Running Bismark for sample EF05-EM06-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:	2706
Mapping efficiency:	27.1%

Sequence pairs with no alignments under any condition:	6355
Sequence pairs did not map uniquely:	939
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:	730	((converted) top strand)
GA/CT/CT:	675	(complementary to (converted) top strand)
GA/CT/GA:	669	(complementary to (converted) bottom strand)
CT/GA/GA:	632	((converted) bottom strand)

Sample EF05-EM06-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF05-EM06-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:	3434
Mapping efficiency:	34.3%

Sequence pairs with no alignments under any condition:	5485
Sequence pairs did not map uniquely:	1081
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:	891	((converted) top strand)
GA/CT/CT:	850	(complementary to (converted) top strand)
GA/CT/GA:	855	(complementary to (converted) bottom strand)
CT/GA/GA:	838	((converted) bottom strand)

Sample EF05-EM06-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF05-EM06-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:	4059
Mapping efficiency:	40.6%

Sequence pairs with no alignments under any condition:	4783
Sequence pairs did not map uniquely:	1158
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:	1046	((converted) top strand)
GA/CT/CT:	1028	(complementary to (converted) top strand)
GA/CT/GA:	990	(complementary to (converted) bottom strand)
CT/GA/GA:	995	((converted) bottom strand)

Sample EF05-EM06-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF05-EM06-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:	4577
Mapping efficiency:	45.8%

Sequence pairs with no alignments under any condition:	4173
Sequence pairs did not map uniquely:	1250
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:	1161	((converted) top strand)
GA/CT/CT:	1174	(complementary to (converted) top strand)
GA/CT/GA:	1131	(complementary to (converted) bottom strand)
CT/GA/GA:	1111	((converted) bottom strand)

Sample EF05-EM06-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF05-EM06-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:	3452
Mapping efficiency:	34.5%

Sequence pairs with no alignments under any condition:	5462
Sequence pairs did not map uniquely:	1086
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:	891	((converted) top strand)
GA/CT/CT:	853	(complementary to (converted) top strand)
GA/CT/GA:	859	(complementary to (converted) bottom strand)
CT/GA/GA:	849	((converted) bottom strand)

Sample EF05-EM06-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF05-EM06-Larvae completed.