Running Bismark for sample CF02-CM02-Zygote with score_min L,0,-0.4
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	994
Mapping efficiency:	9.9%

Sequence pairs with no alignments under any condition:	8487
Sequence pairs did not map uniquely:	519
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:	320	((converted) top strand)
GA/CT/CT:	173	(complementary to (converted) top strand)
GA/CT/GA:	186	(complementary to (converted) bottom strand)
CT/GA/GA:	315	((converted) bottom strand)

Sample CF02-CM02-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF02-CM02-Zygote with score_min L,0,-0.6
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	1389
Mapping efficiency:	13.9%

Sequence pairs with no alignments under any condition:	7984
Sequence pairs did not map uniquely:	627
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:	445	((converted) top strand)
GA/CT/CT:	242	(complementary to (converted) top strand)
GA/CT/GA:	264	(complementary to (converted) bottom strand)
CT/GA/GA:	438	((converted) bottom strand)

Sample CF02-CM02-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF02-CM02-Zygote with score_min L,0,-0.8
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	1759
Mapping efficiency:	17.6%

Sequence pairs with no alignments under any condition:	7523
Sequence pairs did not map uniquely:	718
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:	557	((converted) top strand)
GA/CT/CT:	305	(complementary to (converted) top strand)
GA/CT/GA:	366	(complementary to (converted) bottom strand)
CT/GA/GA:	531	((converted) bottom strand)

Sample CF02-CM02-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF02-CM02-Zygote with score_min L,0,-1.0
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	2209
Mapping efficiency:	22.1%

Sequence pairs with no alignments under any condition:	6971
Sequence pairs did not map uniquely:	820
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:	658	((converted) top strand)
GA/CT/CT:	426	(complementary to (converted) top strand)
GA/CT/GA:	472	(complementary to (converted) bottom strand)
CT/GA/GA:	653	((converted) bottom strand)

Sample CF02-CM02-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF02-CM02-Zygote with score_min L,-1,-0.6
chr NC_035780.1 (65668440 bp)
chr NC_035781.1 (61752955 bp)
chr NC_035782.1 (77061148 bp)
chr NC_035783.1 (59691872 bp)
chr NC_035784.1 (98698416 bp)
chr NC_035785.1 (51258098 bp)
chr NC_035786.1 (57830854 bp)
chr NC_035787.1 (75944018 bp)
chr NC_035788.1 (104168038 bp)
chr NC_035789.1 (32650045 bp)
chr NC_007175.2 (17244 bp)

Number of paired-end alignments with a unique best hit:	1402
Mapping efficiency:	14.0%

Sequence pairs with no alignments under any condition:	7956
Sequence pairs did not map uniquely:	642
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:	441	((converted) top strand)
GA/CT/CT:	246	(complementary to (converted) top strand)
GA/CT/GA:	266	(complementary to (converted) bottom strand)
CT/GA/GA:	449	((converted) bottom strand)

Sample CF02-CM02-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF02-CM02-Zygote completed.