Running Bismark for sample EF07-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:	840
Mapping efficiency:	8.4%

Sequence pairs with no alignments under any condition:	8688
Sequence pairs did not map uniquely:	472
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:	242	((converted) top strand)
GA/CT/CT:	187	(complementary to (converted) top strand)
GA/CT/GA:	176	(complementary to (converted) bottom strand)
CT/GA/GA:	235	((converted) bottom strand)

Sample EF07-EM01-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF07-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:	1084
Mapping efficiency:	10.8%

Sequence pairs with no alignments under any condition:	8357
Sequence pairs did not map uniquely:	559
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:	328	((converted) top strand)
GA/CT/CT:	224	(complementary to (converted) top strand)
GA/CT/GA:	224	(complementary to (converted) bottom strand)
CT/GA/GA:	308	((converted) bottom strand)

Sample EF07-EM01-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF07-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:	1314
Mapping efficiency:	13.1%

Sequence pairs with no alignments under any condition:	8069
Sequence pairs did not map uniquely:	617
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:	403	((converted) top strand)
GA/CT/CT:	265	(complementary to (converted) top strand)
GA/CT/GA:	263	(complementary to (converted) bottom strand)
CT/GA/GA:	383	((converted) bottom strand)

Sample EF07-EM01-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF07-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:	1650
Mapping efficiency:	16.5%

Sequence pairs with no alignments under any condition:	7679
Sequence pairs did not map uniquely:	671
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:	483	((converted) top strand)
GA/CT/CT:	343	(complementary to (converted) top strand)
GA/CT/GA:	339	(complementary to (converted) bottom strand)
CT/GA/GA:	485	((converted) bottom strand)

Sample EF07-EM01-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF07-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:	1115
Mapping efficiency:	11.2%

Sequence pairs with no alignments under any condition:	8326
Sequence pairs did not map uniquely:	559
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:	341	((converted) top strand)
GA/CT/CT:	226	(complementary to (converted) top strand)
GA/CT/GA:	227	(complementary to (converted) bottom strand)
CT/GA/GA:	321	((converted) bottom strand)

Sample EF07-EM01-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample EF07-EM01-Zygote completed.