Running Bismark for sample CF03-CM03-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:	1990
Mapping efficiency:	19.9%

Sequence pairs with no alignments under any condition:	7176
Sequence pairs did not map uniquely:	834
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:	563	((converted) top strand)
GA/CT/CT:	417	(complementary to (converted) top strand)
GA/CT/GA:	470	(complementary to (converted) bottom strand)
CT/GA/GA:	540	((converted) bottom strand)

Sample CF03-CM03-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF03-CM03-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:	2558
Mapping efficiency:	25.6%

Sequence pairs with no alignments under any condition:	6464
Sequence pairs did not map uniquely:	978
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:	697	((converted) top strand)
GA/CT/CT:	545	(complementary to (converted) top strand)
GA/CT/GA:	618	(complementary to (converted) bottom strand)
CT/GA/GA:	698	((converted) bottom strand)

Sample CF03-CM03-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF03-CM03-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:	5836
Sequence pairs did not map uniquely:	1100
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:	842	((converted) top strand)
GA/CT/CT:	655	(complementary to (converted) top strand)
GA/CT/GA:	713	(complementary to (converted) bottom strand)
CT/GA/GA:	854	((converted) bottom strand)

Sample CF03-CM03-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF03-CM03-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:	3586
Mapping efficiency:	35.9%

Sequence pairs with no alignments under any condition:	5173
Sequence pairs did not map uniquely:	1241
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:	984	((converted) top strand)
GA/CT/CT:	790	(complementary to (converted) top strand)
GA/CT/GA:	825	(complementary to (converted) bottom strand)
CT/GA/GA:	987	((converted) bottom strand)

Sample CF03-CM03-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF03-CM03-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:	2594
Mapping efficiency:	25.9%

Sequence pairs with no alignments under any condition:	6419
Sequence pairs did not map uniquely:	987
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:	715	((converted) top strand)
GA/CT/CT:	553	(complementary to (converted) top strand)
GA/CT/GA:	615	(complementary to (converted) bottom strand)
CT/GA/GA:	711	((converted) bottom strand)

Sample CF03-CM03-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF03-CM03-Zygote completed.