Contents of pair:
CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz

Contents of sample_name: CF03-CM05-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:	9658178
Mapping efficiency:	33.9%

Sequence pairs with no alignments under any condition:	15265088
Sequence pairs did not map uniquely:	3566762
Sequence pairs which were discarded because genomic sequence could not be extracted:	6

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2365472	((converted) top strand)
GA/CT/CT:	2457172	(complementary to (converted) top strand)
GA/CT/GA:	2468066	(complementary to (converted) bottom strand)
CT/GA/GA:	2367462	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	9662337
Mapping efficiency:	33.9%

Sequence pairs with no alignments under any condition:	15259909
Sequence pairs did not map uniquely:	3567781
Sequence pairs which were discarded because genomic sequence could not be extracted:	7

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2363287	((converted) top strand)
GA/CT/CT:	2458147	(complementary to (converted) top strand)
GA/CT/GA:	2468209	(complementary to (converted) bottom strand)
CT/GA/GA:	2372687	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	9666372
Mapping efficiency:	33.9%

Sequence pairs with no alignments under any condition:	15255177
Sequence pairs did not map uniquely:	3568478
Sequence pairs which were discarded because genomic sequence could not be extracted:	5

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2363059	((converted) top strand)
GA/CT/CT:	2462093	(complementary to (converted) top strand)
GA/CT/GA:	2468994	(complementary to (converted) bottom strand)
CT/GA/GA:	2372221	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	9662233
Mapping efficiency:	33.9%

Sequence pairs with no alignments under any condition:	15262528
Sequence pairs did not map uniquely:	3565266
Sequence pairs which were discarded because genomic sequence could not be extracted:	4

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2363565	((converted) top strand)
GA/CT/CT:	2457524	(complementary to (converted) top strand)
GA/CT/GA:	2468750	(complementary to (converted) bottom strand)
CT/GA/GA:	2372390	((converted) bottom strand)

All child process successfully finished.CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz	CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz	CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz	CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz	CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz	CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz	CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz	CF03-CM05-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz	

/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_pe.bam	/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_pe.bam	/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_pe.bam	/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM05-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam