Running Bismark for sample CF08-CM05-Larvae 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:	155
Mapping efficiency:	1.6%

Sequence pairs with no alignments under any condition:	9781
Sequence pairs did not map uniquely:	64
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:	50	((converted) top strand)
GA/CT/CT:	31	(complementary to (converted) top strand)
GA/CT/GA:	40	(complementary to (converted) bottom strand)
CT/GA/GA:	34	((converted) bottom strand)

Sample CF08-CM05-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF08-CM05-Larvae 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:	210
Mapping efficiency:	2.1%

Sequence pairs with no alignments under any condition:	9719
Sequence pairs did not map uniquely:	71
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:	64	((converted) top strand)
GA/CT/CT:	50	(complementary to (converted) top strand)
GA/CT/GA:	49	(complementary to (converted) bottom strand)
CT/GA/GA:	47	((converted) bottom strand)

Sample CF08-CM05-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF08-CM05-Larvae 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:	270
Mapping efficiency:	2.7%

Sequence pairs with no alignments under any condition:	9634
Sequence pairs did not map uniquely:	96
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:	82	((converted) top strand)
GA/CT/CT:	64	(complementary to (converted) top strand)
GA/CT/GA:	58	(complementary to (converted) bottom strand)
CT/GA/GA:	66	((converted) bottom strand)

Sample CF08-CM05-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF08-CM05-Larvae 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:	359
Mapping efficiency:	3.6%

Sequence pairs with no alignments under any condition:	9519
Sequence pairs did not map uniquely:	122
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:	108	((converted) top strand)
GA/CT/CT:	81	(complementary to (converted) top strand)
GA/CT/GA:	78	(complementary to (converted) bottom strand)
CT/GA/GA:	92	((converted) bottom strand)

Sample CF08-CM05-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF08-CM05-Larvae 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:	213
Mapping efficiency:	2.1%

Sequence pairs with no alignments under any condition:	9713
Sequence pairs did not map uniquely:	74
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:	64	((converted) top strand)
GA/CT/CT:	51	(complementary to (converted) top strand)
GA/CT/GA:	50	(complementary to (converted) bottom strand)
CT/GA/GA:	48	((converted) bottom strand)

Sample CF08-CM05-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample CF08-CM05-Larvae completed.