Contents of pair:
CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz

Contents of sample_name: CF02-CM02-Zygote

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:	6882716
Mapping efficiency:	13.4%

Sequence pairs with no alignments under any condition:	41938850
Sequence pairs did not map uniquely:	2689896
Sequence pairs which were discarded because genomic sequence could not be extracted:	8

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2082045	((converted) top strand)
GA/CT/CT:	1349788	(complementary to (converted) top strand)
GA/CT/GA:	1357088	(complementary to (converted) bottom strand)
CT/GA/GA:	2093787	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	6883829
Mapping efficiency:	13.4%

Sequence pairs with no alignments under any condition:	41942753
Sequence pairs did not map uniquely:	2684881
Sequence pairs which were discarded because genomic sequence could not be extracted:	10

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2085341	((converted) top strand)
GA/CT/CT:	1350756	(complementary to (converted) top strand)
GA/CT/GA:	1353494	(complementary to (converted) bottom strand)
CT/GA/GA:	2094228	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	6879623
Mapping efficiency:	13.4%

Sequence pairs with no alignments under any condition:	41945382
Sequence pairs did not map uniquely:	2686457
Sequence pairs which were discarded because genomic sequence could not be extracted:	10

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2081026	((converted) top strand)
GA/CT/CT:	1350368	(complementary to (converted) top strand)
GA/CT/GA:	1353502	(complementary to (converted) bottom strand)
CT/GA/GA:	2094717	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	6882351
Mapping efficiency:	13.4%

Sequence pairs with no alignments under any condition:	41941770
Sequence pairs did not map uniquely:	2687341
Sequence pairs which were discarded because genomic sequence could not be extracted:	15

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	2082786	((converted) top strand)
GA/CT/CT:	1350767	(complementary to (converted) top strand)
GA/CT/GA:	1351618	(complementary to (converted) bottom strand)
CT/GA/GA:	2097165	((converted) bottom strand)

All child process successfully finished.CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz	CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz	CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz	CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz	CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz	CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz	CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz	CF02-CM02-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz	

/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF02-CM02-Zygote_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/CF02-CM02-Zygote_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/CF02-CM02-Zygote_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/CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam	

Number of paired-end alignments with a unique best hit:	27528519
Mapping efficiency:	13.4%

Sequence pairs with no alignments under any condition:	167768755
Sequence pairs did not map uniquely:	10748575
Sequence pairs which were discarded because genomic sequence could not be extracted:	43

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	8331198	((converted) top strand)
GA/CT/CT:	5401679	(complementary to (converted) top strand)
GA/CT/GA:	5415702	(complementary to (converted) bottom strand)
CT/GA/GA:	8379897	((converted) bottom strand)

CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt	CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt	CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt	CF02-CM02-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt