Output will be written into the directory: /gscratch/srlab/strigg/analyses/20181004/ Processing paired-end Bismark output file(s) (SAM format): /gscratch/srlab/strigg/analyses/20181004/zr2096_10_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_1_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_2_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_3_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_4_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_5_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_6_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_7_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_8_s1_R1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181004/zr2096_9_s1_R1_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 >>/gscratch/srlab/strigg/analyses/20181004/zr2096_10_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_10_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_10_s1_R1_bismark_bt2_pe.bam: 6293704 Total number duplicated alignments removed: 195026 (3.10%) Duplicated alignments were found at: 163458 different position(s) Total count of deduplicated leftover sequences: 6098678 (96.90% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_1_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_1_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_1_s1_R1_bismark_bt2_pe.bam: 4521751 Total number duplicated alignments removed: 113861 (2.52%) Duplicated alignments were found at: 87450 different position(s) Total count of deduplicated leftover sequences: 4407890 (97.48% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_2_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_2_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_2_s1_R1_bismark_bt2_pe.bam: 7879874 Total number duplicated alignments removed: 296976 (3.77%) Duplicated alignments were found at: 239515 different position(s) Total count of deduplicated leftover sequences: 7582898 (96.23% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_3_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_3_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_3_s1_R1_bismark_bt2_pe.bam: 10170152 Total number duplicated alignments removed: 435847 (4.29%) Duplicated alignments were found at: 329738 different position(s) Total count of deduplicated leftover sequences: 9734305 (95.71% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_4_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_4_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_4_s1_R1_bismark_bt2_pe.bam: 7587322 Total number duplicated alignments removed: 163952 (2.16%) Duplicated alignments were found at: 136766 different position(s) Total count of deduplicated leftover sequences: 7423370 (97.84% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_5_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_5_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_5_s1_R1_bismark_bt2_pe.bam: 10309456 Total number duplicated alignments removed: 436171 (4.23%) Duplicated alignments were found at: 368608 different position(s) Total count of deduplicated leftover sequences: 9873285 (95.77% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_6_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_6_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_6_s1_R1_bismark_bt2_pe.bam: 7735312 Total number duplicated alignments removed: 185029 (2.39%) Duplicated alignments were found at: 153083 different position(s) Total count of deduplicated leftover sequences: 7550283 (97.61% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_7_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_7_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_7_s1_R1_bismark_bt2_pe.bam: 10263535 Total number duplicated alignments removed: 307646 (3.00%) Duplicated alignments were found at: 262839 different position(s) Total count of deduplicated leftover sequences: 9955889 (97.00% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_8_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_8_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_8_s1_R1_bismark_bt2_pe.bam: 9031919 Total number duplicated alignments removed: 303983 (3.37%) Duplicated alignments were found at: 261034 different position(s) Total count of deduplicated leftover sequences: 8727936 (96.63% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181004/zr2096_9_s1_R1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: zr2096_9_s1_R1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181004/zr2096_9_s1_R1_bismark_bt2_pe.bam: 10389381 Total number duplicated alignments removed: 1209178 (11.64%) Duplicated alignments were found at: 999307 different position(s) Total count of deduplicated leftover sequences: 9180203 (88.36% of total)