Running Bismark for sample EF08-EM04-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:	2849
Mapping efficiency:	28.5%

Sequence pairs with no alignments under any condition:	5800
Sequence pairs did not map uniquely:	1351
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:	702	((converted) top strand)
GA/CT/CT:	722	(complementary to (converted) top strand)
GA/CT/GA:	756	(complementary to (converted) bottom strand)
CT/GA/GA:	669	((converted) bottom strand)

Sample EF08-EM04-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF08-EM04-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:	3602
Mapping efficiency:	36.0%

Sequence pairs with no alignments under any condition:	4824
Sequence pairs did not map uniquely:	1574
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:	902	((converted) top strand)
GA/CT/CT:	922	(complementary to (converted) top strand)
GA/CT/GA:	936	(complementary to (converted) bottom strand)
CT/GA/GA:	842	((converted) bottom strand)

Sample EF08-EM04-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF08-EM04-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:	4131
Mapping efficiency:	41.3%

Sequence pairs with no alignments under any condition:	4104
Sequence pairs did not map uniquely:	1765
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:	1037	((converted) top strand)
GA/CT/CT:	1056	(complementary to (converted) top strand)
GA/CT/GA:	1059	(complementary to (converted) bottom strand)
CT/GA/GA:	979	((converted) bottom strand)

Sample EF08-EM04-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF08-EM04-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:	4756
Mapping efficiency:	47.6%

Sequence pairs with no alignments under any condition:	3322
Sequence pairs did not map uniquely:	1922
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:	1217	((converted) top strand)
GA/CT/CT:	1212	(complementary to (converted) top strand)
GA/CT/GA:	1211	(complementary to (converted) bottom strand)
CT/GA/GA:	1116	((converted) bottom strand)

Sample EF08-EM04-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF08-EM04-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:	3640
Mapping efficiency:	36.4%

Sequence pairs with no alignments under any condition:	4782
Sequence pairs did not map uniquely:	1578
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:	919	((converted) top strand)
GA/CT/CT:	926	(complementary to (converted) top strand)
GA/CT/GA:	940	(complementary to (converted) bottom strand)
CT/GA/GA:	855	((converted) bottom strand)

Sample EF08-EM04-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF08-EM04-Larvae completed.