Processing single-end Bismark output file(s) (SAM format): 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam zr1394_10_s456_trimmed_bismark_bt2.bam zr1394_11_s456_trimmed_bismark_bt2.bam zr1394_12_s456_trimmed_bismark_bt2.bam zr1394_13_s456_trimmed_bismark_bt2.bam zr1394_14_s456_trimmed_bismark_bt2.bam zr1394_15_s456_trimmed_bismark_bt2.bam zr1394_16_s456_trimmed_bismark_bt2.bam zr1394_17_s456_trimmed_bismark_bt2.bam zr1394_18_s456_trimmed_bismark_bt2.bam zr1394_1_s456_trimmed_bismark_bt2.bam zr1394_2_s456_trimmed_bismark_bt2.bam zr1394_3_s456_trimmed_bismark_bt2.bam zr1394_4_s456_trimmed_bismark_bt2.bam zr1394_5_s456_trimmed_bismark_bt2.bam zr1394_6_s456_trimmed_bismark_bt2.bam zr1394_7_s456_trimmed_bismark_bt2.bam zr1394_8_s456_trimmed_bismark_bt2.bam zr1394_9_s456_trimmed_bismark_bt2.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 >>1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam: 3662558 Total number duplicated alignments removed: 401216 (10.95%) Duplicated alignments were found at: 249696 different position(s) Total count of deduplicated leftover sequences: 3261342 (89.05% of total) Checking file >>2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam: 4572578 Total number duplicated alignments removed: 553860 (12.11%) Duplicated alignments were found at: 345957 different position(s) Total count of deduplicated leftover sequences: 4018718 (87.89% of total) Checking file >>3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam: 4549927 Total number duplicated alignments removed: 576435 (12.67%) Duplicated alignments were found at: 317721 different position(s) Total count of deduplicated leftover sequences: 3973492 (87.33% of total) Checking file >>4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam: 4527463 Total number duplicated alignments removed: 515221 (11.38%) Duplicated alignments were found at: 327339 different position(s) Total count of deduplicated leftover sequences: 4012242 (88.62% of total) Checking file >>5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam: 4788889 Total number duplicated alignments removed: 605118 (12.64%) Duplicated alignments were found at: 354216 different position(s) Total count of deduplicated leftover sequences: 4183771 (87.36% of total) Checking file >>6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam: 4734709 Total number duplicated alignments removed: 573306 (12.11%) Duplicated alignments were found at: 338393 different position(s) Total count of deduplicated leftover sequences: 4161403 (87.89% of total) Checking file >>7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam: 3976894 Total number duplicated alignments removed: 403813 (10.15%) Duplicated alignments were found at: 263616 different position(s) Total count of deduplicated leftover sequences: 3573081 (89.85% of total) Checking file >>8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in 8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam: 5438263 Total number duplicated alignments removed: 692232 (12.73%) Duplicated alignments were found at: 430170 different position(s) Total count of deduplicated leftover sequences: 4746031 (87.27% of total) Checking file >>zr1394_10_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_10_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_10_s456_trimmed_bismark_bt2.bam: 26440742 Total number duplicated alignments removed: 17149949 (64.86%) Duplicated alignments were found at: 4051647 different position(s) Total count of deduplicated leftover sequences: 9290793 (35.14% of total) Checking file >>zr1394_11_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_11_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_11_s456_trimmed_bismark_bt2.bam: 16280360 Total number duplicated alignments removed: 7765728 (47.70%) Duplicated alignments were found at: 1985022 different position(s) Total count of deduplicated leftover sequences: 8514632 (52.30% of total) Checking file >>zr1394_12_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_12_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_12_s456_trimmed_bismark_bt2.bam: 20852667 Total number duplicated alignments removed: 6676630 (32.02%) Duplicated alignments were found at: 2702461 different position(s) Total count of deduplicated leftover sequences: 14176037 (67.98% of total) Checking file >>zr1394_13_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_13_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_13_s456_trimmed_bismark_bt2.bam: 20464081 Total number duplicated alignments removed: 8773542 (42.87%) Duplicated alignments were found at: 2721914 different position(s) Total count of deduplicated leftover sequences: 11690539 (57.13% of total) Checking file >>zr1394_14_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_14_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_14_s456_trimmed_bismark_bt2.bam: 26512507 Total number duplicated alignments removed: 11489262 (43.34%) Duplicated alignments were found at: 3458285 different position(s) Total count of deduplicated leftover sequences: 15023245 (56.66% of total) Checking file >>zr1394_15_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_15_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_15_s456_trimmed_bismark_bt2.bam: 20793846 Total number duplicated alignments removed: 9547917 (45.92%) Duplicated alignments were found at: 2695647 different position(s) Total count of deduplicated leftover sequences: 11245929 (54.08% of total) Checking file >>zr1394_16_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_16_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_16_s456_trimmed_bismark_bt2.bam: 22191399 Total number duplicated alignments removed: 9778157 (44.06%) Duplicated alignments were found at: 2849964 different position(s) Total count of deduplicated leftover sequences: 12413242 (55.94% of total) Checking file >>zr1394_17_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_17_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_17_s456_trimmed_bismark_bt2.bam: 13373055 Total number duplicated alignments removed: 5209577 (38.96%) Duplicated alignments were found at: 1794464 different position(s) Total count of deduplicated leftover sequences: 8163478 (61.04% of total) Checking file >>zr1394_18_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_18_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_18_s456_trimmed_bismark_bt2.bam: 18831950 Total number duplicated alignments removed: 6252025 (33.20%) Duplicated alignments were found at: 2527208 different position(s) Total count of deduplicated leftover sequences: 12579925 (66.80% of total) Checking file >>zr1394_1_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_1_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_1_s456_trimmed_bismark_bt2.bam: 15141400 Total number duplicated alignments removed: 4480374 (29.59%) Duplicated alignments were found at: 1824236 different position(s) Total count of deduplicated leftover sequences: 10661026 (70.41% of total) Checking file >>zr1394_2_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_2_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_2_s456_trimmed_bismark_bt2.bam: 15412092 Total number duplicated alignments removed: 4686184 (30.41%) Duplicated alignments were found at: 2045834 different position(s) Total count of deduplicated leftover sequences: 10725908 (69.59% of total) Checking file >>zr1394_3_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_3_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_3_s456_trimmed_bismark_bt2.bam: 15387182 Total number duplicated alignments removed: 4468769 (29.04%) Duplicated alignments were found at: 1804376 different position(s) Total count of deduplicated leftover sequences: 10918413 (70.96% of total) Checking file >>zr1394_4_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_4_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_4_s456_trimmed_bismark_bt2.bam: 14451278 Total number duplicated alignments removed: 4498133 (31.13%) Duplicated alignments were found at: 1776509 different position(s) Total count of deduplicated leftover sequences: 9953145 (68.87% of total) Checking file >>zr1394_5_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_5_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_5_s456_trimmed_bismark_bt2.bam: 16372339 Total number duplicated alignments removed: 4080089 (24.92%) Duplicated alignments were found at: 1905839 different position(s) Total count of deduplicated leftover sequences: 12292250 (75.08% of total) Checking file >>zr1394_6_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_6_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_6_s456_trimmed_bismark_bt2.bam: 16168840 Total number duplicated alignments removed: 3828258 (23.68%) Duplicated alignments were found at: 1852339 different position(s) Total count of deduplicated leftover sequences: 12340582 (76.32% of total) Checking file >>zr1394_7_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_7_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_7_s456_trimmed_bismark_bt2.bam: 16017969 Total number duplicated alignments removed: 4832407 (30.17%) Duplicated alignments were found at: 1958540 different position(s) Total count of deduplicated leftover sequences: 11185562 (69.83% of total) Checking file >>zr1394_8_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_8_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_8_s456_trimmed_bismark_bt2.bam: 12549888 Total number duplicated alignments removed: 3674487 (29.28%) Duplicated alignments were found at: 1512253 different position(s) Total count of deduplicated leftover sequences: 8875401 (70.72% of total) Checking file >>zr1394_9_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... samtools view: writing to standard output failed: Broken pipe samtools view: error closing standard output: -1 Output file is: zr1394_9_s456_trimmed_bismark_bt2.deduplicated.bam Total number of alignments analysed in zr1394_9_s456_trimmed_bismark_bt2.bam: 26296063 Total number duplicated alignments removed: 8969760 (34.11%) Duplicated alignments were found at: 3356601 different position(s) Total count of deduplicated leftover sequences: 17326303 (65.89% of total)