Contents of pair:
CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz

Contents of sample_name: CF08-CM04-Larvae

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:	134778
Mapping efficiency:	1.0%

Sequence pairs with no alignments under any condition:	13031056
Sequence pairs did not map uniquely:	51217
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:	36367	((converted) top strand)
GA/CT/CT:	31631	(complementary to (converted) top strand)
GA/CT/GA:	30777	(complementary to (converted) bottom strand)
CT/GA/GA:	36003	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	134340
Mapping efficiency:	1.0%

Sequence pairs with no alignments under any condition:	13031353
Sequence pairs did not map uniquely:	51359
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:	36075	((converted) top strand)
GA/CT/CT:	31421	(complementary to (converted) top strand)
GA/CT/GA:	30921	(complementary to (converted) bottom strand)
CT/GA/GA:	35923	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	134897
Mapping efficiency:	1.0%

Sequence pairs with no alignments under any condition:	13030919
Sequence pairs did not map uniquely:	51236
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:	36518	((converted) top strand)
GA/CT/CT:	31460	(complementary to (converted) top strand)
GA/CT/GA:	30920	(complementary to (converted) bottom strand)
CT/GA/GA:	35999	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	134201
Mapping efficiency:	1.0%

Sequence pairs with no alignments under any condition:	13031372
Sequence pairs did not map uniquely:	51479
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:	36172	((converted) top strand)
GA/CT/CT:	31235	(complementary to (converted) top strand)
GA/CT/GA:	31033	(complementary to (converted) bottom strand)
CT/GA/GA:	35761	((converted) bottom strand)

All child process successfully finished.CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz	CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz	CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz	CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz	CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz	CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz	CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz	CF08-CM04-Larvae_R2_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz	

/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_pe.bam	/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_pe.bam	/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_pe.bam	/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_bismark_bt2_pe.bam	

Number of paired-end alignments with a unique best hit:	538216
Mapping efficiency:	1.0%

Sequence pairs with no alignments under any condition:	52124700
Sequence pairs did not map uniquely:	205291
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:	145132	((converted) top strand)
GA/CT/CT:	125747	(complementary to (converted) top strand)
GA/CT/GA:	123651	(complementary to (converted) bottom strand)
CT/GA/GA:	143686	((converted) bottom strand)

CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt	CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt	CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt	CF08-CM04-Larvae_R1_001.fastp-trim.REPAIRED.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt