Contents of pair:
CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz

Contents of sample_name: CF01-CM02-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:	11666520
Mapping efficiency:	35.0%

Sequence pairs with no alignments under any condition:	16937493
Sequence pairs did not map uniquely:	4746797
Sequence pairs which were discarded because genomic sequence could not be extracted:	20

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2835110	((converted) top strand)
GA/CT/CT:	2994276	(complementary to (converted) top strand)
GA/CT/GA:	2997327	(complementary to (converted) bottom strand)
CT/GA/GA:	2839787	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	11659755
Mapping efficiency:	35.0%

Sequence pairs with no alignments under any condition:	16941665
Sequence pairs did not map uniquely:	4749390
Sequence pairs which were discarded because genomic sequence could not be extracted:	16

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2832625	((converted) top strand)
GA/CT/CT:	2993899	(complementary to (converted) top strand)
GA/CT/GA:	2994489	(complementary to (converted) bottom strand)
CT/GA/GA:	2838726	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	11667217
Mapping efficiency:	35.0%

Sequence pairs with no alignments under any condition:	16936837
Sequence pairs did not map uniquely:	4746756
Sequence pairs which were discarded because genomic sequence could not be extracted:	13

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2833405	((converted) top strand)
GA/CT/CT:	2993939	(complementary to (converted) top strand)
GA/CT/GA:	2997479	(complementary to (converted) bottom strand)
CT/GA/GA:	2842381	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	11663472
Mapping efficiency:	35.0%

Sequence pairs with no alignments under any condition:	16939485
Sequence pairs did not map uniquely:	4747853
Sequence pairs which were discarded because genomic sequence could not be extracted:	18

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2834408	((converted) top strand)
GA/CT/CT:	2995470	(complementary to (converted) top strand)
GA/CT/GA:	2995813	(complementary to (converted) bottom strand)
CT/GA/GA:	2837763	((converted) bottom strand)

All child process successfully finished.CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz	CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.1.gz	CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz	CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.2.gz	CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz	CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.3.gz	CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz	CF01-CM02-Larvae_R2_001.fastp-trim.fq.gz.temp.4.gz	

/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF01-CM02-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/CF01-CM02-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/CF01-CM02-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/CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam	

Number of paired-end alignments with a unique best hit:	46656964
Mapping efficiency:	35.0%

Sequence pairs with no alignments under any condition:	67755480
Sequence pairs did not map uniquely:	18990796
Sequence pairs which were discarded because genomic sequence could not be extracted:	67

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	11335548	((converted) top strand)
GA/CT/CT:	11977584	(complementary to (converted) top strand)
GA/CT/GA:	11985108	(complementary to (converted) bottom strand)
CT/GA/GA:	11358657	((converted) bottom strand)

CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt	CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt	CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt	CF01-CM02-Larvae_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt