what's wrong with that ref
panxiaoguang opened this issue · 1 comments
panxiaoguang commented
INFO Tue Feb 26 11:47:24 CST 2019 Processing chromosome chunk: chrM_1_16571
INFO Tue Feb 26 11:47:24 CST 2019 Processing chromosome chunk: chr1_1_25000000
INFO Tue Feb 26 11:47:24 CST 2019 Processing chromosome chunk: chr1_25000001_50000000
INFO Tue Feb 26 11:47:24 CST 2019 Processing chromosome chunk: chr1_50000001_75000000
java.lang.IllegalArgumentException: Invalid reference index -1
mozack commented
Please confirm that the contigs in your BAM header match the contigs in your reference.