Running Bismark for sample EF03-EM05-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:	2072
Mapping efficiency:	20.7%

Sequence pairs with no alignments under any condition:	7121
Sequence pairs did not map uniquely:	807
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:	518	((converted) top strand)
GA/CT/CT:	491	(complementary to (converted) top strand)
GA/CT/GA:	547	(complementary to (converted) bottom strand)
CT/GA/GA:	516	((converted) bottom strand)

Sample EF03-EM05-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF03-EM05-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:	2820
Mapping efficiency:	28.2%

Sequence pairs with no alignments under any condition:	6176
Sequence pairs did not map uniquely:	1004
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:	707	((converted) top strand)
GA/CT/CT:	683	(complementary to (converted) top strand)
GA/CT/GA:	728	(complementary to (converted) bottom strand)
CT/GA/GA:	702	((converted) bottom strand)

Sample EF03-EM05-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF03-EM05-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:	3406
Mapping efficiency:	34.1%

Sequence pairs with no alignments under any condition:	5405
Sequence pairs did not map uniquely:	1189
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:	860	((converted) top strand)
GA/CT/CT:	812	(complementary to (converted) top strand)
GA/CT/GA:	899	(complementary to (converted) bottom strand)
CT/GA/GA:	835	((converted) bottom strand)

Sample EF03-EM05-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF03-EM05-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:	4045
Mapping efficiency:	40.5%

Sequence pairs with no alignments under any condition:	4650
Sequence pairs did not map uniquely:	1305
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:	1015	((converted) top strand)
GA/CT/CT:	968	(complementary to (converted) top strand)
GA/CT/GA:	1067	(complementary to (converted) bottom strand)
CT/GA/GA:	995	((converted) bottom strand)

Sample EF03-EM05-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF03-EM05-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:	2853
Mapping efficiency:	28.5%

Sequence pairs with no alignments under any condition:	6128
Sequence pairs did not map uniquely:	1019
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:	717	((converted) top strand)
GA/CT/CT:	691	(complementary to (converted) top strand)
GA/CT/GA:	734	(complementary to (converted) bottom strand)
CT/GA/GA:	711	((converted) bottom strand)

Sample EF03-EM05-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF03-EM05-Larvae completed.