Output will be written into the directory: /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.10-bismark-deduplication/
Processing paired-end Bismark output file(s) (SAM format):
CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam


If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads.

Checking file >>CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1


Now testing Bismark result file CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam for positional sorting (which would be bad...)	...passed!
Output file is: CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam:	4232225
Total number duplicated alignments removed:	1032178 (24.39%)
Duplicated alignments were found at:	780590 different position(s)

Total count of deduplicated leftover sequences: 3200047 (75.61% of total)

skipping header line:	@HD	VN:1.0	SO:unsorted
skipping header line:	@SQ	SN:NC_035780.1	LN:65668440
skipping header line:	@SQ	SN:NC_035781.1	LN:61752955
skipping header line:	@SQ	SN:NC_035782.1	LN:77061148
skipping header line:	@SQ	SN:NC_035783.1	LN:59691872
skipping header line:	@SQ	SN:NC_035784.1	LN:98698416
skipping header line:	@SQ	SN:NC_035785.1	LN:51258098
skipping header line:	@SQ	SN:NC_035786.1	LN:57830854
skipping header line:	@SQ	SN:NC_035787.1	LN:75944018
skipping header line:	@SQ	SN:NC_035788.1	LN:104168038
skipping header line:	@SQ	SN:NC_035789.1	LN:32650045
skipping header line:	@SQ	SN:NC_007175.2	LN:17244
skipping header line:	@PG	ID:Bismark	VN:v0.24.0	CL:"bismark --path_to_bowtie2 /home/shared/bowtie2-2.4.4-linux-x86_64 --genome /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/data/Cvirginica_v300 --score_min L,0,-0.6 --parallel 2 --non_directional --samtools_path /home/shared/samtools-1.12 --gzip -p 4 -1 /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz -2 /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/trimmed-fastqs/CF01-CM01-Zygote_R2_001.fastp-trim.20220827.fq.gz --output_dir /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment"
skipping header line:	@PG	ID:samtools	PN:samtools	PP:Bismark	VN:1.12	CL:/home/shared/samtools-1.12/samtools view -bSh -
skipping header line:	@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.12	CL:/home/shared/samtools-1.12/samtools view -h /home/shared/8TB_HDD_01/sam/gitrepos/ceasmallr/output/02.00-bismark-bowtie2-alignment/CF01-CM01-Zygote_R1_001.fastp-trim.20220827.fq.gz.temp.1.gz_bismark_bt2_pe.bam
skipping header line:	@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.12	CL:/home/shared/samtools-1.12/samtools view -bSh -
skipping header line:	@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.12	CL:/home/shared/samtools-1.12/samtools view -h --threads 1 CF01-CM01-Zygote_R1_001.fastp-trim.20220827_bismark_bt2_pe.bam
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1