Running Bismark for sample CF08-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:	1389
Mapping efficiency:	13.9%

Sequence pairs with no alignments under any condition:	7991
Sequence pairs did not map uniquely:	620
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:	396	((converted) top strand)
GA/CT/CT:	328	(complementary to (converted) top strand)
GA/CT/GA:	257	(complementary to (converted) bottom strand)
CT/GA/GA:	408	((converted) bottom strand)

Sample CF08-CM03-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF08-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:	1885
Mapping efficiency:	18.9%

Sequence pairs with no alignments under any condition:	7344
Sequence pairs did not map uniquely:	771
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:	561	((converted) top strand)
GA/CT/CT:	429	(complementary to (converted) top strand)
GA/CT/GA:	364	(complementary to (converted) bottom strand)
CT/GA/GA:	531	((converted) bottom strand)

Sample CF08-CM03-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF08-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:	2356
Mapping efficiency:	23.6%

Sequence pairs with no alignments under any condition:	6770
Sequence pairs did not map uniquely:	874
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:	684	((converted) top strand)
GA/CT/CT:	546	(complementary to (converted) top strand)
GA/CT/GA:	473	(complementary to (converted) bottom strand)
CT/GA/GA:	653	((converted) bottom strand)

Sample CF08-CM03-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF08-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:	2857
Mapping efficiency:	28.6%

Sequence pairs with no alignments under any condition:	6163
Sequence pairs did not map uniquely:	980
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:	803	((converted) top strand)
GA/CT/CT:	674	(complementary to (converted) top strand)
GA/CT/GA:	596	(complementary to (converted) bottom strand)
CT/GA/GA:	784	((converted) bottom strand)

Sample CF08-CM03-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF08-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:	1922
Mapping efficiency:	19.2%

Sequence pairs with no alignments under any condition:	7302
Sequence pairs did not map uniquely:	776
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:	575	((converted) top strand)
GA/CT/CT:	433	(complementary to (converted) top strand)
GA/CT/GA:	372	(complementary to (converted) bottom strand)
CT/GA/GA:	542	((converted) bottom strand)

Sample CF08-CM03-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF08-CM03-Zygote completed.