Running Bismark for sample CF07-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:	914
Mapping efficiency:	9.1%

Sequence pairs with no alignments under any condition:	8683
Sequence pairs did not map uniquely:	403
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:	254	((converted) top strand)
GA/CT/CT:	212	(complementary to (converted) top strand)
GA/CT/GA:	216	(complementary to (converted) bottom strand)
CT/GA/GA:	232	((converted) bottom strand)

Sample CF07-CM02-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF07-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:	1147
Mapping efficiency:	11.5%

Sequence pairs with no alignments under any condition:	8378
Sequence pairs did not map uniquely:	475
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:	326	((converted) top strand)
GA/CT/CT:	256	(complementary to (converted) top strand)
GA/CT/GA:	281	(complementary to (converted) bottom strand)
CT/GA/GA:	284	((converted) bottom strand)

Sample CF07-CM02-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF07-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:	1426
Mapping efficiency:	14.3%

Sequence pairs with no alignments under any condition:	8052
Sequence pairs did not map uniquely:	522
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:	399	((converted) top strand)
GA/CT/CT:	329	(complementary to (converted) top strand)
GA/CT/GA:	338	(complementary to (converted) bottom strand)
CT/GA/GA:	360	((converted) bottom strand)

Sample CF07-CM02-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF07-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:	1809
Mapping efficiency:	18.1%

Sequence pairs with no alignments under any condition:	7572
Sequence pairs did not map uniquely:	619
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:	494	((converted) top strand)
GA/CT/CT:	415	(complementary to (converted) top strand)
GA/CT/GA:	429	(complementary to (converted) bottom strand)
CT/GA/GA:	471	((converted) bottom strand)

Sample CF07-CM02-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF07-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:	1161
Mapping efficiency:	11.6%

Sequence pairs with no alignments under any condition:	8361
Sequence pairs did not map uniquely:	478
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:	329	((converted) top strand)
GA/CT/CT:	260	(complementary to (converted) top strand)
GA/CT/GA:	284	(complementary to (converted) bottom strand)
CT/GA/GA:	288	((converted) bottom strand)

Sample CF07-CM02-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF07-CM02-Zygote completed.