Running Bismark for sample CF01-CM02-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:	2866
Mapping efficiency:	28.7%

Sequence pairs with no alignments under any condition:	5775
Sequence pairs did not map uniquely:	1359
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:	671	((converted) top strand)
GA/CT/CT:	705	(complementary to (converted) top strand)
GA/CT/GA:	769	(complementary to (converted) bottom strand)
CT/GA/GA:	721	((converted) bottom strand)

Sample CF01-CM02-Larvae with score_min L,0,-0.4 processed successfully.
Running Bismark for sample CF01-CM02-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:	3589
Mapping efficiency:	35.9%

Sequence pairs with no alignments under any condition:	4873
Sequence pairs did not map uniquely:	1538
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:	852	((converted) top strand)
GA/CT/CT:	887	(complementary to (converted) top strand)
GA/CT/GA:	965	(complementary to (converted) bottom strand)
CT/GA/GA:	885	((converted) bottom strand)

Sample CF01-CM02-Larvae with score_min L,0,-0.6 processed successfully.
Running Bismark for sample CF01-CM02-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:	4171
Mapping efficiency:	41.7%

Sequence pairs with no alignments under any condition:	4139
Sequence pairs did not map uniquely:	1690
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:	1004	((converted) top strand)
GA/CT/CT:	1023	(complementary to (converted) top strand)
GA/CT/GA:	1109	(complementary to (converted) bottom strand)
CT/GA/GA:	1035	((converted) bottom strand)

Sample CF01-CM02-Larvae with score_min L,0,-0.8 processed successfully.
Running Bismark for sample CF01-CM02-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:	4730
Mapping efficiency:	47.3%

Sequence pairs with no alignments under any condition:	3445
Sequence pairs did not map uniquely:	1825
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:	1190	(complementary to (converted) top strand)
GA/CT/GA:	1256	(complementary to (converted) bottom strand)
CT/GA/GA:	1157	((converted) bottom strand)

Sample CF01-CM02-Larvae with score_min L,0,-1.0 processed successfully.
Running Bismark for sample CF01-CM02-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:	3615
Mapping efficiency:	36.1%

Sequence pairs with no alignments under any condition:	4839
Sequence pairs did not map uniquely:	1546
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:	862	((converted) top strand)
GA/CT/CT:	897	(complementary to (converted) top strand)
GA/CT/GA:	967	(complementary to (converted) bottom strand)
CT/GA/GA:	889	((converted) bottom strand)

Sample CF01-CM02-Larvae with score_min L,-1,-0.6 processed successfully.
All tests for sample CF01-CM02-Larvae completed.