Running Bismark for sample EF04-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:	2950
Mapping efficiency:	29.5%

Sequence pairs with no alignments under any condition:	5871
Sequence pairs did not map uniquely:	1179
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:	630	((converted) top strand)
GA/CT/CT:	844	(complementary to (converted) top strand)
GA/CT/GA:	804	(complementary to (converted) bottom strand)
CT/GA/GA:	672	((converted) bottom strand)

Sample EF04-EM05-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF04-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:	3708
Mapping efficiency:	37.1%

Sequence pairs with no alignments under any condition:	4929
Sequence pairs did not map uniquely:	1363
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:	794	((converted) top strand)
GA/CT/CT:	1052	(complementary to (converted) top strand)
GA/CT/GA:	992	(complementary to (converted) bottom strand)
CT/GA/GA:	870	((converted) bottom strand)

Sample EF04-EM05-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF04-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:	4323
Mapping efficiency:	43.2%

Sequence pairs with no alignments under any condition:	4161
Sequence pairs did not map uniquely:	1516
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:	945	((converted) top strand)
GA/CT/CT:	1199	(complementary to (converted) top strand)
GA/CT/GA:	1159	(complementary to (converted) bottom strand)
CT/GA/GA:	1020	((converted) bottom strand)

Sample EF04-EM05-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF04-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:	4884
Mapping efficiency:	48.8%

Sequence pairs with no alignments under any condition:	3482
Sequence pairs did not map uniquely:	1634
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:	1074	((converted) top strand)
GA/CT/CT:	1354	(complementary to (converted) top strand)
GA/CT/GA:	1305	(complementary to (converted) bottom strand)
CT/GA/GA:	1151	((converted) bottom strand)

Sample EF04-EM05-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF04-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:	3743
Mapping efficiency:	37.4%

Sequence pairs with no alignments under any condition:	4882
Sequence pairs did not map uniquely:	1375
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:	807	((converted) top strand)
GA/CT/CT:	1062	(complementary to (converted) top strand)
GA/CT/GA:	1000	(complementary to (converted) bottom strand)
CT/GA/GA:	874	((converted) bottom strand)

Sample EF04-EM05-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF04-EM05-Larvae completed.