Processing paired-end Bismark output file(s) (SAM format):
zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam	zr2096_9_s1_R1_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 >>zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

...passed!
Output file is: zr2096_10_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_10_s1_R1_val_1_bismark_bt2_pe.bam:	7840800
Total number duplicated alignments removed:	292715 (3.73%)
Duplicated alignments were found at:	246728 different position(s)

Total count of deduplicated leftover sequences: 7548085 (96.27% of total)

Checking file >>zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_1_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_1_s1_R1_val_1_bismark_bt2_pe.bam:	5862943
Total number duplicated alignments removed:	408029 (6.96%)
Duplicated alignments were found at:	178632 different position(s)

Total count of deduplicated leftover sequences: 5454914 (93.04% of total)

Checking file >>zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_2_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_2_s1_R1_val_1_bismark_bt2_pe.bam:	12405477
Total number duplicated alignments removed:	781960 (6.30%)
Duplicated alignments were found at:	549300 different position(s)

Total count of deduplicated leftover sequences: 11623517 (93.70% of total)

Checking file >>zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_3_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_3_s1_R1_val_1_bismark_bt2_pe.bam:	13093746
Total number duplicated alignments removed:	660853 (5.05%)
Duplicated alignments were found at:	513074 different position(s)

Total count of deduplicated leftover sequences: 12432893 (94.95% of total)

Checking file >>zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_4_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_4_s1_R1_val_1_bismark_bt2_pe.bam:	10958111
Total number duplicated alignments removed:	302583 (2.76%)
Duplicated alignments were found at:	257083 different position(s)

Total count of deduplicated leftover sequences: 10655528 (97.24% of total)

Checking file >>zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_5_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_5_s1_R1_val_1_bismark_bt2_pe.bam:	13585388
Total number duplicated alignments removed:	724362 (5.33%)
Duplicated alignments were found at:	605546 different position(s)

Total count of deduplicated leftover sequences: 12861026 (94.67% of total)

Checking file >>zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_6_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_6_s1_R1_val_1_bismark_bt2_pe.bam:	10919623
Total number duplicated alignments removed:	332524 (3.05%)
Duplicated alignments were found at:	278765 different position(s)

Total count of deduplicated leftover sequences: 10587099 (96.95% of total)

Checking file >>zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_7_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_7_s1_R1_val_1_bismark_bt2_pe.bam:	12618338
Total number duplicated alignments removed:	447800 (3.55%)
Duplicated alignments were found at:	388990 different position(s)

Total count of deduplicated leftover sequences: 12170538 (96.45% of total)

Checking file >>zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_8_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_8_s1_R1_val_1_bismark_bt2_pe.bam:	11642729
Total number duplicated alignments removed:	547980 (4.71%)
Duplicated alignments were found at:	437695 different position(s)

Total count of deduplicated leftover sequences: 11094749 (95.29% of total)

Checking file >>zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam<< for signs of file truncation...

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
...passed!
Output file is: zr2096_9_s1_R1_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in zr2096_9_s1_R1_val_1_bismark_bt2_pe.bam:	13327617
Total number duplicated alignments removed:	1741377 (13.07%)
Duplicated alignments were found at:	1421061 different position(s)

Total count of deduplicated leftover sequences: 11586240 (86.93% of total)

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1