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niuhuifei / popoolation2

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Error: mpileup2sync #8

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. creating mpileup as per directions in tutorial but using my own sequence data
2. java -Xmx4g -jar ~/popoolation2/mpileup2sync.jar --fastq-type illumina 
--min-qual 20 --input IY_std3L.mpileup --output IY_std3L.sync
3.

What is the expected output? What do you see instead?
SHould get a sync file, but instead I get an error saying: 

Exception in thread "main" java.lang.IllegalArgumentException: An error occured 
during parsing of the mpileup;
Please make sure you are a.) using the correct encoding and b.) using the 
correct mpileup format
    at BatchProcessor.processBatch(BatchProcessor.java:43)
    at Mpileup2SyncFramework.run(Mpileup2SyncFramework.java:55)
    at CommandLineParser.parseArguments(CommandLineParser.java:67)
    at Mpileup2syncMain.main(Mpileup2syncMain.java:17)

What version of the product are you using? On what operating system?

Please provide any additional information below.

Original issue reported on code.google.com by rahulvr...@gmail.com on 11 Oct 2012 at 4:44

GoogleCodeExporter commented 9 years ago 
can you paste a short example of your mpileup file, maybee
- the encoding is sanger
- or something may be wrong with the mpileup file

Original comment by RoKof...@gmail.com on 30 Oct 2012 at 8:11