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:	532162
Total number duplicated alignments removed:	1367 (0.26%)
Duplicated alignments were found at:	1302 different position(s)

Total count of deduplicated leftover sequences: 530795 (99.74% 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:	288473
Total number duplicated alignments removed:	9143 (3.17%)
Duplicated alignments were found at:	4833 different position(s)

Total count of deduplicated leftover sequences: 279330 (96.83% 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:	503476
Total number duplicated alignments removed:	5358 (1.06%)
Duplicated alignments were found at:	3256 different position(s)

Total count of deduplicated leftover sequences: 498118 (98.94% 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:	526409
Total number duplicated alignments removed:	1361 (0.26%)
Duplicated alignments were found at:	1266 different position(s)

Total count of deduplicated leftover sequences: 525048 (99.74% 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:	541137
Total number duplicated alignments removed:	783 (0.14%)
Duplicated alignments were found at:	737 different position(s)

Total count of deduplicated leftover sequences: 540354 (99.86% 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:	520106
Total number duplicated alignments removed:	1247 (0.24%)
Duplicated alignments were found at:	1147 different position(s)

Total count of deduplicated leftover sequences: 518859 (99.76% 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:	545007
Total number duplicated alignments removed:	820 (0.15%)
Duplicated alignments were found at:	778 different position(s)

Total count of deduplicated leftover sequences: 544187 (99.85% 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:	518103
Total number duplicated alignments removed:	769 (0.15%)
Duplicated alignments were found at:	751 different position(s)

Total count of deduplicated leftover sequences: 517334 (99.85% 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:	481891
Total number duplicated alignments removed:	2585 (0.54%)
Duplicated alignments were found at:	1880 different position(s)

Total count of deduplicated leftover sequences: 479306 (99.46% 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:	506536
Total number duplicated alignments removed:	2728 (0.54%)
Duplicated alignments were found at:	2521 different position(s)

Total count of deduplicated leftover sequences: 503808 (99.46% of total)

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