Running Bismark for sample EF06-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:	1778
Mapping efficiency:	17.8%

Sequence pairs with no alignments under any condition:	7535
Sequence pairs did not map uniquely:	687
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:	457	((converted) top strand)
GA/CT/CT:	458	(complementary to (converted) top strand)
GA/CT/GA:	432	(complementary to (converted) bottom strand)
CT/GA/GA:	431	((converted) bottom strand)

Sample EF06-EM06-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF06-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:	2487
Mapping efficiency:	24.9%

Sequence pairs with no alignments under any condition:	6650
Sequence pairs did not map uniquely:	863
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:	636	((converted) top strand)
GA/CT/CT:	633	(complementary to (converted) top strand)
GA/CT/GA:	622	(complementary to (converted) bottom strand)
CT/GA/GA:	596	((converted) bottom strand)

Sample EF06-EM06-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF06-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:	3177
Mapping efficiency:	31.8%

Sequence pairs with no alignments under any condition:	5828
Sequence pairs did not map uniquely:	995
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:	797	((converted) top strand)
GA/CT/CT:	816	(complementary to (converted) top strand)
GA/CT/GA:	801	(complementary to (converted) bottom strand)
CT/GA/GA:	763	((converted) bottom strand)

Sample EF06-EM06-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF06-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:	3868
Mapping efficiency:	38.7%

Sequence pairs with no alignments under any condition:	4974
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:	962	((converted) top strand)
GA/CT/CT:	988	(complementary to (converted) top strand)
GA/CT/GA:	974	(complementary to (converted) bottom strand)
CT/GA/GA:	944	((converted) bottom strand)

Sample EF06-EM06-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF06-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:	2527
Mapping efficiency:	25.3%

Sequence pairs with no alignments under any condition:	6599
Sequence pairs did not map uniquely:	874
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:	644	((converted) top strand)
GA/CT/CT:	647	(complementary to (converted) top strand)
GA/CT/GA:	635	(complementary to (converted) bottom strand)
CT/GA/GA:	601	((converted) bottom strand)

Sample EF06-EM06-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF06-EM06-Larvae completed.