2020-12-09 17:10:31,376 [main] INFO - Aligining reads to exon sequences for GSM4481414
2020-12-09 17:10:31,380 [main] WARN - Bowtie has already been run for C:\Users\GYD\DataRepository\SRRData\GSE148801\SRR11557592.fastq
**2020-12-09 17:10:31,471 [main] ERROR - Error parsing Bowtie output file**
java.lang.StringIndexOutOfBoundsException: String index out of range: -1
	at java.lang.String.substring(String.java:1967)
	at splicetool.analyze.align.BowtieResults.sameRead(BowtieResults.java:459)
	at splicetool.analyze.align.BowtieResults.handleDegenRead(BowtieResults.java:179)
	at splicetool.analyze.align.BowtieResults.getNext(BowtieResults.java:135)
	at splicetool.analyze.ImportReads.alignReads(ImportReads.java:182)
	at splicetool.analyze.ImportReads.main(ImportReads.java:627)
2020-12-09 17:10:31,473 [main] ERROR -   Line: SRR11557592.8045 D90VQ5P1:154:H
2020-12-09 17:10:31,473 [main] INFO - Completed: Aligining reads to exon sequences.
2020-12-09 17:10:35,147 [main] ERROR - Error allocating degenerate reads. 
java.lang.ArrayIndexOutOfBoundsException: 1
	at splicetool.analyze.ImportReads.allocateDegenReads(ImportReads.java:315)
	at splicetool.analyze.ImportReads.main(ImportReads.java:639)