Running Bismark for sample EF07-EM03-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:	2691
Mapping efficiency:	26.9%

Sequence pairs with no alignments under any condition:	6134
Sequence pairs did not map uniquely:	1175
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:	587	((converted) top strand)
GA/CT/CT:	673	(complementary to (converted) top strand)
GA/CT/GA:	759	(complementary to (converted) bottom strand)
CT/GA/GA:	672	((converted) bottom strand)

Sample EF07-EM03-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF07-EM03-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:	3253
Mapping efficiency:	32.5%

Sequence pairs with no alignments under any condition:	5430
Sequence pairs did not map uniquely:	1317
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:	716	((converted) top strand)
GA/CT/CT:	814	(complementary to (converted) top strand)
GA/CT/GA:	910	(complementary to (converted) bottom strand)
CT/GA/GA:	813	((converted) bottom strand)

Sample EF07-EM03-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF07-EM03-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:	3723
Mapping efficiency:	37.2%

Sequence pairs with no alignments under any condition:	4845
Sequence pairs did not map uniquely:	1432
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:	833	((converted) top strand)
GA/CT/CT:	921	(complementary to (converted) top strand)
GA/CT/GA:	1031	(complementary to (converted) bottom strand)
CT/GA/GA:	938	((converted) bottom strand)

Sample EF07-EM03-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF07-EM03-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:	4257
Mapping efficiency:	42.6%

Sequence pairs with no alignments under any condition:	4201
Sequence pairs did not map uniquely:	1542
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:	976	((converted) top strand)
GA/CT/CT:	1052	(complementary to (converted) top strand)
GA/CT/GA:	1156	(complementary to (converted) bottom strand)
CT/GA/GA:	1073	((converted) bottom strand)

Sample EF07-EM03-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF07-EM03-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:	3265
Mapping efficiency:	32.6%

Sequence pairs with no alignments under any condition:	5407
Sequence pairs did not map uniquely:	1328
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:	720	((converted) top strand)
GA/CT/CT:	815	(complementary to (converted) top strand)
GA/CT/GA:	917	(complementary to (converted) bottom strand)
CT/GA/GA:	813	((converted) bottom strand)

Sample EF07-EM03-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF07-EM03-Larvae completed.