Cant find BAM input file or BAM index file

[zhutao1009]

when I run the step 2 of Retroseq, the software tell me: Cant find BAM input file or BAM index file here is my whole command: step 1: retroseq.pl -discover -bam MD1_INDEL_realigned.bam -output MD1_candidates.tab -eref eref.tab -align #no error message step2: retroseq.pl -call -bam MD1_INDEL_realigned.bam -input MD1_candidates.tab -ref PK_ref.fa -output Retroswq_MD1.vcf here is the error message: RetroSeq: A tool for discovery of transposable elements from short read alignments

Version: 1.5 Author: Thomas Keane ([email protected])

Cant find BAM input file or BAM index file: MD1_INDEL_realigned.bam ############## By the way, I'm using the samtools version: 0.1.19