Running Bismark for sample CF04-CM04-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:	1942
Mapping efficiency:	19.4%

Sequence pairs with no alignments under any condition:	7231
Sequence pairs did not map uniquely:	827
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:	534	((converted) top strand)
GA/CT/CT:	382	(complementary to (converted) top strand)
GA/CT/GA:	451	(complementary to (converted) bottom strand)
CT/GA/GA:	575	((converted) bottom strand)

Sample CF04-CM04-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF04-CM04-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:	2514
Mapping efficiency:	25.1%

Sequence pairs with no alignments under any condition:	6495
Sequence pairs did not map uniquely:	991
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:	699	((converted) top strand)
GA/CT/CT:	501	(complementary to (converted) top strand)
GA/CT/GA:	572	(complementary to (converted) bottom strand)
CT/GA/GA:	742	((converted) bottom strand)

Sample CF04-CM04-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF04-CM04-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:	3064
Mapping efficiency:	30.6%

Sequence pairs with no alignments under any condition:	5823
Sequence pairs did not map uniquely:	1113
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:	855	((converted) top strand)
GA/CT/CT:	604	(complementary to (converted) top strand)
GA/CT/GA:	699	(complementary to (converted) bottom strand)
CT/GA/GA:	906	((converted) bottom strand)

Sample CF04-CM04-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF04-CM04-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:	3585
Mapping efficiency:	35.9%

Sequence pairs with no alignments under any condition:	5167
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:	995	((converted) top strand)
GA/CT/CT:	739	(complementary to (converted) top strand)
GA/CT/GA:	809	(complementary to (converted) bottom strand)
CT/GA/GA:	1042	((converted) bottom strand)

Sample CF04-CM04-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF04-CM04-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:	2562
Mapping efficiency:	25.6%

Sequence pairs with no alignments under any condition:	6442
Sequence pairs did not map uniquely:	996
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:	712	((converted) top strand)
GA/CT/CT:	509	(complementary to (converted) top strand)
GA/CT/GA:	582	(complementary to (converted) bottom strand)
CT/GA/GA:	759	((converted) bottom strand)

Sample CF04-CM04-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF04-CM04-Zygote completed.