Running Bismark for sample EF06-EM01-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:	2770
Mapping efficiency:	27.7%

Sequence pairs with no alignments under any condition:	6116
Sequence pairs did not map uniquely:	1114
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:	639	((converted) top strand)
GA/CT/CT:	762	(complementary to (converted) top strand)
GA/CT/GA:	746	(complementary to (converted) bottom strand)
CT/GA/GA:	623	((converted) bottom strand)

Sample EF06-EM01-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF06-EM01-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:	3403
Mapping efficiency:	34.0%

Sequence pairs with no alignments under any condition:	5320
Sequence pairs did not map uniquely:	1277
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:	816	((converted) top strand)
GA/CT/CT:	904	(complementary to (converted) top strand)
GA/CT/GA:	902	(complementary to (converted) bottom strand)
CT/GA/GA:	781	((converted) bottom strand)

Sample EF06-EM01-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF06-EM01-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:	3925
Mapping efficiency:	39.2%

Sequence pairs with no alignments under any condition:	4682
Sequence pairs did not map uniquely:	1393
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:	943	((converted) top strand)
GA/CT/CT:	1042	(complementary to (converted) top strand)
GA/CT/GA:	1033	(complementary to (converted) bottom strand)
CT/GA/GA:	907	((converted) bottom strand)

Sample EF06-EM01-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF06-EM01-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:	4492
Mapping efficiency:	44.9%

Sequence pairs with no alignments under any condition:	4007
Sequence pairs did not map uniquely:	1501
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:	1075	((converted) top strand)
GA/CT/CT:	1172	(complementary to (converted) top strand)
GA/CT/GA:	1180	(complementary to (converted) bottom strand)
CT/GA/GA:	1065	((converted) bottom strand)

Sample EF06-EM01-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF06-EM01-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:	3438
Mapping efficiency:	34.4%

Sequence pairs with no alignments under any condition:	5282
Sequence pairs did not map uniquely:	1280
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:	822	((converted) top strand)
GA/CT/CT:	921	(complementary to (converted) top strand)
GA/CT/GA:	912	(complementary to (converted) bottom strand)
CT/GA/GA:	783	((converted) bottom strand)

Sample EF06-EM01-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF06-EM01-Larvae completed.