methylpy has took long time.

[Biomamba]

Dear author:
Thank you for develop such a useful tools for WGBS. I have run a methylpy pipeline for one month at least. How ever, my output sam files are still renewed. My log is displayed below. Can you tell me if my pipeline is finished? Why my alignment rate was so limited? Thank you!
Begin splitting reads for libA
Wed Jan 18 02:03:30 2023

Begin trimming reads for libA
Wed Jan 18 08:52:46 2023

Begin converting reads for libA
Wed Jan 18 13:51:28 2023

Begin Running Bowtie2 for libA
Wed Jan 18 21:54:19 2023

253212453 reads; of these:
253212453 (100.00%) were paired; of these:
181751703 (71.78%) aligned concordantly 0 times
44514905 (17.58%) aligned concordantly exactly 1 time
26945845 (10.64%) aligned concordantly >1 times
28.22% overall alignment rate
Processing forward strand hits
Tue Jan 31 16:52:22 2023

[yupenghe]

This job takes unusually long and I would recommend to kill it if it is still running.

What was the command you were using? Can you take a subset of R1/R2 data and try running methylpy on it with and without --pbat option to check the mapping rate?

[Biomamba]

Thank you for your reply. I will give the test data a try. However, I don't set the pbat option. Is it a default option?
Following is my code:
methylpy paired-end-pipeline
--read1-files 02.clip.reads/${sample}.clip.1.fq.gz
--read2-files 02.clip.reads/${sample}.clip.2.fq.gz
--sample ${sample}
--forward-ref /home/biomamba/biosoft/library.file/bowtie4wgbs/GRCm39_f
--reverse-ref /home/biomamba/biosoft/library.file/bowtie4wgbs/GRCm39_r
--ref-fasta /home/biomamba/biosoft/library.file/GCF_000001635.27_GRCm39_genomic.fna
--num-procs 8
--remove-clonal True
--path-to-output 03.meth