abra2 error java.lang.NumberFormatException

Question

[chiyong4783]

Hello, I have constructed a graph-based pan-genome using MC, and then I used VG to align short-read data to the pan-genome. When I used abra2, the following error occurred. What could be the reason for this??

Answer 1

[phage1]

inputs need to be sorted and indexed. can you confirm you are doing this?

samtools sort input.bam -o sorted.bam
samtools index sorted.bam

or some such should result in a .bai index file

[chiyong4783]

I encountered an issue while replacing the BAM file header. Thank you for your comment.