Running Bismark for sample EF02-EM02-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:	1703
Mapping efficiency:	17.0%

Sequence pairs with no alignments under any condition:	7445
Sequence pairs did not map uniquely:	852
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:	495	((converted) top strand)
GA/CT/CT:	369	(complementary to (converted) top strand)
GA/CT/GA:	378	(complementary to (converted) bottom strand)
CT/GA/GA:	461	((converted) bottom strand)

Sample EF02-EM02-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF02-EM02-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:	2365
Mapping efficiency:	23.6%

Sequence pairs with no alignments under any condition:	6558
Sequence pairs did not map uniquely:	1077
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:	681	((converted) top strand)
GA/CT/CT:	542	(complementary to (converted) top strand)
GA/CT/GA:	504	(complementary to (converted) bottom strand)
CT/GA/GA:	638	((converted) bottom strand)

Sample EF02-EM02-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF02-EM02-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:	2968
Mapping efficiency:	29.7%

Sequence pairs with no alignments under any condition:	5753
Sequence pairs did not map uniquely:	1279
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:	847	((converted) top strand)
GA/CT/CT:	664	(complementary to (converted) top strand)
GA/CT/GA:	637	(complementary to (converted) bottom strand)
CT/GA/GA:	820	((converted) bottom strand)

Sample EF02-EM02-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF02-EM02-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:	3718
Mapping efficiency:	37.2%

Sequence pairs with no alignments under any condition:	4790
Sequence pairs did not map uniquely:	1492
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:	1051	((converted) top strand)
GA/CT/CT:	827	(complementary to (converted) top strand)
GA/CT/GA:	822	(complementary to (converted) bottom strand)
CT/GA/GA:	1018	((converted) bottom strand)

Sample EF02-EM02-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF02-EM02-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:	2399
Mapping efficiency:	24.0%

Sequence pairs with no alignments under any condition:	6507
Sequence pairs did not map uniquely:	1094
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:	701	((converted) top strand)
GA/CT/CT:	545	(complementary to (converted) top strand)
GA/CT/GA:	509	(complementary to (converted) bottom strand)
CT/GA/GA:	644	((converted) bottom strand)

Sample EF02-EM02-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample EF02-EM02-Zygote completed.