what is going wrong? i am uploading right now the SearchGUI files to my google drive account. will send the link off-list as soon as the upload is done.

thanks already, u

Peptide Shaker Report

Fri Feb 12 10:58:29 PST 2016 Importing sequences from 1512_UP_human_CanIsoCon_concatenated_target_decoy.fasta. Fri Feb 12 10:58:32 PST 2016 FASTA file import completed. Fri Feb 12 10:58:32 PST 2016 Importing gene mappings. Fri Feb 12 10:58:34 PST 2016 Establishing local database connection. Fri Feb 12 10:58:35 PST 2016 Reading identification files. Fri Feb 12 10:58:35 PST 2016 Parsing MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.comet.pep.xml. Fri Feb 12 10:58:38 PST 2016 Loading spectra for MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.comet.pep.xml. Fri Feb 12 10:58:38 PST 2016 Importing MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.mgf Fri Feb 12 10:58:38 PST 2016 MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.mgf imported. Fri Feb 12 10:58:39 PST 2016 Collecting peptides to map. Fri Feb 12 10:58:40 PST 2016 Mapping peptides to proteins. Fri Feb 12 11:02:45 PST 2016 Importing PSMs from MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.comet.pep.xml Fri Feb 12 11:02:45 PST 2016 An error occurred: null Fri Feb 12 11:02:45 PST 2016 Please contact the developers (https://github.com/compomics/peptide-shaker/issues).

Fri Feb 12 11:02:45 PST 2016 Importing Data Canceled

Peptide Shaker Log

Fri Feb 12 08:58:38 PST 2016: PeptideShaker version 1.7.5. Memory given to the Java virtual machine: 13981188096. Total amount of memory in the Java virtual machine: 163053568. Free memory: 131627536. Java version: 1.8.0_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: 1.8.0_71 os.name: Windows 7 memory: 46.8/163.1 processors available: 8 useCommandThread: false java.lang.NullPointerException at com.compomics.util.experiment.biology.Peptide.getPotentialModificationSites(Peptide.java:898) at com.compomics.util.experiment.biology.PTMFactory.getExpectedPTMs(PTMFactory.java:404) at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:580) at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:416) at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:66) at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1459) 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)

[hbarsnes]

Hi Ulrich,

Thanks for the data. We'll have a look at it next week and get back to you. Probably another strange PTM related issue that nobody's come across before, as you're pretty good at those. ;)

Best regards, Harald

[ulrich-eckhard]

yeah, must be my special gift - and being my own nemesis! ;-)

On Fri, Feb 12, 2016 at 2:41 PM, Harald Barsnes notifications@github.com wrote:

Hi Ulrich,

Thanks for the data. We'll have a look at it next week and get back to you. Probably another strange PTM related issue that nobody's come across before, as you're pretty good at those. ;)

Best regards, Harald

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-183515044 .

[ulrich-eckhard]

and thanks already!

On Fri, Feb 12, 2016 at 2:43 PM, Ulrich Eckhard ulrich.eckhard@gmail.com wrote:

yeah, must be my special gift - and being my own nemesis! ;-)

On Fri, Feb 12, 2016 at 2:41 PM, Harald Barsnes notifications@github.com wrote:

Hi Ulrich,

Thanks for the data. We'll have a look at it next week and get back to you. Probably another strange PTM related issue that nobody's come across before, as you're pretty good at those. ;)

Best regards, Harald

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-183515044 .

[anupshah14]

Hi Guys,

I recently had a similar issue. I search the data using SearchGUI 2.6.1. It has successfully completed search using X!Tandom and created a zip file. I got error while importing to Peptideshaker 1.7.6. Here are last few lines of peptideshaker report

Fri Feb 19 18:27:02 AEST 2016 Computing assumptions probabilities. Fri Feb 19 18:27:02 AEST 2016 Saving assumptions probabilities. Fri Feb 19 18:27:16 AEST 2016 Selecting best peptide per spectrum. Fri Feb 19 18:27:59 AEST 2016 Computing PSM probabilities. Fri Feb 19 18:27:59 AEST 2016 Scoring PTMs in PSMs (D-score and A-score) Fri Feb 19 18:27:59 AEST 2016 An error occurred: null Fri Feb 19 18:27:59 AEST 2016 Please contact the developers (https://github.com/compomics/peptide-shaker/issues).

Fri Feb 19 18:27:59 AEST 2016 Importing Data Canceled!

Not sure if I have done something wrong here.

Thanks Anup

[mvaudel]

Dear Anup,

Would it be possible for you to send us the log of the tool (available via the Help -> Bug Report menu), and eventually also the paramters file?

Apologies for the inconvenience,

Marc

[anupshah14]

Hi Marc, I was using the option to visualise the report in Peptideshaker after search completion. But when I tried to open the zip file in Peptide shaker separately I would load my results. Still I will send you the files.

Anup

[mvaudel]

Hi again,

Great to read that it worked out in the end, and thanks for the log you sent. Would it be possible to send me the log of PeptideShaker as well?

Thank you,

Marc

[Nyaradzo]

Hi Marc,

I have been experiencing the same problem.

error is below and I have attached the log.

Tue Feb 23 14:10:55 CAT 2016 2 identified spectra (0.1%) did not present a valid peptide. Tue Feb 23 14:10:55 CAT 2016 4 of the best scoring peptides were excluded by the import filters: Tue Feb 23 14:10:55 CAT 2016 - 100.0% peptide mapping to both target and decoy. Tue Feb 23 14:10:55 CAT 2016 Parsing 3B_5ul.myrimatch.mzid. Tue Feb 23 14:11:05 CAT 2016 Loading spectra for 3B_5ul.myrimatch.mzid. Tue Feb 23 14:11:05 CAT 2016 Importing PSMs from 3B_5ul.myrimatch.mzid Tue Feb 23 14:14:26 CAT 2016 An error occurred: Error while loading spectrum 3B_5ul.471.471. File:"3B_5ul.raw", NativeID:"controllerType=0 controllerNumber=1 scan=471" of file 3B_5ul.mgf. Tue Feb 23 14:14:26 CAT 2016 Please contact the developers (https://github.com/compomics/peptide-shaker/issues).

Tue Feb 23 14:14:26 CAT 2016 Importing Data Canceled!

Nyari Importing data error2.txt

[mvaudel]

Hi Nyari,

It seems like these is a problem when reading your files. Can you send me the log of the tool? It is available under the "Help" > "Bug Report" menu which you can access at the tool startup or in the main interface.

Apologizes for the inconvenience,

Marc

[Nyaradzo]

Hi Marc,

Please find attached the log

Nyari

From: Marc Vaudel [mailto:notifications@github.com] Sent: 24 February 2016 12:06 PM To: compomics/peptide-shaker Cc: Nyari Chigorimbo Subject: Re: [peptide-shaker] Loading results into PeptideShaker fails. (#138)

Hi Nyari,

It seems like these is a problem when reading your files. Can you send me the log of the tool? It is available under the "Help" > "Bug Report" menu which you can access at the tool startup or in the main interface.

Apologizes for the inconvenience,

Marc

— Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/138#issuecomment-188173453.

Reindexing: Human_TrypsinProteins9Dec15.fasta. Reindexing: Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta.

makeblastdb command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\makeblastdb\windows\makeblastdb -in Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -dbtype prot

tide index command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-index F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta fasta-index --overwrite T --mods-spec M+15.994915,C+57.021464 --nterm-peptide-mods-spec 1E-18.010565,1Q-17.026549,1C-17.026549,1X+42.010565 --decoy-format none --missed-cleavages 2 --output-dir crux-output --peptide-list F --verbosity 30 --min-length 6 --max-length 30 --min-mass 200.0 --max-mass 7200.0 --monoisotopic-precursor T --clip-nterm-methionine F --enzyme trypsin --digestion full-digest

xtandem command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\tandem C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\input_searchGUI.xml

myrimatch command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MyriMatch\windows\windows_64bit\myrimatch -cpus 4 -ProteinDatabase "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -OutputFormat mzIdentML -workdir "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp" -OutputSuffix .myrimatch -DecoyPrefix "" -MinPeptideLength 8 -MaxPeptideLength 30 -MaxResultRank 10 -SpectrumListFilters "" -FragmentMzTolerance "0.5 daltons" -MonoPrecursorMzTolerance "10.0 ppm" -PrecursorMzToleranceRule "mono" -StaticMods "M 15.994915 C 57.021464" -DynamicMods "(E 0 -18.010565 (Q 1 -17.026549 (C 2 -17.026549 ( 3 42.010565" -MaxDynamicMods 2 -StatusUpdateFrequency 10 -NumChargeStates 4+ -TicCutoffPercentage 0.98 -MinPeptideMass 0.0 -MaxPeptideMass 10000.0 -UseSmartPlusThreeModel true -ComputeXCorr false -NumIntensityClasses 3 -ClassSizeMultiplier 2 -NumBatches 50 -MaxPeakCount 300 -MonoisotopeAdjustmentSet [0,1] -FragmentationAutoRule false -FragmentationRule "cid" -CleavageRules "Trypsin" -MinTerminiCleavages 2 -MaxMissedCleavages 2

ms amanda command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\MSAmanda.exe "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\settings_SearchGUI.xml" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.ms-amanda.csv"

ms-gf+ command: "C:\Program Files\Java\jre1.8.0_71\bin\java" -Xms128M -Xmx4096M -jar "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\MSGFPlus.jar" -s "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -d "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" -o "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.msgf.mzid" -t 10.0ppm -tda 0 -mod "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\params\Mods.txt" -minCharge 2 -maxCharge 4 -inst 3 -thread 4 -m 3 -e 1 -ntt 2 -protocol 0 -minLength 8 -maxLength 30 -n 10 -addFeatures 0 -ti "0,1"

omssa command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\OMSSA\windows\omssacl -w -to 0.5 -te 10.0 -teppm -e 0 -zl 2 -zh 4 -zt 3 -ti 1 -tex 1446.94 -cl 0.0 -ch 0.2 -ci 5.0E-4 -w1 27 -w2 14 -h1 2 -h2 2 -hl 30 -hc 30 -hm 2 -hs 4 -ht 6 -mm 128 -zoh 2 -z1 0.95 -pc 1 -sb1 0 -sp 100 -scorp 0.5 -is 0.0 -ir 0.0 -ii 0.01 -v 2 -he 100.0 -tez 1 -zcc 2 -cp 0 -no 8 -nox 30 -tom 0 -tem 0 -i 1,4 -mf 119,120 -mv 121,122,123,124 -d Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -fm C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf -ox "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.omx" -nt 4

comet command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Comet\windows\windows_64bit\comet.exe C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf

java.io.FileNotFoundException: Source 'C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.comet.pep.xml' does not exist at org.apache.commons.io.FileUtils.moveFile(FileUtils.java:1805) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2107) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

makeblastdb command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\makeblastdb\windows\makeblastdb -in Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -dbtype prot

tide index command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-index F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta fasta-index --overwrite T --mods-spec M+15.994915,C+57.021464 --nterm-peptide-mods-spec 1E-18.010565,1Q-17.026549,1C-17.026549,1X+42.010565 --decoy-format none --missed-cleavages 2 --output-dir crux-output --peptide-list F --verbosity 30 --min-length 6 --max-length 30 --min-mass 200.0 --max-mass 7200.0 --monoisotopic-precursor T --clip-nterm-methionine F --enzyme trypsin --digestion full-digest

xtandem command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\tandem C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\input_searchGUI.xml

myrimatch command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MyriMatch\windows\windows_64bit\myrimatch -cpus 4 -ProteinDatabase "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -OutputFormat mzIdentML -workdir "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp" -OutputSuffix .myrimatch -DecoyPrefix "" -MinPeptideLength 8 -MaxPeptideLength 30 -MaxResultRank 10 -SpectrumListFilters "" -FragmentMzTolerance "0.5 daltons" -MonoPrecursorMzTolerance "10.0 ppm" -PrecursorMzToleranceRule "mono" -StaticMods "M 15.994915 C 57.021464" -DynamicMods "(E 0 -18.010565 (Q 1 -17.026549 (C 2 -17.026549 ( 3 42.010565" -MaxDynamicMods 2 -StatusUpdateFrequency 10 -NumChargeStates 4+ -TicCutoffPercentage 0.98 -MinPeptideMass 0.0 -MaxPeptideMass 10000.0 -UseSmartPlusThreeModel true -ComputeXCorr false -NumIntensityClasses 3 -ClassSizeMultiplier 2 -NumBatches 50 -MaxPeakCount 300 -MonoisotopeAdjustmentSet [0,1] -FragmentationAutoRule false -FragmentationRule "cid" -CleavageRules "Trypsin" -MinTerminiCleavages 2 -MaxMissedCleavages 2

ms amanda command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\MSAmanda.exe "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\settings_SearchGUI.xml" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.ms-amanda.csv"

ms-gf+ command: "C:\Program Files\Java\jre1.8.0_71\bin\java" -Xms128M -Xmx4096M -jar "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\MSGFPlus.jar" -s "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -d "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" -o "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.msgf.mzid" -t 10.0ppm -tda 0 -mod "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\params\Mods.txt" -minCharge 2 -maxCharge 4 -inst 3 -thread 4 -m 3 -e 1 -ntt 2 -protocol 0 -minLength 8 -maxLength 30 -n 10 -addFeatures 0 -ti "0,1"

omssa command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\OMSSA\windows\omssacl -w -to 0.5 -te 10.0 -teppm -e 0 -zl 2 -zh 4 -zt 3 -ti 1 -tex 1446.94 -cl 0.0 -ch 0.2 -ci 5.0E-4 -w1 27 -w2 14 -h1 2 -h2 2 -hl 30 -hc 30 -hm 2 -hs 4 -ht 6 -mm 128 -zoh 2 -z1 0.95 -pc 1 -sb1 0 -sp 100 -scorp 0.5 -is 0.0 -ir 0.0 -ii 0.01 -v 2 -he 100.0 -tez 1 -zcc 2 -cp 0 -no 8 -nox 30 -tom 0 -tem 0 -i 1,4 -mf 119,120 -mv 121,122,123,124 -d Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -fm C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf -ox "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.omx" -nt 4

comet command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Comet\windows\windows_64bit\comet.exe C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf

tide search command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-search --compute-sp F C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\temp\peak_lists\1A_Nyari_Epic.ms2 fasta-index --overwrite T --top-match 10 --precursor-window 10.0 --precursor-window-type ppm --fileroot 1A_Nyari_Epic --exact-p-value F --output-dir crux-output --spectrum-min-mz 0.0 --min-peaks 20 --spectrum-charge all --remove-precursor-peak F --remove-precursor-tolerance 1.5 --print-search-progress 1000 --use-flanking-peaks F --use-neutral-loss-peaks F --mz-bin-width 0.02 --mz-bin-offset 0.0 --concat F --txt-output T --sqt-output F --pepxml-output F --mzid-output F --pin-output F --verbosity 30

java.io.FileNotFoundException: Source 'C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux-output\1A_Nyari_Epic.tide-search.target.txt' does not exist at org.apache.commons.io.FileUtils.moveFile(FileUtils.java:1805) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2147) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

makeblastdb command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\makeblastdb\windows\makeblastdb -in Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -dbtype prot

tide index command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-index F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta fasta-index --overwrite T --mods-spec M+15.994915,C+57.021464 --nterm-peptide-mods-spec 1E-18.010565,1Q-17.026549,1C-17.026549,1X+42.010565 --decoy-format none --missed-cleavages 2 --output-dir crux-output --peptide-list F --verbosity 30 --min-length 6 --max-length 30 --min-mass 200.0 --max-mass 7200.0 --monoisotopic-precursor T --clip-nterm-methionine F --enzyme trypsin --digestion full-digest

xtandem command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\tandem C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\input_searchGUI.xml

myrimatch command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MyriMatch\windows\windows_64bit\myrimatch -cpus 4 -ProteinDatabase "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -OutputFormat mzIdentML -workdir "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp" -OutputSuffix .myrimatch -DecoyPrefix "" -MinPeptideLength 8 -MaxPeptideLength 30 -MaxResultRank 10 -SpectrumListFilters "" -FragmentMzTolerance "0.5 daltons" -MonoPrecursorMzTolerance "10.0 ppm" -PrecursorMzToleranceRule "mono" -StaticMods "M 15.994915 C 57.021464" -DynamicMods "(E 0 -18.010565 (Q 1 -17.026549 (C 2 -17.026549 ( 3 42.010565" -MaxDynamicMods 2 -StatusUpdateFrequency 10 -NumChargeStates 4+ -TicCutoffPercentage 0.98 -MinPeptideMass 0.0 -MaxPeptideMass 10000.0 -UseSmartPlusThreeModel true -ComputeXCorr false -NumIntensityClasses 3 -ClassSizeMultiplier 2 -NumBatches 50 -MaxPeakCount 300 -MonoisotopeAdjustmentSet [0,1] -FragmentationAutoRule false -FragmentationRule "cid" -CleavageRules "Trypsin" -MinTerminiCleavages 2 -MaxMissedCleavages 2

ms amanda command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\MSAmanda.exe "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\settings_SearchGUI.xml" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.ms-amanda.csv"

ms-gf+ command: "C:\Program Files\Java\jre1.8.0_71\bin\java" -Xms128M -Xmx4096M -jar "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\MSGFPlus.jar" -s "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -d "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" -o "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.msgf.mzid" -t 10.0ppm -tda 0 -mod "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\params\Mods.txt" -minCharge 2 -maxCharge 4 -inst 3 -thread 4 -m 3 -e 1 -ntt 2 -protocol 0 -minLength 8 -maxLength 30 -n 10 -addFeatures 0 -ti "0,1"

omssa command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\OMSSA\windows\omssacl -w -to 0.5 -te 10.0 -teppm -e 0 -zl 2 -zh 4 -zt 3 -ti 1 -tex 1446.94 -cl 0.0 -ch 0.2 -ci 5.0E-4 -w1 27 -w2 14 -h1 2 -h2 2 -hl 30 -hc 30 -hm 2 -hs 4 -ht 6 -mm 128 -zoh 2 -z1 0.95 -pc 1 -sb1 0 -sp 100 -scorp 0.5 -is 0.0 -ir 0.0 -ii 0.01 -v 2 -he 100.0 -tez 1 -zcc 2 -cp 0 -no 8 -nox 30 -tom 0 -tem 0 -i 1,4 -mf 119,120 -mv 121,122,123,124 -d Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -fm C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf -ox "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy.SearchGUI_temp\1A_Nyari_Epic.omx" -nt 4

comet command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Comet\windows\windows_64bit\comet.exe C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf

tide search command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-search --compute-sp F C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\temp\peak_lists\1A_Nyari_Epic.ms2 fasta-index --overwrite T --top-match 10 --precursor-window 10.0 --precursor-window-type ppm --fileroot 1A_Nyari_Epic --exact-p-value F --output-dir crux-output --spectrum-min-mz 0.0 --min-peaks 20 --spectrum-charge all --remove-precursor-peak F --remove-precursor-tolerance 1.5 --print-search-progress 1000 --use-flanking-peaks F --use-neutral-loss-peaks F --mz-bin-width 0.02 --mz-bin-offset 0.0 --concat F --txt-output T --sqt-output F --pepxml-output F --mzid-output F --pin-output F --verbosity 30

java.io.FileNotFoundException: Source 'C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux-output\1A_Nyari_Epic.tide-search.target.txt' does not exist at org.apache.commons.io.FileUtils.moveFile(FileUtils.java:1805) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2147) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

makeblastdb command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\makeblastdb\windows\makeblastdb -in Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -dbtype prot

tide index command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-index F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta fasta-index --overwrite T --mods-spec M+15.994915,C+57.021464 --nterm-peptide-mods-spec 1E-18.010565,1Q-17.026549,1C-17.026549,1X+42.010565 --decoy-format none --missed-cleavages 2 --output-dir crux-output --peptide-list F --verbosity 30 --min-length 6 --max-length 30 --min-mass 200.0 --max-mass 7200.0 --monoisotopic-precursor T --clip-nterm-methionine F --enzyme trypsin --digestion full-digest

xtandem command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\tandem C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\XTandem\windows\windows_64bit\input_searchGUI.xml

myrimatch command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MyriMatch\windows\windows_64bit\myrimatch -cpus 4 -ProteinDatabase "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -OutputFormat mzIdentML -workdir "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\one.SearchGUI_temp" -OutputSuffix .myrimatch -DecoyPrefix "" -MinPeptideLength 8 -MaxPeptideLength 30 -MaxResultRank 10 -SpectrumListFilters "" -FragmentMzTolerance "0.5 daltons" -MonoPrecursorMzTolerance "10.0 ppm" -PrecursorMzToleranceRule "mono" -StaticMods "M 15.994915 C 57.021464" -DynamicMods "(E 0 -18.010565 (Q 1 -17.026549 (C 2 -17.026549 ( 3 42.010565" -MaxDynamicMods 2 -StatusUpdateFrequency 10 -NumChargeStates 4+ -TicCutoffPercentage 0.98 -MinPeptideMass 0.0 -MaxPeptideMass 10000.0 -UseSmartPlusThreeModel true -ComputeXCorr false -NumIntensityClasses 3 -ClassSizeMultiplier 2 -NumBatches 50 -MaxPeakCount 300 -MonoisotopeAdjustmentSet [0,1] -FragmentationAutoRule false -FragmentationRule "cid" -CleavageRules "Trypsin" -MinTerminiCleavages 2 -MaxMissedCleavages 2

ms amanda command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\MSAmanda.exe "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS Amanda\windows\settings_SearchGUI.xml" "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\one.SearchGUI_temp\1A_Nyari_Epic.ms-amanda.csv"

ms-gf+ command: "C:\Program Files\Java\jre1.8.0_71\bin\java" -Xms128M -Xmx4096M -jar "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\MSGFPlus.jar" -s "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf" -d "F:\Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta" -o "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\one.SearchGUI_temp\1A_Nyari_Epic.msgf.mzid" -t 10.0ppm -tda 0 -mod "C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\MS-GF+\params\Mods.txt" -minCharge 2 -maxCharge 4 -inst 3 -thread 4 -m 3 -e 1 -ntt 2 -protocol 0 -minLength 8 -maxLength 30 -n 10 -addFeatures 0 -ti "0,1"

omssa command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\OMSSA\windows\omssacl -w -to 0.5 -te 10.0 -teppm -e 0 -zl 2 -zh 4 -zt 3 -ti 1 -tex 1446.94 -cl 0.0 -ch 0.2 -ci 5.0E-4 -w1 27 -w2 14 -h1 2 -h2 2 -hl 30 -hc 30 -hm 2 -hs 4 -ht 6 -mm 128 -zoh 2 -z1 0.95 -pc 1 -sb1 0 -sp 100 -scorp 0.5 -is 0.0 -ir 0.0 -ii 0.01 -v 2 -he 100.0 -tez 1 -zcc 2 -cp 0 -no 8 -nox 30 -tom 0 -tem 0 -i 1,4 -mf 119,120 -mv 121,122,123,124 -d Human_TrypsinProteins9Dec15_concatenated_target_decoy.fasta -fm C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf -ox "C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\one.SearchGUI_temp\1A_Nyari_Epic.omx" -nt 4

comet command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Comet\windows\windows_64bit\comet.exe C:\Users\Nyari Chigorimbo\Documents\Proteomics\InGel Epic\Pilots Easy\1A_Nyari_Epic.mgf

tide search command: C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux tide-search --compute-sp F C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\temp\peak_lists\1A_Nyari_Epic.ms2 fasta-index --overwrite T --top-match 10 --precursor-window 10.0 --precursor-window-type ppm --fileroot 1A_Nyari_Epic --exact-p-value F --output-dir crux-output --spectrum-min-mz 0.0 --min-peaks 20 --spectrum-charge all --remove-precursor-peak F --remove-precursor-tolerance 1.5 --print-search-progress 1000 --use-flanking-peaks F --use-neutral-loss-peaks F --mz-bin-width 0.02 --mz-bin-offset 0.0 --concat F --txt-output T --sqt-output F --pepxml-output F --mzid-output F --pin-output F --verbosity 30

java.io.FileNotFoundException: Source 'C:\Users\Nyari Chigorimbo\Documents\Proteomics Bioinformatics\Day 2 Monday\searching mass spectral data\software\SearchGUI-2.6.5\resources\Tide\windows\windows_64bit\crux-output\1A_Nyari_Epic.tide-search.target.txt' does not exist at org.apache.commons.io.FileUtils.moveFile(FileUtils.java:1805) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:2147) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)

[Nyaradzo]

Apologies, that was the search gui log attached here is the peptide shaker one,

Nyari

From: Marc Vaudel [mailto:notifications@github.com] Sent: 24 February 2016 12:06 PM To: compomics/peptide-shaker Cc: Nyari Chigorimbo Subject: Re: [peptide-shaker] Loading results into PeptideShaker fails. (#138)

Hi Nyari,

It seems like these is a problem when reading your files. Can you send me the log of the tool? It is available under the "Help" > "Bug Report" menu which you can access at the tool startup or in the main interface.

Apologizes for the inconvenience,

Marc

— Reply to this email directly or view it on GitHubhttps://github.com/compomics/peptide-shaker/issues/138#issuecomment-188173453.

Mon Feb 15 09:47:49 CAT 2016: PeptideShaker version 1.7.6. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 163053568. Free memory: 130530640. Java version: 1.8.0_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: 1.8.0_71 os.name: Windows 7 memory: 47.2/163.1 processors available: 4 useCommandThread: false

Mon Feb 22 09:42:37 CAT 2016: PeptideShaker version 1.7.6. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 163053568. Free memory: 130506656. Java version: 1.8.0_73. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_73 os.name: Windows 7 memory: 47.3/163.1 processors available: 4 useCommandThread: false Reindexing: Uniprot_human_proteome_Feb2016_concatenated_target_decoy.fasta. (changes in the file detected) Reindexing: Uniprot_human_proteome_Feb2016_concatenated_target_decoy.fasta. java.io.EOFException: no more data available - expected end tags to close start tag from line 28490 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...ass="318.218798" assumed_charge="1" index="461" retention_time_sec... @28490:318 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1885) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:149) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:686) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at com.compomics.util.io.compression.ZipUtils.unzip(ZipUtils.java:243) at eu.isas.peptideshaker.gui.PeptideShakerGUI$102.run(PeptideShakerGUI.java:5379) java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at com.compomics.util.io.compression.ZipUtils.unzip(ZipUtils.java:243) at eu.isas.peptideshaker.gui.PeptideShakerGUI$102.run(PeptideShakerGUI.java:5379)

Tue Feb 23 11:28:22 CAT 2016: PeptideShaker version 1.7.6. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 97346328. Java version: 1.8.0_73. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_73 os.name: Windows 7 memory: 45.4/163.1 processors available: 4 useCommandThread: false java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at com.compomics.util.io.compression.ZipUtils.unzip(ZipUtils.java:243) at eu.isas.peptideshaker.gui.PeptideShakerGUI$102.run(PeptideShakerGUI.java:5379) java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at com.compomics.util.io.compression.ZipUtils.unzip(ZipUtils.java:243) at eu.isas.peptideshaker.gui.PeptideShakerGUI$102.run(PeptideShakerGUI.java:5379) java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at java.util.zip.ZipFile.(Unknown Source) at com.compomics.util.io.compression.ZipUtils.unzip(ZipUtils.java:243) at eu.isas.peptideshaker.gui.NewDialog.loadZipFile(NewDialog.java:2242) at eu.isas.peptideshaker.gui.NewDialog.loadIdInputFiles(NewDialog.java:2127) at eu.isas.peptideshaker.gui.NewDialog.access$2500(NewDialog.java:63) at eu.isas.peptideshaker.gui.NewDialog$37.run(NewDialog.java:1190) java.io.EOFException: no more data available - expected end tags to close start tag from line 132302 and start tag from line 132298 and start tag from line 132233 and start tag from line 132232 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...rch_score name="deltacnstar" value="0.000"/>\r\n <search_score na... @132302:21 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1885) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:456) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:686) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 404638 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...recursor_neutral_mass="1100.213339" assumed_charge="3" index="7840... @404638:272 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:149) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 441854 and start tag from line 441775 and start tag from line 441774 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...tein="tr|H0YH40_REVERSED|H0YH40_REVERSED_HUMAN" num_tot_proteins="... @441854:165 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:149) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 181567 and start tag from line 181560 and start tag from line 181503 and start tag from line 181502 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n <search_sc... @181568:15 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:456) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 595647 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...5317" end_scan="5317" precursor_neutralmass="371.167894" assumed... @595647:249 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1885) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:149) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 34294 and start tag from line 34291 and start tag from line 34290 and start tag from line 34276 and start tag from line 34275 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ... position="6" mass="160.030649"/>\r\n <mod_aminoacid_mass positi... @34294:32 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1885) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:356) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 87152 and start tag from line 87103 and start tag from line 87102 and start tag from line 3 and start tag from line 2, parser stopped on END_TAG seen ...score" value="13.7"/>\r\n ... @87157:44 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1112) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:456) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 411130 and start tag from line 411148 and start tag from line 411147 and start tag from line 411096 and start tag from line 411095 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...d_peptide="AAGKEVPLPSNPILM[147]AYGSISPSAYVLEIFK">\r\n <mod_amino... @411149:16 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:356) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 129889 and start tag from line 129879 and start tag from line 129815 and start tag from line 129814 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n <search_score... @129890:18 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:456) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 233661 and start tag from line 233658 and start tag from line 233621 and start tag from line 233620 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n <search... @233662:12 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:456) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:186) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.EOFException: no more data available - expected end tags to close start tag from line 337720 and start tag from line 337598 and start tag from line 337597 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...tide="CGQEDSGDGCDDLR" peptide_prev_aa="R" peptide_next_aa="D" prot... @337720:99 at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919) at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928) at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1885) at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740) at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095) at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:149) at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:698) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:688) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:482) at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:438) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) java.io.IOException: The network path was not found at java.io.RandomAccessFile.readBytes(Native Method) at java.io.RandomAccessFile.read(Unknown Source) at uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.fillBuffer(BufferedRandomAccessFile.java:80) at uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.getNextLine(BufferedRandomAccessFile.java:165) at com.compomics.util.experiment.io.massspectrometry.MgfReader.getSpectrum(MgfReader.java:920) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:789) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:728) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:746) at eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection.getBestHit(BestMatchSelection.java:636) at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:672) at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:416) at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:66) at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1459) 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) java.io.IOException: The network path was not found at java.io.RandomAccessFile.readBytes(Native Method) at java.io.RandomAccessFile.read(Unknown Source) at uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.fillBuffer(BufferedRandomAccessFile.java:80) at uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile.getNextLine(BufferedRandomAccessFile.java:165) at com.compomics.util.experiment.io.massspectrometry.MgfReader.getSpectrum(MgfReader.java:920) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:789) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:728) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:746) at eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection.getBestHit(BestMatchSelection.java:636) at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:672) at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:416) at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:66) at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1459) 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) java.lang.IllegalArgumentException: Error while loading spectrum 3B_5ul.471.471. File:"3B_5ul.raw", NativeID:"controllerType=0 controllerNumber=1 scan=471" of file 3B_5ul.mgf. at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:799) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:796) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:728) at com.compomics.util.experiment.massspectrometry.SpectrumFactory.getSpectrum(SpectrumFactory.java:746) at eu.isas.peptideshaker.scoring.psm_scoring.BestMatchSelection.getBestHit(BestMatchSelection.java:636) at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:672) at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:416) at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:66) at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1459) 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)

[mvaudel]

Hi again and thanks for the files,

It seems that you are running into several problems here: the Comet pepXML files seem to be empty, and the tool does not find the mgf files corresponding to the identification results.

Can you make the zip file containing the identification results available to us, and make sure that the mgf files used for the search are available to the tool?

Best regards,

Marc

[Nyaradzo]

Hi, The zip file without the MGF's is 1Gb. do we have another option?

Nyari

[mvaudel]

Hi again,

Can you try to unzip it, and send me one of the pep xml files responsible for the error?

Best regards,

Marc

2016-02-24 13:28 GMT+01:00 Nyaradzo notifications@github.com:

Hi, The zip file without the MGF's is 1Gb. do we have another option?

Nyari

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-188227922 .

[Nyaradzo]

Good Morning,

8E_5ul.comet.pep.zip

[mvaudel]

Hi again and thank you for these files.

8E_5ul.comet.pep.xml is empty and seems to be the problem. Can you send us 8E_5ul.mgf as well?

I will make sure that the tool does not break on empty files in the future. Do you see any reason why Comet did not work on this file? Was there any error message?

Best regards,

Marc

2016-02-25 9:29 GMT+01:00 Nyaradzo notifications@github.com:

Good Morning,

8E_5ul.comet.pep.zip https://github.com/compomics/peptide-shaker/files/146126/8E_5ul.comet.pep.zip

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-188668026 .

[ulrich-eckhard]

Hey Harald and Marc, trying to hijack my thread again! ;-) did you have time to check my dimethyl data? provided them via my google drive account. thanks in advance u

[hbarsnes]

Hi Ulrich,

Yes, we think we've located the problem and are working on a fix. A new version will hopefully be out soon.

Best regards, Harald

[ulrich-eckhard]

cool cool ... thanks already On Mar 1, 2016 10:31 AM, "Harald Barsnes" notifications@github.com wrote:

Hi Ulrich,

Yes, we think we've located the problem and are working on a fix. A new version will hopefully be out soon.

Best regards, Harald

— Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-190843780 .

[ulrich-eckhard]

Hey Harald,

finally found time to play with my duplex dimethyl data with the latest SG release. but as I wanted to have the dm0@K only with dm0@Nter and not with dm6@Nter, I hijacked SG as you suggested (https://github.com/compomics/searchgui/issues/72).

but now I can't load the X! Tandem results into PeptideShaker. The file looks good I think. but maybe you spot something obvious.

i will upload the data to my google drive and send you a link. will also put my parameter file there, so that you can see what I did.

guess you will figure it out quickly, all the best u

[hbarsnes]

i will upload the data to my google drive and send you a link. will also put my parameter file there, so that you can see what I did.

I'm still waiting for that link right..?

[ulrich-eckhard]

seems you are! sorry for that! :-)

On Fri, Mar 18, 2016 at 10:01 AM, Harald Barsnes notifications@github.com wrote:

i will upload the data to my google drive and send you a link. will also put my parameter file there, so that you can see what I did.

I'm still waiting for that link right..?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-198454786

[hbarsnes]

Hi Ulrich,

The new PeptideShaker version is finally out. It should fix the problem with the "Dimethylation of peptide N-term 2H(4)" and "Dimethylation of peptide N-term" modifications.

Best regards, Harald

[ulrich-eckhard]

should find time over the weekend to give it a shot.

fingers crossed!

On Fri, Apr 1, 2016 at 6:35 AM, Harald Barsnes notifications@github.com wrote:

Hi Ulrich,

The new PeptideShaker version is finally out. It should fix the problem with the "Dimethylation of peptide N-term 2H(4)" and "Dimethylation of peptide N-term" modifications.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/compomics/peptide-shaker/issues/138#issuecomment-204397993

[hbarsnes]

(Issue assumed fixed. If this is not the case, please let us know and we'll reopen the issue.)