Contents of pair:
CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz

Contents of sample_name: CF03-CM03-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:	6801123
Mapping efficiency:	20.8%

Sequence pairs with no alignments under any condition:	23544973
Sequence pairs did not map uniquely:	2389330
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:	1907759	((converted) top strand)
GA/CT/CT:	1491364	(complementary to (converted) top strand)
GA/CT/GA:	1493062	(complementary to (converted) bottom strand)
CT/GA/GA:	1908928	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	6795059
Mapping efficiency:	20.8%

Sequence pairs with no alignments under any condition:	23554219
Sequence pairs did not map uniquely:	2386148
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:	1903236	((converted) top strand)
GA/CT/CT:	1492115	(complementary to (converted) top strand)
GA/CT/GA:	1492269	(complementary to (converted) bottom strand)
CT/GA/GA:	1907435	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	6793595
Mapping efficiency:	20.8%

Sequence pairs with no alignments under any condition:	23555428
Sequence pairs did not map uniquely:	2386403
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:	1901109	((converted) top strand)
GA/CT/CT:	1490977	(complementary to (converted) top strand)
GA/CT/GA:	1490902	(complementary to (converted) bottom strand)
CT/GA/GA:	1910601	((converted) bottom strand)

Number of paired-end alignments with a unique best hit:	6797063
Mapping efficiency:	20.8%

Sequence pairs with no alignments under any condition:	23549520
Sequence pairs did not map uniquely:	2388843
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:	1903547	((converted) top strand)
GA/CT/CT:	1490676	(complementary to (converted) top strand)
GA/CT/GA:	1491757	(complementary to (converted) bottom strand)
CT/GA/GA:	1911078	((converted) bottom strand)

All child process successfully finished.CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz	CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.1.gz	CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz	CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.2.gz	CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz	CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.3.gz	CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz	CF03-CM03-Zygote_R2_001.fastp-trim.fq.gz.temp.4.gz	

/gscratch/srlab/kdurkin1/kathleen-coral/project/output/02.01-bismark-bowtie2-alignment-SLURM-array/CF03-CM03-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/CF03-CM03-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/CF03-CM03-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/CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_pe.bam	

Number of paired-end alignments with a unique best hit:	27186840
Mapping efficiency:	20.8%

Sequence pairs with no alignments under any condition:	94204140
Sequence pairs did not map uniquely:	9550724
Sequence pairs which were discarded because genomic sequence could not be extracted:	25

Number of sequence pairs with unique best (first) alignment came from the bowtie output:
CT/GA/CT:	7615651	((converted) top strand)
GA/CT/CT:	5965132	(complementary to (converted) top strand)
GA/CT/GA:	5967990	(complementary to (converted) bottom strand)
CT/GA/GA:	7638042	((converted) bottom strand)

CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.1.gz_bismark_bt2_PE_report.txt	CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.2.gz_bismark_bt2_PE_report.txt	CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.3.gz_bismark_bt2_PE_report.txt	CF03-CM03-Zygote_R1_001.fastp-trim.fq.gz.temp.4.gz_bismark_bt2_PE_report.txt