Running Bismark for sample CF03-CM05-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:	2542
Mapping efficiency:	25.4%

Sequence pairs with no alignments under any condition:	6363
Sequence pairs did not map uniquely:	1095
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:	640	((converted) top strand)
GA/CT/CT:	664	(complementary to (converted) top strand)
GA/CT/GA:	635	(complementary to (converted) bottom strand)
CT/GA/GA:	603	((converted) bottom strand)

Sample CF03-CM05-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF03-CM05-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:	3397
Mapping efficiency:	34.0%

Sequence pairs with no alignments under any condition:	5262
Sequence pairs did not map uniquely:	1341
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:	843	((converted) top strand)
GA/CT/CT:	897	(complementary to (converted) top strand)
GA/CT/GA:	836	(complementary to (converted) bottom strand)
CT/GA/GA:	821	((converted) bottom strand)

Sample CF03-CM05-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF03-CM05-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:	4061
Mapping efficiency:	40.6%

Sequence pairs with no alignments under any condition:	4405
Sequence pairs did not map uniquely:	1534
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:	977	((converted) top strand)
GA/CT/CT:	1082	(complementary to (converted) top strand)
GA/CT/GA:	1027	(complementary to (converted) bottom strand)
CT/GA/GA:	975	((converted) bottom strand)

Sample CF03-CM05-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF03-CM05-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:	4662
Mapping efficiency:	46.6%

Sequence pairs with no alignments under any condition:	3679
Sequence pairs did not map uniquely:	1659
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:	1111	((converted) top strand)
GA/CT/CT:	1226	(complementary to (converted) top strand)
GA/CT/GA:	1184	(complementary to (converted) bottom strand)
CT/GA/GA:	1141	((converted) bottom strand)

Sample CF03-CM05-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF03-CM05-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:	3444
Mapping efficiency:	34.4%

Sequence pairs with no alignments under any condition:	5211
Sequence pairs did not map uniquely:	1345
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:	856	((converted) top strand)
GA/CT/CT:	913	(complementary to (converted) top strand)
GA/CT/GA:	849	(complementary to (converted) bottom strand)
CT/GA/GA:	826	((converted) bottom strand)

Sample CF03-CM05-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample CF03-CM05-Larvae completed.