Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190806_v074/
Processing paired-end Bismark output file(s) (SAM format):
/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_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/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam:	7025362
Total number duplicated alignments removed:	1875252 (26.69%)
Duplicated alignments were found at:	1025167 different position(s)

Total count of deduplicated leftover sequences: 5150110 (73.31% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam:	9918239
Total number duplicated alignments removed:	2423092 (24.43%)
Duplicated alignments were found at:	1235195 different position(s)

Total count of deduplicated leftover sequences: 7495147 (75.57% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam:	13828640
Total number duplicated alignments removed:	3695743 (26.73%)
Duplicated alignments were found at:	1989541 different position(s)

Total count of deduplicated leftover sequences: 10132897 (73.27% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam:	10236936
Total number duplicated alignments removed:	3030160 (29.60%)
Duplicated alignments were found at:	1684943 different position(s)

Total count of deduplicated leftover sequences: 7206776 (70.40% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam:	7811982
Total number duplicated alignments removed:	2608881 (33.40%)
Duplicated alignments were found at:	1463448 different position(s)

Total count of deduplicated leftover sequences: 5203101 (66.60% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam:	7892255
Total number duplicated alignments removed:	2308469 (29.25%)
Duplicated alignments were found at:	1344013 different position(s)

Total count of deduplicated leftover sequences: 5583786 (70.75% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam:	5810273
Total number duplicated alignments removed:	1616015 (27.81%)
Duplicated alignments were found at:	924266 different position(s)

Total count of deduplicated leftover sequences: 4194258 (72.19% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190806_v074/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam:	6848668
Total number duplicated alignments removed:	1928180 (28.15%)
Duplicated alignments were found at:	1172653 different position(s)

Total count of deduplicated leftover sequences: 4920488 (71.85% of total)