Output will be written into the directory: /gscratch/srlab/strigg/analyses/20181101/ Processing paired-end Bismark output file(s) (SAM format): /gscratch/srlab/strigg/analyses/20181101/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam /gscratch/srlab/strigg/analyses/20181101/EPI-44_S41_L005_R1_001_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 >>/gscratch/srlab/strigg/analyses/20181101/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam: 12933060 Total number duplicated alignments removed: 2202000 (17.03%) Duplicated alignments were found at: 866582 different position(s) Total count of deduplicated leftover sequences: 10731060 (82.97% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam: 18819411 Total number duplicated alignments removed: 3289942 (17.48%) Duplicated alignments were found at: 1465170 different position(s) Total count of deduplicated leftover sequences: 15529469 (82.52% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam: 16700962 Total number duplicated alignments removed: 2902189 (17.38%) Duplicated alignments were found at: 1205947 different position(s) Total count of deduplicated leftover sequences: 13798773 (82.62% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam: 16425059 Total number duplicated alignments removed: 3210217 (19.54%) Duplicated alignments were found at: 1167016 different position(s) Total count of deduplicated leftover sequences: 13214842 (80.46% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam: 17801176 Total number duplicated alignments removed: 3686649 (20.71%) Duplicated alignments were found at: 1301846 different position(s) Total count of deduplicated leftover sequences: 14114527 (79.29% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam: 15315195 Total number duplicated alignments removed: 2626295 (17.15%) Duplicated alignments were found at: 1081964 different position(s) Total count of deduplicated leftover sequences: 12688900 (82.85% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam: 14110653 Total number duplicated alignments removed: 2690816 (19.07%) Duplicated alignments were found at: 1046227 different position(s) Total count of deduplicated leftover sequences: 11419837 (80.93% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam: 15451363 Total number duplicated alignments removed: 2999531 (19.41%) Duplicated alignments were found at: 1137914 different position(s) Total count of deduplicated leftover sequences: 12451832 (80.59% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam: 17332078 Total number duplicated alignments removed: 3597067 (20.75%) Duplicated alignments were found at: 1368716 different position(s) Total count of deduplicated leftover sequences: 13735011 (79.25% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam: 16590771 Total number duplicated alignments removed: 3134922 (18.90%) Duplicated alignments were found at: 1179791 different position(s) Total count of deduplicated leftover sequences: 13455849 (81.10% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam: 12824444 Total number duplicated alignments removed: 2239644 (17.46%) Duplicated alignments were found at: 1072351 different position(s) Total count of deduplicated leftover sequences: 10584800 (82.54% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 15678404 Total number duplicated alignments removed: 3148783 (20.08%) Duplicated alignments were found at: 1317281 different position(s) Total count of deduplicated leftover sequences: 12529621 (79.92% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam: 14204942 Total number duplicated alignments removed: 4313588 (30.37%) Duplicated alignments were found at: 2327005 different position(s) Total count of deduplicated leftover sequences: 9891354 (69.63% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam: 16499291 Total number duplicated alignments removed: 5114942 (31.00%) Duplicated alignments were found at: 2744629 different position(s) Total count of deduplicated leftover sequences: 11384349 (69.00% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam: 14957895 Total number duplicated alignments removed: 5875438 (39.28%) Duplicated alignments were found at: 2834725 different position(s) Total count of deduplicated leftover sequences: 9082457 (60.72% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam: 13267422 Total number duplicated alignments removed: 4091356 (30.84%) Duplicated alignments were found at: 2245389 different position(s) Total count of deduplicated leftover sequences: 9176066 (69.16% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam: 9081303 Total number duplicated alignments removed: 2742296 (30.20%) Duplicated alignments were found at: 1480604 different position(s) Total count of deduplicated leftover sequences: 6339007 (69.80% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam: 16691335 Total number duplicated alignments removed: 4980013 (29.84%) Duplicated alignments were found at: 2445777 different position(s) Total count of deduplicated leftover sequences: 11711322 (70.16% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam: 11759160 Total number duplicated alignments removed: 3445175 (29.30%) Duplicated alignments were found at: 1869164 different position(s) Total count of deduplicated leftover sequences: 8313985 (70.70% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam: 11112785 Total number duplicated alignments removed: 2821038 (25.39%) Duplicated alignments were found at: 1479892 different position(s) Total count of deduplicated leftover sequences: 8291747 (74.61% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam: 14896437 Total number duplicated alignments removed: 4386955 (29.45%) Duplicated alignments were found at: 2477168 different position(s) Total count of deduplicated leftover sequences: 10509482 (70.55% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam: 13137265 Total number duplicated alignments removed: 4109932 (31.28%) Duplicated alignments were found at: 2083215 different position(s) Total count of deduplicated leftover sequences: 9027333 (68.72% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam: 11640293 Total number duplicated alignments removed: 3116295 (26.77%) Duplicated alignments were found at: 1555878 different position(s) Total count of deduplicated leftover sequences: 8523998 (73.23% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam: 13917954 Total number duplicated alignments removed: 3882364 (27.89%) Duplicated alignments were found at: 1795882 different position(s) Total count of deduplicated leftover sequences: 10035590 (72.11% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam: 14423415 Total number duplicated alignments removed: 3699607 (25.65%) Duplicated alignments were found at: 1936538 different position(s) Total count of deduplicated leftover sequences: 10723808 (74.35% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam: 19526957 Total number duplicated alignments removed: 6093978 (31.21%) Duplicated alignments were found at: 2948652 different position(s) Total count of deduplicated leftover sequences: 13432979 (68.79% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam: 15686974 Total number duplicated alignments removed: 4456475 (28.41%) Duplicated alignments were found at: 2064215 different position(s) Total count of deduplicated leftover sequences: 11230499 (71.59% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam: 18577099 Total number duplicated alignments removed: 4814378 (25.92%) Duplicated alignments were found at: 2199179 different position(s) Total count of deduplicated leftover sequences: 13762721 (74.08% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam: 11777721 Total number duplicated alignments removed: 3400697 (28.87%) Duplicated alignments were found at: 1750799 different position(s) Total count of deduplicated leftover sequences: 8377024 (71.13% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam: 6124376 Total number duplicated alignments removed: 2201339 (35.94%) Duplicated alignments were found at: 1111310 different position(s) Total count of deduplicated leftover sequences: 3923037 (64.06% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam: 13511277 Total number duplicated alignments removed: 3984035 (29.49%) Duplicated alignments were found at: 2001573 different position(s) Total count of deduplicated leftover sequences: 9527242 (70.51% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam: 10921771 Total number duplicated alignments removed: 3214011 (29.43%) Duplicated alignments were found at: 1619429 different position(s) Total count of deduplicated leftover sequences: 7707760 (70.57% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam: 13850429 Total number duplicated alignments removed: 3604979 (26.03%) Duplicated alignments were found at: 1926218 different position(s) Total count of deduplicated leftover sequences: 10245450 (73.97% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam: 16538141 Total number duplicated alignments removed: 4182646 (25.29%) Duplicated alignments were found at: 2240623 different position(s) Total count of deduplicated leftover sequences: 12355495 (74.71% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam: 8505647 Total number duplicated alignments removed: 2679573 (31.50%) Duplicated alignments were found at: 1516663 different position(s) Total count of deduplicated leftover sequences: 5826074 (68.50% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam: 13470954 Total number duplicated alignments removed: 3956750 (29.37%) Duplicated alignments were found at: 2155026 different position(s) Total count of deduplicated leftover sequences: 9514204 (70.63% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam: 8085337 Total number duplicated alignments removed: 2287403 (28.29%) Duplicated alignments were found at: 1153045 different position(s) Total count of deduplicated leftover sequences: 5797934 (71.71% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam: 11475974 Total number duplicated alignments removed: 2987985 (26.04%) Duplicated alignments were found at: 1392172 different position(s) Total count of deduplicated leftover sequences: 8487989 (73.96% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam: 14321289 Total number duplicated alignments removed: 3855826 (26.92%) Duplicated alignments were found at: 1699307 different position(s) Total count of deduplicated leftover sequences: 10465463 (73.08% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam: 16992612 Total number duplicated alignments removed: 5344954 (31.45%) Duplicated alignments were found at: 2603231 different position(s) Total count of deduplicated leftover sequences: 11647658 (68.55% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam: 15730938 Total number duplicated alignments removed: 4327800 (27.51%) Duplicated alignments were found at: 2219103 different position(s) Total count of deduplicated leftover sequences: 11403138 (72.49% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam: 11600087 Total number duplicated alignments removed: 3506517 (30.23%) Duplicated alignments were found at: 1879035 different position(s) Total count of deduplicated leftover sequences: 8093570 (69.77% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam: 8919143 Total number duplicated alignments removed: 3084323 (34.58%) Duplicated alignments were found at: 1646333 different position(s) Total count of deduplicated leftover sequences: 5834820 (65.42% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam: 8942620 Total number duplicated alignments removed: 2677909 (29.95%) Duplicated alignments were found at: 1500648 different position(s) Total count of deduplicated leftover sequences: 6264711 (70.05% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam: 6639172 Total number duplicated alignments removed: 1925651 (29.00%) Duplicated alignments were found at: 1041289 different position(s) Total count of deduplicated leftover sequences: 4713521 (71.00% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam: 7704618 Total number duplicated alignments removed: 2205404 (28.62%) Duplicated alignments were found at: 1307240 different position(s) Total count of deduplicated leftover sequences: 5499214 (71.38% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam: 11088022 Total number duplicated alignments removed: 3127264 (28.20%) Duplicated alignments were found at: 1534888 different position(s) Total count of deduplicated leftover sequences: 7960758 (71.80% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam: 14915064 Total number duplicated alignments removed: 5591422 (37.49%) Duplicated alignments were found at: 2897008 different position(s) Total count of deduplicated leftover sequences: 9323642 (62.51% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam: 13451347 Total number duplicated alignments removed: 5031715 (37.41%) Duplicated alignments were found at: 2720422 different position(s) Total count of deduplicated leftover sequences: 8419632 (62.59% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam: 16878077 Total number duplicated alignments removed: 5949512 (35.25%) Duplicated alignments were found at: 3317643 different position(s) Total count of deduplicated leftover sequences: 10928565 (64.75% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam: 13055046 Total number duplicated alignments removed: 4831602 (37.01%) Duplicated alignments were found at: 2726221 different position(s) Total count of deduplicated leftover sequences: 8223444 (62.99% of total) Checking file >>/gscratch/srlab/strigg/analyses/20181101/EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in /gscratch/srlab/strigg/analyses/20181101/EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam: 7701905 Total number duplicated alignments removed: 2550122 (33.11%) Duplicated alignments were found at: 1554741 different position(s) Total count of deduplicated leftover sequences: 5151783 (66.89% of total)