Output will be written into the directory: /gscratch/srlab/strigg/analyses/20190415_10K/
Processing paired-end Bismark output file(s) (SAM format):
/gscratch/srlab/strigg/analyses/20190415_10K/Tank2-025-026_R1_001_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190415_10K/Tank2-025-026_trim_R1_001_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190415_10K/Tank3-15-16_R1_001_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190415_10K/Tank3-15-16_trim_R1_001_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 >>/gscratch/srlab/strigg/analyses/20190415_10K/Tank2-025-026_R1_001_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: Tank2-025-026_R1_001_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190415_10K/Tank2-025-026_R1_001_bismark_bt2_pe.bam:	44222014
Total number duplicated alignments removed:	4089205 (9.25%)
Duplicated alignments were found at:	3434427 different position(s)

Total count of deduplicated leftover sequences: 40132809 (90.75% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190415_10K/Tank2-025-026_trim_R1_001_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: Tank2-025-026_trim_R1_001_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190415_10K/Tank2-025-026_trim_R1_001_bismark_bt2_pe.bam:	42892839
Total number duplicated alignments removed:	3932820 (9.17%)
Duplicated alignments were found at:	3410251 different position(s)

Total count of deduplicated leftover sequences: 38960019 (90.83% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190415_10K/Tank3-15-16_R1_001_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: Tank3-15-16_R1_001_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190415_10K/Tank3-15-16_R1_001_bismark_bt2_pe.bam:	32660140
Total number duplicated alignments removed:	2547287 (7.80%)
Duplicated alignments were found at:	2151243 different position(s)

Total count of deduplicated leftover sequences: 30112853 (92.20% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190415_10K/Tank3-15-16_trim_R1_001_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: Tank3-15-16_trim_R1_001_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190415_10K/Tank3-15-16_trim_R1_001_bismark_bt2_pe.bam:	31686658
Total number duplicated alignments removed:	2444863 (7.72%)
Duplicated alignments were found at:	2140207 different position(s)

Total count of deduplicated leftover sequences: 29241795 (92.28% of total)