Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth3.fastp-trim.202003064031_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth3.fastp-trim.202003064031_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:	263
Mapping efficiency:	0.0% 
Sequence pairs with no alignments under any condition:	9999737
Sequence pairs did not map uniquely:	0
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	62	((converted) top strand)
GA/CT/CT:	98	(complementary to (converted) top strand)
GA/CT/GA:	56	(complementary to (converted) bottom strand)
CT/GA/GA:	44	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	13928

Total methylated C's in CpG context:	602
Total methylated C's in CHG context:	708
Total methylated C's in CHH context:	904
Total methylated C's in Unknown context:	16

Total unmethylated C's in CpG context:	3226
Total unmethylated C's in CHG context:	3598
Total unmethylated C's in CHH context:	4890
Total unmethylated C's in Unknown context:	20

C methylated in CpG context:	15.7%
C methylated in CHG context:	16.4%
C methylated in CHH context:	15.6%
C methylated in unknown context (CN or CHN):	44.4%


Bismark completed in 0d 0h 7m 37s