Running Bismark for sample CF05-CM05-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:	1941
Mapping efficiency:	19.4%

Sequence pairs with no alignments under any condition:	7256
Sequence pairs did not map uniquely:	803
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:	496	((converted) top strand)
GA/CT/CT:	448	(complementary to (converted) top strand)
GA/CT/GA:	489	(complementary to (converted) bottom strand)
CT/GA/GA:	508	((converted) bottom strand)

Sample CF05-CM05-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF05-CM05-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:	2528
Mapping efficiency:	25.3%

Sequence pairs with no alignments under any condition:	6478
Sequence pairs did not map uniquely:	994
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:	646	((converted) top strand)
GA/CT/CT:	585	(complementary to (converted) top strand)
GA/CT/GA:	630	(complementary to (converted) bottom strand)
CT/GA/GA:	667	((converted) bottom strand)

Sample CF05-CM05-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF05-CM05-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:	3083
Mapping efficiency:	30.8%

Sequence pairs with no alignments under any condition:	5792
Sequence pairs did not map uniquely:	1125
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:	793	((converted) top strand)
GA/CT/CT:	702	(complementary to (converted) top strand)
GA/CT/GA:	765	(complementary to (converted) bottom strand)
CT/GA/GA:	823	((converted) bottom strand)

Sample CF05-CM05-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF05-CM05-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:	3654
Mapping efficiency:	36.5%

Sequence pairs with no alignments under any condition:	5098
Sequence pairs did not map uniquely:	1248
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:	925	((converted) top strand)
GA/CT/CT:	857	(complementary to (converted) top strand)
GA/CT/GA:	903	(complementary to (converted) bottom strand)
CT/GA/GA:	969	((converted) bottom strand)

Sample CF05-CM05-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF05-CM05-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:	2566
Mapping efficiency:	25.7%

Sequence pairs with no alignments under any condition:	6417
Sequence pairs did not map uniquely:	1017
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:	660	((converted) top strand)
GA/CT/CT:	593	(complementary to (converted) top strand)
GA/CT/GA:	639	(complementary to (converted) bottom strand)
CT/GA/GA:	674	((converted) bottom strand)

Sample CF05-CM05-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF05-CM05-Zygote completed.