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Old 10-29-2012, 08:27 AM   #1
moritzsch
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Location: Germany

Join Date: May 2012
Posts: 2
Default Varscan exception error

Hi,

I received the following error running Varscan.
I have run the program with the same command before without any problems:

Min coverage: 8x for Normal, 6x for Tumor
Min reads2: 2
Min strands2: 1
Min var freq: 0.2
Min freq for hom: 0.75
Normal purity: 1.0
Tumor purity: 0.6
Min avg qual: 10
P-value thresh: 0.99
Somatic p-value: 0.05
Exception in thread "main" java.lang.NumberFormatException: For input string: ":###AEHDAIJ#JE(DDG4EE#EDJEEEDJ>EIFGHFGJJJI)>JHIJHFIIGC#IDI=0GH?JG#G*FJFF#.IJFFICJGCIIEEIC#DJDD##DHDD#@DCCDC@"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:492)
at java.lang.Integer.parseInt(Integer.java:527)
at net.sf.varscan.Somatic.<init>(Somatic.java:898)
at net.sf.varscan.VarScan.somatic(VarScan.java:282)
at net.sf.varscan.VarScan.main(VarScan.java:188)

any help?

Thanks
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Old 11-08-2012, 07:42 AM   #2
dkoboldt
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Default

This is a parsing error, usually encountered when VarScan is given an input file that's not the expected format. Can you provide your full command, as well as an excerpt from each of your input file(s)?
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Old 11-08-2012, 08:09 AM   #3
moritzsch
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Location: Germany

Join Date: May 2012
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thanks, in the meantime I solved it
the pileup did not look properly and position and reference base were missing.

chr14..,..,,..,....,,,,..,,....,..,..,*,.,.C.,.,,,.,,.^X,^Z.^-. :###AEHDAIJ#JE(DDG4EE#EDJEEEDJ>EIFGHFGJJJI)>JHIJHFIIGC#IDI=0GH?JG#G*FJFF#.IJFFICJGCIIEEIC#DJDD##DHDD#@DCCDC@ Z>]>E]]E>2>>]]]>>>]]>>]]]]]]]]0]]]>]2]]]]]>>]]]]]]]>]]>]]>WWWWWWU>XUXXXX>VXX+XXXXXVXXXXXX>ZZZZ>>ZZZZWZZZZXZ-
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