Running Bismark for sample EF03-EM04-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:	2219
Mapping efficiency:	22.2%

Sequence pairs with no alignments under any condition:	6812
Sequence pairs did not map uniquely:	969
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:	542	(complementary to (converted) top strand)
GA/CT/GA:	489	(complementary to (converted) bottom strand)
CT/GA/GA:	548	((converted) bottom strand)

Sample EF03-EM04-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample EF03-EM04-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:	3043
Mapping efficiency:	30.4%

Sequence pairs with no alignments under any condition:	5738
Sequence pairs did not map uniquely:	1219
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:	863	((converted) top strand)
GA/CT/CT:	727	(complementary to (converted) top strand)
GA/CT/GA:	663	(complementary to (converted) bottom strand)
CT/GA/GA:	790	((converted) bottom strand)

Sample EF03-EM04-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample EF03-EM04-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:	3707
Mapping efficiency:	37.1%

Sequence pairs with no alignments under any condition:	4889
Sequence pairs did not map uniquely:	1404
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:	1072	((converted) top strand)
GA/CT/CT:	859	(complementary to (converted) top strand)
GA/CT/GA:	806	(complementary to (converted) bottom strand)
CT/GA/GA:	970	((converted) bottom strand)

Sample EF03-EM04-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample EF03-EM04-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:	4473
Mapping efficiency:	44.7%

Sequence pairs with no alignments under any condition:	4002
Sequence pairs did not map uniquely:	1525
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:	1307	((converted) top strand)
GA/CT/CT:	1031	(complementary to (converted) top strand)
GA/CT/GA:	957	(complementary to (converted) bottom strand)
CT/GA/GA:	1178	((converted) bottom strand)

Sample EF03-EM04-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample EF03-EM04-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:	3091
Mapping efficiency:	30.9%

Sequence pairs with no alignments under any condition:	5684
Sequence pairs did not map uniquely:	1225
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:	871	((converted) top strand)
GA/CT/CT:	740	(complementary to (converted) top strand)
GA/CT/GA:	671	(complementary to (converted) bottom strand)
CT/GA/GA:	809	((converted) bottom strand)

Sample EF03-EM04-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample EF03-EM04-Larvae completed.