Output will be written into the directory: /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/bismark/
Processing Bismark output file(s) (SAM format):
../data/bismark/SRR6995994.nonCG_filtered.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 >>../data/bismark/SRR6995994.nonCG_filtered.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error reading file "../data/bismark/SRR6995994.nonCG_filtered.bam": Broken pipe
samtools view: error closing standard output: -1

Output file is: SRR6995994.nonCG_filtered.deduplicated.bam


Total number of alignments analysed in ../data/bismark/SRR6995994.nonCG_filtered.bam:	557683
Total number duplicated alignments removed:	364926 (65.44%)
Duplicated alignments were found at:	68331 different position(s)

Total count of deduplicated leftover sequences: 192757 (34.56% 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:v0.25.1	CL:"bismark --genome ../data/genome/bismark --non_directional --score_min L,0,-0.6 --parallel 6 --output_dir ../data/bismark --temp_dir ../data/bismark ../data/trimmed-reads/SRR6995994_trimmed.fq.gz"
skipping header line:	@PG	ID:samtools	PN:samtools	PP:Bismark	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -bSh -
skipping header line:	@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h /mmfs1/gscratch/scrubbed/sr320/github/project-gulf/data/bismark/SRR6995994_trimmed.fq.gz.temp.1_bismark_bt2.bam
skipping header line:	@PG	ID:samtools.2	PN:samtools	PP:samtools.1	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view --threads 4 -bSh -
skipping header line:	@PG	ID:samtools.3	PN:samtools	PP:samtools.2	VN:1.22.1	CL:samtools view -h ../data/bismark/SRR6995994.bam
skipping header line:	@PG	ID:samtools.4	PN:samtools	PP:samtools.3	VN:1.22.1	CL:samtools view -bS -
skipping header line:	@PG	ID:samtools.5	PN:samtools	PP:samtools.4	VN:1.22.1	CL:/mmfs1/gscratch/srlab/sr320/miniforge3/envs/myflow/bin/samtools view -h --threads 1 ../data/bismark/SRR6995994.nonCG_filtered.bam