the error when dedup the sam when use the bismak

[Jiangjiangzhang6]

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

[FelixKrueger]

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?