Running Bismark for sample CF06-CM02-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:	1604
Mapping efficiency:	16.0%

Sequence pairs with no alignments under any condition:	7789
Sequence pairs did not map uniquely:	607
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:	404	((converted) top strand)
GA/CT/CT:	399	(complementary to (converted) top strand)
GA/CT/GA:	415	(complementary to (converted) bottom strand)
CT/GA/GA:	386	((converted) bottom strand)

Sample CF06-CM02-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF06-CM02-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:	2270
Mapping efficiency:	22.7%

Sequence pairs with no alignments under any condition:	6950
Sequence pairs did not map uniquely:	780
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:	569	((converted) top strand)
GA/CT/CT:	534	(complementary to (converted) top strand)
GA/CT/GA:	583	(complementary to (converted) bottom strand)
CT/GA/GA:	584	((converted) bottom strand)

Sample CF06-CM02-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF06-CM02-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:	2794
Mapping efficiency:	27.9%

Sequence pairs with no alignments under any condition:	6300
Sequence pairs did not map uniquely:	906
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:	692	((converted) top strand)
GA/CT/CT:	658	(complementary to (converted) top strand)
GA/CT/GA:	717	(complementary to (converted) bottom strand)
CT/GA/GA:	727	((converted) bottom strand)

Sample CF06-CM02-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF06-CM02-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:	3360
Mapping efficiency:	33.6%

Sequence pairs with no alignments under any condition:	5605
Sequence pairs did not map uniquely:	1035
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:	835	((converted) top strand)
GA/CT/CT:	798	(complementary to (converted) top strand)
GA/CT/GA:	873	(complementary to (converted) bottom strand)
CT/GA/GA:	854	((converted) bottom strand)

Sample CF06-CM02-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF06-CM02-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:	2293
Mapping efficiency:	22.9%

Sequence pairs with no alignments under any condition:	6918
Sequence pairs did not map uniquely:	789
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:	578	((converted) top strand)
GA/CT/CT:	543	(complementary to (converted) top strand)
GA/CT/GA:	585	(complementary to (converted) bottom strand)
CT/GA/GA:	587	((converted) bottom strand)

Sample CF06-CM02-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample CF06-CM02-Larvae completed.