Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth9.fastp-trim.202003062409_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth9.fastp-trim.202003062409_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/lambda/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Option '--non_directional' specified: alignments to all strands were being performed (OT, OB, CTOT, CTOB)

Final Alignment report
======================
Sequence pairs analysed in total:	10000000
Number of paired-end alignments with a unique best hit:	309
Mapping efficiency:	0.0% 
Sequence pairs with no alignments under any condition:	9999668
Sequence pairs did not map uniquely:	23
Sequence pairs which were discarded because genomic sequence could not be extracted:	0

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	55	((converted) top strand)
GA/CT/CT:	74	(complementary to (converted) top strand)
GA/CT/GA:	106	(complementary to (converted) bottom strand)
CT/GA/GA:	74	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	12324

Total methylated C's in CpG context:	465
Total methylated C's in CHG context:	632
Total methylated C's in CHH context:	913
Total methylated C's in Unknown context:	6

Total unmethylated C's in CpG context:	2583
Total unmethylated C's in CHG context:	2788
Total unmethylated C's in CHH context:	4943
Total unmethylated C's in Unknown context:	28

C methylated in CpG context:	15.3%
C methylated in CHG context:	18.5%
C methylated in CHH context:	15.6%
C methylated in unknown context (CN or CHN):	17.6%


Bismark completed in 0d 0h 7m 13s