yupenghe/methylpy

methylpy single-end-pipeline error

Opened this issue · 2 comments

hengbingao commented

Hi, Yupeng,
when I run methylpy single-end-pipeline --read-files ${i}_1.fastq.gz --sample fetal_cortex --forward-ref $MYGROUP/genome/hg38/methy_hg38_f --reverse-ref $MYGROUP/genome/hg38/methy_hg38_r --ref-fasta genome/hg38.fa --num-procs 20 --bgzip True,
some error were: cutadapt: error: unrecognized arguments: -f and subprocess.CalledProcessError: Command '['rm', 'SRR901379_map_libA_split_trimmed_0', 'SRR901379_map_libA_split_trimmed_1', 'SRR9']' returned non-zero exit status 1.
Begin splitting reads for SRR9.
I wonder how to fix this error, I have install the methylpy in conda. thanks!

yupenghe commented

Hey what is your cutadapt version? Could you try version 1.9?

hengbingao commented

It is 4.6, may I could have a try with version 1.9.
Thank you so much for your advices, Yupeng.