Davieni4yashiro

yes,the chloroplast genome is included in my reference genome. And the idxstats of bam file looks fine. 

hi yupeng, I found that the last line of the problemmatic allc file is shifted, leaving a blank in fields[4]  And when I delete the last line and run...

[pics.zip](https://github.com/yupenghe/methylpy/files/9533156/pics.zip)

yes it is

Hi, the test files are enclosed in the zip file. And for problematic samples, 2 BAM_FILEs were generated by `methylpy paired-end-pipeline`: `no_clonal.bam` and `no_clonal.bam.read2flipped.bam`. I did what you told me...

[chrC.fa.zip](https://github.com/yupenghe/methylpy/files/9539517/chrC.fa.zip) Thanks!

It does help! Thanks so much!