Running Bismark for sample EF05-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:	2237
Mapping efficiency:	22.4%

Sequence pairs with no alignments under any condition:	6801
Sequence pairs did not map uniquely:	962
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:	553	((converted) top strand)
GA/CT/CT:	602	(complementary to (converted) top strand)
GA/CT/GA:	565	(complementary to (converted) bottom strand)
CT/GA/GA:	517	((converted) bottom strand)

Sample EF05-EM01-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF05-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:	2917
Mapping efficiency:	29.2%

Sequence pairs with no alignments under any condition:	5914
Sequence pairs did not map uniquely:	1169
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:	710	((converted) top strand)
GA/CT/CT:	777	(complementary to (converted) top strand)
GA/CT/GA:	749	(complementary to (converted) bottom strand)
CT/GA/GA:	681	((converted) bottom strand)

Sample EF05-EM01-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF05-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:	3499
Mapping efficiency:	35.0%

Sequence pairs with no alignments under any condition:	5197
Sequence pairs did not map uniquely:	1304
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:	858	((converted) top strand)
GA/CT/CT:	907	(complementary to (converted) top strand)
GA/CT/GA:	902	(complementary to (converted) bottom strand)
CT/GA/GA:	832	((converted) bottom strand)

Sample EF05-EM01-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF05-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:	4075
Mapping efficiency:	40.8%

Sequence pairs with no alignments under any condition:	4472
Sequence pairs did not map uniquely:	1453
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:	997	((converted) top strand)
GA/CT/CT:	1054	(complementary to (converted) top strand)
GA/CT/GA:	1043	(complementary to (converted) bottom strand)
CT/GA/GA:	981	((converted) bottom strand)

Sample EF05-EM01-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF05-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:	2955
Mapping efficiency:	29.6%

Sequence pairs with no alignments under any condition:	5876
Sequence pairs did not map uniquely:	1169
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:	715	((converted) top strand)
GA/CT/CT:	785	(complementary to (converted) top strand)
GA/CT/GA:	756	(complementary to (converted) bottom strand)
CT/GA/GA:	699	((converted) bottom strand)

Sample EF05-EM01-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF05-EM01-Larvae completed.