Output will be written into the directory: /gscratch/srlab/strigg/analyses/20190214_10K/
Processing paired-end Bismark output file(s) (SAM format):
/gscratch/srlab/strigg/analyses/20190214_10K/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190214_10K/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190214_10K/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20190214_10K/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_10K/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_10K/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam:	13025293
Total number duplicated alignments removed:	2492731 (19.14%)
Duplicated alignments were found at:	973800 different position(s)

Total count of deduplicated leftover sequences: 10532562 (80.86% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190214_10K/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_10K/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam:	15835414
Total number duplicated alignments removed:	2965373 (18.73%)
Duplicated alignments were found at:	1159592 different position(s)

Total count of deduplicated leftover sequences: 12870041 (81.27% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190214_10K/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_10K/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam:	16928820
Total number duplicated alignments removed:	3232662 (19.10%)
Duplicated alignments were found at:	1272082 different position(s)

Total count of deduplicated leftover sequences: 13696158 (80.90% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20190214_10K/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_10K/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam:	15041361
Total number duplicated alignments removed:	2670153 (17.75%)
Duplicated alignments were found at:	1083772 different position(s)

Total count of deduplicated leftover sequences: 12371208 (82.25% of total)