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The end-of-file marker seems to be absent from your BAM file. As the error text suggests this could be because the input file is truncated (did the Bismark mapping complete alright, is the mapping report complete?). Or, is there a chance the file is not in BAM format? Can you run samtools view -H clean_..._bismark_hisat2_pe.bam to see the header?
bismark
the map command : /bismark --genome_folder ../01.hap1 --hisat2 --non_directional -1 ../clean_ZHM1H.R1.fastq.gz -2 ../clean_ZHM1H.R2.fastq.gz -p 5 -L 30 -N 1 -o hap1 #--output_dir ./ --bam hap1_bismark_hisat2_pe.bam
my friends, what's wrong with it, hope your reply
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