Running Bismark for sample CF06-CM01-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:	1677
Mapping efficiency:	16.8%

Sequence pairs with no alignments under any condition:	7569
Sequence pairs did not map uniquely:	754
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:	438	((converted) top strand)
GA/CT/CT:	405	(complementary to (converted) top strand)
GA/CT/GA:	368	(complementary to (converted) bottom strand)
CT/GA/GA:	466	((converted) bottom strand)

Sample CF06-CM01-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF06-CM01-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:	2354
Mapping efficiency:	23.5%

Sequence pairs with no alignments under any condition:	6679
Sequence pairs did not map uniquely:	967
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:	632	((converted) top strand)
GA/CT/CT:	553	(complementary to (converted) top strand)
GA/CT/GA:	523	(complementary to (converted) bottom strand)
CT/GA/GA:	646	((converted) bottom strand)

Sample CF06-CM01-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF06-CM01-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:	2991
Mapping efficiency:	29.9%

Sequence pairs with no alignments under any condition:	5918
Sequence pairs did not map uniquely:	1091
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:	807	((converted) top strand)
GA/CT/CT:	701	(complementary to (converted) top strand)
GA/CT/GA:	681	(complementary to (converted) bottom strand)
CT/GA/GA:	802	((converted) bottom strand)

Sample CF06-CM01-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF06-CM01-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:	3644
Mapping efficiency:	36.4%

Sequence pairs with no alignments under any condition:	5109
Sequence pairs did not map uniquely:	1247
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:	986	((converted) top strand)
GA/CT/CT:	856	(complementary to (converted) top strand)
GA/CT/GA:	838	(complementary to (converted) bottom strand)
CT/GA/GA:	964	((converted) bottom strand)

Sample CF06-CM01-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF06-CM01-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:	2398
Mapping efficiency:	24.0%

Sequence pairs with no alignments under any condition:	6634
Sequence pairs did not map uniquely:	968
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:	644	((converted) top strand)
GA/CT/CT:	561	(complementary to (converted) top strand)
GA/CT/GA:	536	(complementary to (converted) bottom strand)
CT/GA/GA:	657	((converted) bottom strand)

Sample CF06-CM01-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF06-CM01-Zygote completed.