{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/138","repository_url":"https://api.github.com/repos/compomics/peptide-shaker","labels_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/138/labels{/name}","comments_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/138/comments","events_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/138/events","html_url":"https://github.com/compomics/peptide-shaker/issues/138","id":133318973,"number":138,"title":"Loading results into PeptideShaker fails.","user":{"login":"ulriche","id":13509447,"avatar_url":"https://avatars.githubusercontent.com/u/13509447?v=3","gravatar_id":"","url":"https://api.github.com/users/ulriche","html_url":"https://github.com/ulriche","followers_url":"https://api.github.com/users/ulriche/followers","following_url":"https://api.github.com/users/ulriche/following{/other_user}","gists_url":"https://api.github.com/users/ulriche/gists{/gist_id}","starred_url":"https://api.github.com/users/ulriche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ulriche/subscriptions","organizations_url":"https://api.github.com/users/ulriche/orgs","repos_url":"https://api.github.com/users/ulriche/repos","events_url":"https://api.github.com/users/ulriche/events{/privacy}","received_events_url":"https://api.github.com/users/ulriche/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/compomics/peptide-shaker/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"mvaudel","id":11632644,"avatar_url":"https://avatars.githubusercontent.com/u/11632644?v=3","gravatar_id":"","url":"https://api.github.com/users/mvaudel","html_url":"https://github.com/mvaudel","followers_url":"https://api.github.com/users/mvaudel/followers","following_url":"https://api.github.com/users/mvaudel/following{/other_user}","gists_url":"https://api.github.com/users/mvaudel/gists{/gist_id}","starred_url":"https://api.github.com/users/mvaudel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mvaudel/subscriptions","organizations_url":"https://api.github.com/users/mvaudel/orgs","repos_url":"https://api.github.com/users/mvaudel/repos","events_url":"https://api.github.com/users/mvaudel/events{/privacy}","received_events_url":"https://api.github.com/users/mvaudel/received_events","type":"User","site_admin":false},"milestone":null,"comments":0,"created_at":"2016-02-12T19:08:22Z","updated_at":"2016-02-12T22:41:40Z","closed_at":null,"body":"Hey Marc and Harald,\r\n\r\ni 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.\r\n\r\ncan you have a quick look into that, or have a quick idea what is going wrong?\r\ni 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.\r\n\r\nthanks already,\r\nu\r\n\r\n\r\nPeptide Shaker Report\r\n===\r\n\r\nFri Feb 12 10:58:29 PST 2016        Importing sequences from 1512_UP_human_CanIsoCon_concatenated_target_decoy.fasta.\r\nFri Feb 12 10:58:32 PST 2016        FASTA file import completed.\r\nFri Feb 12 10:58:32 PST 2016        Importing gene mappings.\r\nFri Feb 12 10:58:34 PST 2016        Establishing local database connection.\r\nFri Feb 12 10:58:35 PST 2016        Reading identification files.\r\nFri Feb 12 10:58:35 PST 2016        Parsing MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.comet.pep.xml.\r\nFri Feb 12 10:58:38 PST 2016        Loading spectra for MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.comet.pep.xml.\r\nFri Feb 12 10:58:38 PST 2016        Importing MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.mgf\r\nFri Feb 12 10:58:38 PST 2016        MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.mgf imported.\r\nFri Feb 12 10:58:39 PST 2016        Collecting peptides to map.\r\nFri Feb 12 10:58:40 PST 2016        Mapping peptides to proteins.\r\nFri Feb 12 11:02:45 PST 2016        Importing PSMs from MegaGum_preT_UE-QC1B_F12_01_4545_uncalib_4.3.110.comet.pep.xml\r\nFri Feb 12 11:02:45 PST 2016        An error occurred: null\r\nFri Feb 12 11:02:45 PST 2016        Please contact the developers (https://github.com/compomics/peptide-shaker/issues).\r\n\r\nFri Feb 12 11:02:45 PST 2016        Importing Data Canceled\r\n\r\nPeptide Shaker Log\r\n===\r\nFri Feb 12 08:58:38 PST 2016: PeptideShaker version 1.7.5.\r\nMemory given to the Java virtual machine: 13981188096.\r\nTotal amount of memory in the Java virtual machine: 163053568.\r\nFree memory: 131627536.\r\nJava version: 1.8.0_71.\r\n1714 script command tokens\r\n(C) 2009 Jmol Development\r\nJmol Version: 12.0.43  2011-05-03 14:21\r\njava.vendor: Oracle Corporation\r\njava.version: 1.8.0_71\r\nos.name: Windows 7\r\nmemory: 46.8/163.1\r\nprocessors available: 8\r\nuseCommandThread: false\r\njava.lang.NullPointerException\r\n\tat com.compomics.util.experiment.biology.Peptide.getPotentialModificationSites(Peptide.java:898)\r\n\tat com.compomics.util.experiment.biology.PTMFactory.getExpectedPTMs(PTMFactory.java:404)\r\n\tat eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:580)\r\n\tat eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:416)\r\n\tat eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:66)\r\n\tat eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1459)\r\n\tat java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)\r\n\tat java.util.concurrent.FutureTask.run(Unknown Source)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)\r\n\tat java.lang.Thread.run(Unknown Source)\r\n"},"comment":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/comments/183515044","html_url":"https://github.com/compomics/peptide-shaker/issues/138#issuecomment-183515044","issue_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/138","id":183515044,"user":{"login":"hbarsnes","id":13151214,"avatar_url":"https://avatars.githubusercontent.com/u/13151214?v=3","gravatar_id":"","url":"https://api.github.com/users/hbarsnes","html_url":"https://github.com/hbarsnes","followers_url":"https://api.github.com/users/hbarsnes/followers","following_url":"https://api.github.com/users/hbarsnes/following{/other_user}","gists_url":"https://api.github.com/users/hbarsnes/gists{/gist_id}","starred_url":"https://api.github.com/users/hbarsnes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbarsnes/subscriptions","organizations_url":"https://api.github.com/users/hbarsnes/orgs","repos_url":"https://api.github.com/users/hbarsnes/repos","events_url":"https://api.github.com/users/hbarsnes/events{/privacy}","received_events_url":"https://api.github.com/users/hbarsnes/received_events","type":"User","site_admin":false},"created_at":"2016-02-12T22:41:40Z","updated_at":"2016-02-12T22:41:40Z","body":"Hi Ulrich,\r\n\r\nThanks 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. ;)\r\n\r\nBest regards,\r\nHarald"}}