how to acquire or calculate the mapping efficiency using methylpy?

[InfiniteLaugh]

Hello, as a new learner of methylpy I am curious about how to acquire mapping efficiency, since it seems not shown in the output result in total. I used to use bismark, and the mapping efficiency is about 40-60%, which is quite low when compared with other plant species. I have looked through bowtie2 report but it seems different from this.
Therefore i try to replace it this methylpy.

my code is as follows:
methylpy paired-end-pipeline --read1-files ../samplename_clean.1.fq.gz --read2-files ../samplename_clean.2.fq.gz --sample samplename --forward-ref ../methypy_ref/genome_f --reverse-ref ../methypy_ref/genome_r --ref-fasta ../fasta --num-procs 20 --trim-reads False --compress-output True --remove-clonal True --path-to-picard /direction_to_picard/software/

my result report is as follows:

Begin splitting reads for libA
Mon Feb 13 00:52:04 2023

No trimming applied on reads
Mon Feb 13 01:08:03 2023

Begin converting reads for libA
Mon Feb 13 01:08:03 2023

Begin Running Bowtie2 for libA
Mon Feb 13 01:09:03 2023

109022310 reads; of these:
  109022310 (100.00%) were paired; of these:
    52732411 (48.37%) aligned concordantly 0 times
    30919854 (28.36%) aligned concordantly exactly 1 time
    25370045 (23.27%) aligned concordantly >1 times
51.63% overall alignment rate
Processing forward strand hits
Mon Feb 13 02:53:36 2023

109022310 reads; of these:
  109022310 (100.00%) were paired; of these:
    52872328 (48.50%) aligned concordantly 0 times
    30919684 (28.36%) aligned concordantly exactly 1 time
    25230298 (23.14%) aligned concordantly >1 times
51.50% overall alignment rate
Processing reverse strand hits
Mon Feb 13 04:42:43 2023

Bismark result is as follows:

Final Alignment report
======================
Sequence pairs analysed in total:	109022310
Number of paired-end alignments with a unique best hit:	50998056
Mapping efficiency:	46.8% 
Sequence pairs with no alignments under any condition:	46756311
Sequence pairs did not map uniquely:	11267943
Sequence pairs which were discarded because genomic sequence could not be extracted:	101

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	25516794	((converted) top strand)
GA/CT/CT:	0	(complementary to (converted) top strand)
GA/CT/GA:	0	(complementary to (converted) bottom strand)
CT/GA/GA:	25481161	((converted) bottom strand)

Number of alignments to (merely theoretical) complementary strands being rejected in total:	0

Thank you and looking forward to the anawer.

[yupenghe]

it is in the output file. For example:

There are 93996 total input reads
Mon May  3 22:15:54 2021

There are 88982 uniquely mapping reads, 94.6657304566 percent remaining
Mon May  3 22:15:54 2021

[InfiniteLaugh]

Thank you so much for your answer. May i ask is there any way to output these information to a certain file like Bismark. For I have many sample to analyze, and currently these information were output to one file named nohup.out. Will > sample.name.txt after each line of code works?

[yupenghe]

Yes you can do something like METHYLPY COMMAND >sample_name.out.txt 2> sample_name.err.txt to get the output message and output error for each sample.