Running Bismark for sample EF08-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:	3207
Mapping efficiency:	32.1%

Sequence pairs with no alignments under any condition:	5323
Sequence pairs did not map uniquely:	1470
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:	771	((converted) top strand)
GA/CT/CT:	868	(complementary to (converted) top strand)
GA/CT/GA:	822	(complementary to (converted) bottom strand)
CT/GA/GA:	746	((converted) bottom strand)

Sample EF08-EM03-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF08-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:	3821
Mapping efficiency:	38.2%

Sequence pairs with no alignments under any condition:	4556
Sequence pairs did not map uniquely:	1623
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:	918	((converted) top strand)
GA/CT/CT:	1030	(complementary to (converted) top strand)
GA/CT/GA:	963	(complementary to (converted) bottom strand)
CT/GA/GA:	910	((converted) bottom strand)

Sample EF08-EM03-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF08-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:	4282
Mapping efficiency:	42.8%

Sequence pairs with no alignments under any condition:	3979
Sequence pairs did not map uniquely:	1739
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:	1036	((converted) top strand)
GA/CT/CT:	1128	(complementary to (converted) top strand)
GA/CT/GA:	1072	(complementary to (converted) bottom strand)
CT/GA/GA:	1046	((converted) bottom strand)

Sample EF08-EM03-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF08-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:	4858
Mapping efficiency:	48.6%

Sequence pairs with no alignments under any condition:	3293
Sequence pairs did not map uniquely:	1849
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:	1171	((converted) top strand)
GA/CT/CT:	1266	(complementary to (converted) top strand)
GA/CT/GA:	1220	(complementary to (converted) bottom strand)
CT/GA/GA:	1201	((converted) bottom strand)

Sample EF08-EM03-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF08-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:	3844
Mapping efficiency:	38.4%

Sequence pairs with no alignments under any condition:	4524
Sequence pairs did not map uniquely:	1632
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:	925	((converted) top strand)
GA/CT/CT:	1022	(complementary to (converted) top strand)
GA/CT/GA:	975	(complementary to (converted) bottom strand)
CT/GA/GA:	922	((converted) bottom strand)

Sample EF08-EM03-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF08-EM03-Larvae completed.