java -Xmx70g -cp socrates-1.13.1-jar-with-dependencies.jar au.edu.wehi.socrates.BAMStratifier ../onestepPGSPGD/20190613/IonXpress_005_rawlib.bam
Stratify BAM file ../onestepPGSPGD/20190613/IonXpress_005_rawlib.bam with option values:
threads = 1
min mapq = 5
min long sc length = 25
min avg soft clip base quality = 5
min aligned percent identity = 95
remove duplicates = true
java.lang.NumberFormatException: For input string: "null"
at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.base/java.lang.Integer.parseInt(Integer.java:652)
at java.base/java.lang.Integer.parseInt(Integer.java:770)
at au.edu.wehi.socrates.util.SAMFileInfo.getLibraryReadLengths(SAMFileInfo.java:104)
at au.edu.wehi.socrates.BAMStratifier.(BAMStratifier.java:121)
at au.edu.wehi.socrates.BAMStratifier.main(BAMStratifier.java:842)
Exception in thread "main" java.lang.NullPointerException
at au.edu.wehi.socrates.BAMStratifier.(BAMStratifier.java:123)
at au.edu.wehi.socrates.BAMStratifier.main(BAMStratifier.java:842)
java -Xmx70g -cp socrates-1.13.1-jar-with-dependencies.jar au.edu.wehi.socrates.BAMStratifier ../onestepPGSPGD/20190613/IonXpress_005_rawlib.bam
Stratify BAM file ../onestepPGSPGD/20190613/IonXpress_005_rawlib.bam with option values:
threads = 1
min mapq = 5
min long sc length = 25
min avg soft clip base quality = 5
min aligned percent identity = 95
remove duplicates = true
java.lang.NumberFormatException: For input string: "null"
at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.base/java.lang.Integer.parseInt(Integer.java:652)
at java.base/java.lang.Integer.parseInt(Integer.java:770)
at au.edu.wehi.socrates.util.SAMFileInfo.getLibraryReadLengths(SAMFileInfo.java:104)
at au.edu.wehi.socrates.BAMStratifier.(BAMStratifier.java:121)
at au.edu.wehi.socrates.BAMStratifier.main(BAMStratifier.java:842)
Exception in thread "main" java.lang.NullPointerException
at au.edu.wehi.socrates.BAMStratifier.(BAMStratifier.java:123)
at au.edu.wehi.socrates.BAMStratifier.main(BAMStratifier.java:842)