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: 185 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 185 (100.00% 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 ...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: 91 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 91 (100.00% 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 ...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: 176 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 176 (100.00% 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 ...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: 194 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 194 (100.00% 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 ...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: 195 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 195 (100.00% 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 ...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: 182 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 182 (100.00% 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 ...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: 217 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 217 (100.00% 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 ...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: 211 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 211 (100.00% 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 ...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: 175 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 175 (100.00% 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 ...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: 164 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 164 (100.00% of total)