Bismark report for: /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth5.fastp-trim.202003051832_R1_001.fastq.gz and /gscratch/scrubbed/samwhite/outputs/20200305_methcompare_fastp_trimming/Meth5.fastp-trim.202003051832_R2_001.fastq.gz (version: v0.21.0)
Bismark was run with Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/froger/Pact_Genome/ with the specified options: -q --score-min L,0,-0.2 -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:	10000
Number of paired-end alignments with a unique best hit:	4679
Mapping efficiency:	46.8% 
Sequence pairs with no alignments under any condition:	4465
Sequence pairs did not map uniquely:	856
Sequence pairs which were discarded because genomic sequence could not be extracted:	9

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	1155	((converted) top strand)
GA/CT/CT:	1206	(complementary to (converted) top strand)
GA/CT/GA:	1246	(complementary to (converted) bottom strand)
CT/GA/GA:	1063	((converted) bottom strand)

Final Cytosine Methylation Report
=================================
Total number of C's analysed:	207199

Total methylated C's in CpG context:	5612
Total methylated C's in CHG context:	340
Total methylated C's in CHH context:	645
Total methylated C's in Unknown context:	2

Total unmethylated C's in CpG context:	40228
Total unmethylated C's in CHG context:	40618
Total unmethylated C's in CHH context:	119756
Total unmethylated C's in Unknown context:	77

C methylated in CpG context:	12.2%
C methylated in CHG context:	0.8%
C methylated in CHH context:	0.5%
C methylated in unknown context (CN or CHN):	2.5%


Bismark completed in 0d 0h 1m 29s