Output will be written into the directory: /home/sam/analyses/20180531_oly_bismark_deduplication/ Processing single-end Bismark output file(s) (SAM format): /home/sam/analyses/20180507_oly_methylseq_bismark/1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_10_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_11_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_12_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_13_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_14_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_15_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_16_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_17_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_18_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_1_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_2_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_3_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_4_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_5_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_6_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_7_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_8_s456_trimmed_bismark_bt2.bam /home/sam/analyses/20180507_oly_methylseq_bismark/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 >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/1_ATCACG_L001_R1_001_trimmed_bismark_bt2.bam: 401918 Total number duplicated alignments removed: 13624 (3.39%) Duplicated alignments were found at: 10092 different position(s) Total count of deduplicated leftover sequences: 388294 (96.61% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/2_CGATGT_L001_R1_001_trimmed_bismark_bt2.bam: 398541 Total number duplicated alignments removed: 12455 (3.13%) Duplicated alignments were found at: 9062 different position(s) Total count of deduplicated leftover sequences: 386086 (96.87% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/3_TTAGGC_L001_R1_001_trimmed_bismark_bt2.bam: 401184 Total number duplicated alignments removed: 15498 (3.86%) Duplicated alignments were found at: 9462 different position(s) Total count of deduplicated leftover sequences: 385686 (96.14% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/4_TGACCA_L001_R1_001_trimmed_bismark_bt2.bam: 402878 Total number duplicated alignments removed: 12403 (3.08%) Duplicated alignments were found at: 9571 different position(s) Total count of deduplicated leftover sequences: 390475 (96.92% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/5_ACAGTG_L001_R1_001_trimmed_bismark_bt2.bam: 398539 Total number duplicated alignments removed: 13674 (3.43%) Duplicated alignments were found at: 9449 different position(s) Total count of deduplicated leftover sequences: 384865 (96.57% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/6_GCCAAT_L001_R1_001_trimmed_bismark_bt2.bam: 394874 Total number duplicated alignments removed: 12839 (3.25%) Duplicated alignments were found at: 8957 different position(s) Total count of deduplicated leftover sequences: 382035 (96.75% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/7_CAGATC_L001_R1_001_trimmed_bismark_bt2.bam: 398470 Total number duplicated alignments removed: 10607 (2.66%) Duplicated alignments were found at: 8442 different position(s) Total count of deduplicated leftover sequences: 387863 (97.34% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/8_ACTTGA_L001_R1_001_trimmed_bismark_bt2.bam: 395985 Total number duplicated alignments removed: 11116 (2.81%) Duplicated alignments were found at: 8286 different position(s) Total count of deduplicated leftover sequences: 384869 (97.19% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_10_s456_trimmed_bismark_bt2.bam: 348453 Total number duplicated alignments removed: 34500 (9.90%) Duplicated alignments were found at: 21036 different position(s) Total count of deduplicated leftover sequences: 313953 (90.10% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_11_s456_trimmed_bismark_bt2.bam: 303938 Total number duplicated alignments removed: 27179 (8.94%) Duplicated alignments were found at: 16512 different position(s) Total count of deduplicated leftover sequences: 276759 (91.06% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_12_s456_trimmed_bismark_bt2.bam: 357770 Total number duplicated alignments removed: 9891 (2.76%) Duplicated alignments were found at: 7518 different position(s) Total count of deduplicated leftover sequences: 347879 (97.24% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_13_s456_trimmed_bismark_bt2.bam: 324641 Total number duplicated alignments removed: 17428 (5.37%) Duplicated alignments were found at: 12024 different position(s) Total count of deduplicated leftover sequences: 307213 (94.63% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_14_s456_trimmed_bismark_bt2.bam: 307789 Total number duplicated alignments removed: 14656 (4.76%) Duplicated alignments were found at: 10305 different position(s) Total count of deduplicated leftover sequences: 293133 (95.24% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_15_s456_trimmed_bismark_bt2.bam: 312101 Total number duplicated alignments removed: 20488 (6.56%) Duplicated alignments were found at: 13495 different position(s) Total count of deduplicated leftover sequences: 291613 (93.44% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_16_s456_trimmed_bismark_bt2.bam: 306132 Total number duplicated alignments removed: 17258 (5.64%) Duplicated alignments were found at: 11600 different position(s) Total count of deduplicated leftover sequences: 288874 (94.36% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_17_s456_trimmed_bismark_bt2.bam: 323587 Total number duplicated alignments removed: 18679 (5.77%) Duplicated alignments were found at: 12798 different position(s) Total count of deduplicated leftover sequences: 304908 (94.23% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_18_s456_trimmed_bismark_bt2.bam: 348298 Total number duplicated alignments removed: 11400 (3.27%) Duplicated alignments were found at: 8398 different position(s) Total count of deduplicated leftover sequences: 336898 (96.73% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_1_s456_trimmed_bismark_bt2.bam: 329419 Total number duplicated alignments removed: 11287 (3.43%) Duplicated alignments were found at: 7962 different position(s) Total count of deduplicated leftover sequences: 318132 (96.57% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_2_s456_trimmed_bismark_bt2.bam: 340656 Total number duplicated alignments removed: 10294 (3.02%) Duplicated alignments were found at: 7716 different position(s) Total count of deduplicated leftover sequences: 330362 (96.98% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_3_s456_trimmed_bismark_bt2.bam: 324066 Total number duplicated alignments removed: 11059 (3.41%) Duplicated alignments were found at: 7665 different position(s) Total count of deduplicated leftover sequences: 313007 (96.59% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_4_s456_trimmed_bismark_bt2.bam: 327730 Total number duplicated alignments removed: 12448 (3.80%) Duplicated alignments were found at: 8829 different position(s) Total count of deduplicated leftover sequences: 315282 (96.20% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_5_s456_trimmed_bismark_bt2.bam: 351188 Total number duplicated alignments removed: 8184 (2.33%) Duplicated alignments were found at: 6214 different position(s) Total count of deduplicated leftover sequences: 343004 (97.67% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_6_s456_trimmed_bismark_bt2.bam: 354174 Total number duplicated alignments removed: 7527 (2.13%) Duplicated alignments were found at: 5757 different position(s) Total count of deduplicated leftover sequences: 346647 (97.87% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_7_s456_trimmed_bismark_bt2.bam: 327124 Total number duplicated alignments removed: 10823 (3.31%) Duplicated alignments were found at: 7689 different position(s) Total count of deduplicated leftover sequences: 316301 (96.69% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_8_s456_trimmed_bismark_bt2.bam: 329450 Total number duplicated alignments removed: 11886 (3.61%) Duplicated alignments were found at: 8635 different position(s) Total count of deduplicated leftover sequences: 317564 (96.39% of total) Checking file >>/home/sam/analyses/20180507_oly_methylseq_bismark/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 /home/sam/analyses/20180507_oly_methylseq_bismark/zr1394_9_s456_trimmed_bismark_bt2.bam: 345938 Total number duplicated alignments removed: 9557 (2.76%) Duplicated alignments were found at: 7288 different position(s) Total count of deduplicated leftover sequences: 336381 (97.24% of total)