{"action":"closed","issue":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/197","repository_url":"https://api.github.com/repos/compomics/peptide-shaker","labels_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/197/labels{/name}","comments_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/197/comments","events_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/197/events","html_url":"https://github.com/compomics/peptide-shaker/issues/197","id":170523284,"number":197,"title":"Getting StringIndexOutOfBoundsException with PeptideShakerCLI","user":{"login":"max-l","id":192660,"avatar_url":"https://avatars.githubusercontent.com/u/192660?v=3","gravatar_id":"","url":"https://api.github.com/users/max-l","html_url":"https://github.com/max-l","followers_url":"https://api.github.com/users/max-l/followers","following_url":"https://api.github.com/users/max-l/following{/other_user}","gists_url":"https://api.github.com/users/max-l/gists{/gist_id}","starred_url":"https://api.github.com/users/max-l/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/max-l/subscriptions","organizations_url":"https://api.github.com/users/max-l/orgs","repos_url":"https://api.github.com/users/max-l/repos","events_url":"https://api.github.com/users/max-l/events{/privacy}","received_events_url":"https://api.github.com/users/max-l/received_events","type":"User","site_admin":false},"labels":[{"id":251120700,"url":"https://api.github.com/repos/compomics/peptide-shaker/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"closed","locked":false,"assignee":{"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},"assignees":[{"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}],"milestone":null,"comments":7,"created_at":"2016-08-10T21:28:23Z","updated_at":"2017-01-06T23:54:29Z","closed_at":"2017-01-06T23:54:29Z","body":"Hello, PeptideShakerCLI is crashing with the following stack trace (see below)\n\nI can provide the input file if that is of any help\n\nOut of  5188 runs of peptideshakerCLI, I get 946 such failures\n\n```\nMon Aug 08 22:48:40 EDT 2016 Importing PSMs from j7497.comet.pep.xml\n10% 20% 30% 40% 50% 60% 70% 80% 90%\nMon Aug 08 22:49:22 EDT 2016 336 identified spectra (3.3%) did not present a valid peptide.\nMon Aug 08 22:49:22 EDT 2016 21144 of the best scoring peptides were excluded by the import filters:\nMon Aug 08 22:49:22 EDT 2016     - 37.0% peptide length less than 8 or greater than 30.\nMon Aug 08 22:49:22 EDT 2016     - 62.8% peptide presenting high mass or isotopic deviation.\nMon Aug 08 22:49:22 EDT 2016 Parsing j7497.msgf.mzid.\n10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\nMon Aug 08 22:49:27 EDT 2016 Loading spectra for j7497.msgf.mzid.\n10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\nMon Aug 08 22:49:27 EDT 2016 Collecting peptides to map.\n10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\nMon Aug 08 22:49:28 EDT 2016 Mapping peptides to proteins.\n10% 20% 30% 40% 50% 60% 70% 80% 90% 100%\nMon Aug 08 22:49:28 EDT 2016 Importing PSMs from j7497.msgf.mzid\n10% 20% 30% 40% 50% 60%java.lang.StringIndexOutOfBoundsException: String index out of range: 24\n    at java.lang.String.substring(String.java:1907)\n    at com.compomics.util.experiment.biology.Protein.isNTerm(Protein.java:257)\n    at com.compomics.util.experiment.biology.Peptide.isNterm(Peptide.java:639)\n    at com.compomics.util.experiment.biology.Peptide.getPotentialModificationSites(Peptide.java:911)\n    at com.compomics.util.experiment.biology.PTMFactory.getExpectedPTMs(PTMFactory.java:404)\n    at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:589)\n    at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:422)\n    at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:68)\n    at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1473)\n    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)\n    at java.util.concurrent.FutureTask.run(FutureTask.java:262)\n    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\n    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\n    at java.lang.Thread.run(Thread.java:745)\n\nMon Aug 08 22:49:32 EDT 2016 PeptideShaker Processing Canceled.\n<CompomicsError>PeptideShaker processing canceled. See the PeptideShaker log for details.</CompomicsError>\n\n```\n"}}
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