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If you do not have a alignment file in the SAM format you may want to start with Introduction to mapping.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[main_samview] fail to read the header from "03_Output/mapping/bowtie/REL606.5.sam".