Output will be written into the directory: /gscratch/srlab/strigg/analyses/20190214_30K/
Processing paired-end Bismark output file(s) (SAM format):
/gscratch/srlab/strigg/analyses/20190214_30K/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190214_30K/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190214_30K/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190214_30K/EPI-120_S32_L005_R1_001_val_1_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/20190214_30K/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190214_30K/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam:	15600077
Total number duplicated alignments removed:	2723291 (17.46%)
Duplicated alignments were found at:	1171198 different position(s)

Total count of deduplicated leftover sequences: 12876786 (82.54% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190214_30K/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190214_30K/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam:	14908234
Total number duplicated alignments removed:	2626788 (17.62%)
Duplicated alignments were found at:	1117697 different position(s)

Total count of deduplicated leftover sequences: 12281446 (82.38% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190214_30K/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190214_30K/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam:	15855321
Total number duplicated alignments removed:	2815636 (17.76%)
Duplicated alignments were found at:	1216468 different position(s)

Total count of deduplicated leftover sequences: 13039685 (82.24% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190214_30K/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20190214_30K/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam:	14219508
Total number duplicated alignments removed:	2412714 (16.97%)
Duplicated alignments were found at:	1047169 different position(s)

Total count of deduplicated leftover sequences: 11806794 (83.03% of total)