Contents of pair:
CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz

Contents of sample_name: CF03-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:	13849016
Mapping efficiency:	46.2%

Sequence pairs with no alignments under any condition:	10653643
Sequence pairs did not map uniquely:	5451142
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:	3302251	((converted) top strand)
GA/CT/CT:	3617224	(complementary to (converted) top strand)
GA/CT/GA:	3619176	(complementary to (converted) bottom strand)
CT/GA/GA:	3310361	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	13845530
Mapping efficiency:	46.2%

Sequence pairs with no alignments under any condition:	10654498
Sequence pairs did not map uniquely:	5453774
Sequence pairs which were discarded because genomic sequence could not be extracted:	3

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	3301104	((converted) top strand)
GA/CT/CT:	3612926	(complementary to (converted) top strand)
GA/CT/GA:	3620989	(complementary to (converted) bottom strand)
CT/GA/GA:	3310508	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	13848432
Mapping efficiency:	46.2%

Sequence pairs with no alignments under any condition:	10655181
Sequence pairs did not map uniquely:	5450189
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:	3301191	((converted) top strand)
GA/CT/CT:	3615558	(complementary to (converted) top strand)
GA/CT/GA:	3618939	(complementary to (converted) bottom strand)
CT/GA/GA:	3312740	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	13852578
Mapping efficiency:	46.2%

Sequence pairs with no alignments under any condition:	10651918
Sequence pairs did not map uniquely:	5449305
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:	3304848	((converted) top strand)
GA/CT/CT:	3616277	(complementary to (converted) top strand)
GA/CT/GA:	3618180	(complementary to (converted) bottom strand)
CT/GA/GA:	3313268	((converted) bottom strand)

All child process successfully finished.CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz	CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz	CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz	CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz	CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz	CF03-CM04-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz	CF03-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz	CF03-CM04-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-CM04-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-CM04-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-CM04-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-CM04-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam