Running Bismark for sample CF01-CM01-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:	953
Mapping efficiency:	9.5%

Sequence pairs with no alignments under any condition:	8598
Sequence pairs did not map uniquely:	449
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:	289	((converted) top strand)
GA/CT/CT:	214	(complementary to (converted) top strand)
GA/CT/GA:	220	(complementary to (converted) bottom strand)
CT/GA/GA:	230	((converted) bottom strand)

Sample CF01-CM01-Zygote with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF01-CM01-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:	1284
Mapping efficiency:	12.8%

Sequence pairs with no alignments under any condition:	8163
Sequence pairs did not map uniquely:	553
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:	373	((converted) top strand)
GA/CT/CT:	298	(complementary to (converted) top strand)
GA/CT/GA:	291	(complementary to (converted) bottom strand)
CT/GA/GA:	322	((converted) bottom strand)

Sample CF01-CM01-Zygote with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF01-CM01-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:	1601
Mapping efficiency:	16.0%

Sequence pairs with no alignments under any condition:	7758
Sequence pairs did not map uniquely:	641
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:	456	((converted) top strand)
GA/CT/CT:	373	(complementary to (converted) top strand)
GA/CT/GA:	372	(complementary to (converted) bottom strand)
CT/GA/GA:	400	((converted) bottom strand)

Sample CF01-CM01-Zygote with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF01-CM01-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:	1994
Mapping efficiency:	19.9%

Sequence pairs with no alignments under any condition:	7263
Sequence pairs did not map uniquely:	743
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:	563	((converted) top strand)
GA/CT/CT:	456	(complementary to (converted) top strand)
GA/CT/GA:	467	(complementary to (converted) bottom strand)
CT/GA/GA:	508	((converted) bottom strand)

Sample CF01-CM01-Zygote with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF01-CM01-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:	1313
Mapping efficiency:	13.1%

Sequence pairs with no alignments under any condition:	8135
Sequence pairs did not map uniquely:	552
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:	379	((converted) top strand)
GA/CT/CT:	303	(complementary to (converted) top strand)
GA/CT/GA:	302	(complementary to (converted) bottom strand)
CT/GA/GA:	329	((converted) bottom strand)

Sample CF01-CM01-Zygote with score_min L,-1,-0.6 processed successfully.
All tests for sample CF01-CM01-Zygote completed.