Running Bismark for sample EF01-EM01-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:	1565
Mapping efficiency:	15.7%

Sequence pairs with no alignments under any condition:	7763
Sequence pairs did not map uniquely:	672
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:	397	((converted) top strand)
GA/CT/CT:	357	(complementary to (converted) top strand)
GA/CT/GA:	392	(complementary to (converted) bottom strand)
CT/GA/GA:	419	((converted) bottom strand)

Sample EF01-EM01-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF01-EM01-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:	2194
Mapping efficiency:	21.9%

Sequence pairs with no alignments under any condition:	6957
Sequence pairs did not map uniquely:	849
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:	559	((converted) top strand)
GA/CT/CT:	505	(complementary to (converted) top strand)
GA/CT/GA:	555	(complementary to (converted) bottom strand)
CT/GA/GA:	575	((converted) bottom strand)

Sample EF01-EM01-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF01-EM01-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:	2682
Mapping efficiency:	26.8%

Sequence pairs with no alignments under any condition:	6366
Sequence pairs did not map uniquely:	952
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:	631	(complementary to (converted) top strand)
GA/CT/GA:	679	(complementary to (converted) bottom strand)
CT/GA/GA:	728	((converted) bottom strand)

Sample EF01-EM01-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF01-EM01-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:	3277
Mapping efficiency:	32.8%

Sequence pairs with no alignments under any condition:	5637
Sequence pairs did not map uniquely:	1086
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:	792	((converted) top strand)
GA/CT/CT:	800	(complementary to (converted) top strand)
GA/CT/GA:	814	(complementary to (converted) bottom strand)
CT/GA/GA:	871	((converted) bottom strand)

Sample EF01-EM01-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF01-EM01-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:	2228
Mapping efficiency:	22.3%

Sequence pairs with no alignments under any condition:	6918
Sequence pairs did not map uniquely:	854
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:	559	((converted) top strand)
GA/CT/CT:	515	(complementary to (converted) top strand)
GA/CT/GA:	558	(complementary to (converted) bottom strand)
CT/GA/GA:	596	((converted) bottom strand)

Sample EF01-EM01-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample EF01-EM01-Zygote completed.