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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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NumberFormatException in varscan somatic #55

Open Jasondai9 opened 3 years ago

Jasondai9 commented 3 years ago

Hello,

I am using Varscan somatic 2.4.4 to call variants with this command and got an error.

This is the command: varscan somatic /path/to/mpileup /path/to/output --mpileup 1 --output-vcf --tumor-purity 1

This is the error message

[mpileup] 2 samples in 2 input files
Input Parameter Threw Exception: For input string: "true"
java.lang.NumberFormatException: For input string: "true"
at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
at java.lang.Double.parseDouble(Double.java:538)
at net.sf.varscan.Somatic.<init>(Somatic.java:171)
at net.sf.varscan.VarScan.somatic(VarScan.java:277)
at net.sf.varscan.VarScan.main(VarScan.java:199)
Window size: 10
Window SNPs: 3
Indel margin: 3
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
Input stream not ready, waiting for 5 seconds...
ERROR: Gave up waiting after 500 seconds...
Yuzheyuzhe commented 2 years ago

Hello, I got the same question and do not know the reason. Do you solve this problem? If possible, could you please share the solution, thank you very much!