HMMRATAC
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Exception in thread "main" java.util.InputMismatchException
Hello,
I run
samtools view -H C1.FINAL.BAM | perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}' > genomeinfo/C1.FINAL.BAM
java -jar ~/HMMRATAC_V1.2.10_exe.jar -b C1.FINAL.BAM -i C1.FINAL.BAM.bai -g genomeinfo/C1.FINAL.BAM
But got this error:
Exception in thread "main" java.util.InputMismatchException
at java.base/java.util.Scanner.throwFor(Scanner.java:939)
at java.base/java.util.Scanner.next(Scanner.java:1594)
at java.base/java.util.Scanner.nextInt(Scanner.java:2258)
at java.base/java.util.Scanner.nextInt(Scanner.java:2212)
at GenomeFileReaders.GenomeFileReader.<init>(GenomeFileReader.java:65)
at HMMR_ATAC.Main_HMMR_Driver.main(Main_HMMR_Driver.java:165)
Can you please let me know how can I fix it?
Thanks a lot.