Running Bismark for sample CF03-CM04-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:	3849
Mapping efficiency:	38.5%

Sequence pairs with no alignments under any condition:	4455
Sequence pairs did not map uniquely:	1696
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:	910	((converted) top strand)
GA/CT/CT:	995	(complementary to (converted) top strand)
GA/CT/GA:	1044	(complementary to (converted) bottom strand)
CT/GA/GA:	900	((converted) bottom strand)

Sample CF03-CM04-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF03-CM04-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:	4611
Mapping efficiency:	46.1%

Sequence pairs with no alignments under any condition:	3510
Sequence pairs did not map uniquely:	1879
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:	1122	((converted) top strand)
GA/CT/CT:	1184	(complementary to (converted) top strand)
GA/CT/GA:	1222	(complementary to (converted) bottom strand)
CT/GA/GA:	1083	((converted) bottom strand)

Sample CF03-CM04-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF03-CM04-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:	5188
Mapping efficiency:	51.9%

Sequence pairs with no alignments under any condition:	2809
Sequence pairs did not map uniquely:	2003
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:	1258	((converted) top strand)
GA/CT/CT:	1322	(complementary to (converted) top strand)
GA/CT/GA:	1366	(complementary to (converted) bottom strand)
CT/GA/GA:	1242	((converted) bottom strand)

Sample CF03-CM04-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF03-CM04-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:	5712
Mapping efficiency:	57.1%

Sequence pairs with no alignments under any condition:	2172
Sequence pairs did not map uniquely:	2116
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:	1396	((converted) top strand)
GA/CT/CT:	1454	(complementary to (converted) top strand)
GA/CT/GA:	1496	(complementary to (converted) bottom strand)
CT/GA/GA:	1366	((converted) bottom strand)

Sample CF03-CM04-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF03-CM04-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:	4650
Mapping efficiency:	46.5%

Sequence pairs with no alignments under any condition:	3468
Sequence pairs did not map uniquely:	1882
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:	1127	((converted) top strand)
GA/CT/CT:	1194	(complementary to (converted) top strand)
GA/CT/GA:	1232	(complementary to (converted) bottom strand)
CT/GA/GA:	1097	((converted) bottom strand)

Sample CF03-CM04-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample CF03-CM04-Larvae completed.