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Rappsilber-Laboratory / XiSearch

XiSearch
Apache License 2.0
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CSVinFDR fails #53

Open jayieh opened 4 years ago

jayieh commented 4 years ago

Hi,

I am running xiSEARCH 1.7.6.1 in combo with xiFDR-2.1.2 (via GUI on a win server 2012 and java 8.0.2410).

After a successful search, I receive the following error msg:

Sep 09, 2020 5:28:11 PM org.rappsilber.fdr.XiCSVinFDR main INFO: seeting up csv input Sep 09, 2020 5:28:11 PM org.rappsilber.fdr.XiCSVinFDR main INFO: Read datafrom CSV Sep 09, 2020 5:28:11 PM org.rappsilber.fdr.CSVinFDR readCSV SEVERE: Unexecpted exception while parsing line 28 java.text.ParseException: Don't know how to handle different numbers of protein accessions and descriptions Sep 09, 2020 5:28:11 PM rappsilber.ui.LoggingStatus setStatus INFO: Error while running FDR at org.rappsilber.fdr.CSVinFDR.readCSV(CSVinFDR.java:348) at org.rappsilber.fdr.XiCSVinFDR.readCSV(XiCSVinFDR.java:621) at org.rappsilber.fdr.XiCSVinFDR.main(XiCSVinFDR.java:392) at org.rappsilber.fdr.CommandLine.main(CommandLine.java:49)

Sep 09, 2020 5:28:11 PM org.rappsilber.fdr.XiCSVinFDR main SEVERE: Error while reading file: D:\juergen\200827_#20_046_ABR79-88\20200908_Xi1.7.6.1.csv

I also included the first 50 lines of the results csv

Do you have a hint on what the issue might be?

Best

Jürgen

20200908_Xi1.7.6.1__1st_50_lines.txt

andzajan commented 3 years ago

Hi, probably this is already too late to respond, but I did encounter exactly the same issue, solution was to have Uniprot style sequence headers. Foer example:

>sp|P08518|RPB2_nice_protein