Output will be written into the directory: /gscratch/srlab/strigg/analyses/20181011/
Processing paired-end Bismark output file(s) (SAM format):
/gscratch/srlab/strigg/analyses/20181011/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/srlab/strigg/analyses/20181011/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/20181011/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/20181011/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.bam:	6566
Total number duplicated alignments removed:	98 (1.49%)
Duplicated alignments were found at:	52 different position(s)

Total count of deduplicated leftover sequences: 6468 (98.51% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.bam:	6534
Total number duplicated alignments removed:	81 (1.24%)
Duplicated alignments were found at:	32 different position(s)

Total count of deduplicated leftover sequences: 6453 (98.76% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.bam:	6413
Total number duplicated alignments removed:	68 (1.06%)
Duplicated alignments were found at:	32 different position(s)

Total count of deduplicated leftover sequences: 6345 (98.94% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.bam:	6557
Total number duplicated alignments removed:	131 (2.00%)
Duplicated alignments were found at:	63 different position(s)

Total count of deduplicated leftover sequences: 6426 (98.00% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.bam:	6381
Total number duplicated alignments removed:	83 (1.30%)
Duplicated alignments were found at:	54 different position(s)

Total count of deduplicated leftover sequences: 6298 (98.70% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.bam:	6484
Total number duplicated alignments removed:	73 (1.13%)
Duplicated alignments were found at:	29 different position(s)

Total count of deduplicated leftover sequences: 6411 (98.87% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.bam:	6570
Total number duplicated alignments removed:	77 (1.17%)
Duplicated alignments were found at:	45 different position(s)

Total count of deduplicated leftover sequences: 6493 (98.83% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.bam:	6539
Total number duplicated alignments removed:	89 (1.36%)
Duplicated alignments were found at:	55 different position(s)

Total count of deduplicated leftover sequences: 6450 (98.64% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.bam:	6308
Total number duplicated alignments removed:	104 (1.65%)
Duplicated alignments were found at:	53 different position(s)

Total count of deduplicated leftover sequences: 6204 (98.35% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.bam:	6210
Total number duplicated alignments removed:	97 (1.56%)
Duplicated alignments were found at:	41 different position(s)

Total count of deduplicated leftover sequences: 6113 (98.44% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.bam:	6301
Total number duplicated alignments removed:	53 (0.84%)
Duplicated alignments were found at:	36 different position(s)

Total count of deduplicated leftover sequences: 6248 (99.16% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.bam:	6395
Total number duplicated alignments removed:	93 (1.45%)
Duplicated alignments were found at:	49 different position(s)

Total count of deduplicated leftover sequences: 6302 (98.55% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.bam:	5988
Total number duplicated alignments removed:	28 (0.47%)
Duplicated alignments were found at:	22 different position(s)

Total count of deduplicated leftover sequences: 5960 (99.53% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.bam:	5726
Total number duplicated alignments removed:	41 (0.72%)
Duplicated alignments were found at:	25 different position(s)

Total count of deduplicated leftover sequences: 5685 (99.28% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.bam:	6086
Total number duplicated alignments removed:	66 (1.08%)
Duplicated alignments were found at:	30 different position(s)

Total count of deduplicated leftover sequences: 6020 (98.92% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.bam:	5635
Total number duplicated alignments removed:	33 (0.59%)
Duplicated alignments were found at:	26 different position(s)

Total count of deduplicated leftover sequences: 5602 (99.41% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.bam:	6199
Total number duplicated alignments removed:	78 (1.26%)
Duplicated alignments were found at:	39 different position(s)

Total count of deduplicated leftover sequences: 6121 (98.74% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.bam:	5615
Total number duplicated alignments removed:	80 (1.42%)
Duplicated alignments were found at:	38 different position(s)

Total count of deduplicated leftover sequences: 5535 (98.58% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.bam:	5264
Total number duplicated alignments removed:	42 (0.80%)
Duplicated alignments were found at:	20 different position(s)

Total count of deduplicated leftover sequences: 5222 (99.20% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.bam:	5446
Total number duplicated alignments removed:	55 (1.01%)
Duplicated alignments were found at:	24 different position(s)

Total count of deduplicated leftover sequences: 5391 (98.99% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.bam:	6307
Total number duplicated alignments removed:	34 (0.54%)
Duplicated alignments were found at:	25 different position(s)

Total count of deduplicated leftover sequences: 6273 (99.46% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.bam:	6048
Total number duplicated alignments removed:	58 (0.96%)
Duplicated alignments were found at:	33 different position(s)

Total count of deduplicated leftover sequences: 5990 (99.04% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.bam:	5889
Total number duplicated alignments removed:	40 (0.68%)
Duplicated alignments were found at:	27 different position(s)

Total count of deduplicated leftover sequences: 5849 (99.32% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.bam:	5499
Total number duplicated alignments removed:	69 (1.25%)
Duplicated alignments were found at:	36 different position(s)

Total count of deduplicated leftover sequences: 5430 (98.75% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.bam:	6224
Total number duplicated alignments removed:	58 (0.93%)
Duplicated alignments were found at:	33 different position(s)

Total count of deduplicated leftover sequences: 6166 (99.07% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.bam:	5601
Total number duplicated alignments removed:	59 (1.05%)
Duplicated alignments were found at:	31 different position(s)

Total count of deduplicated leftover sequences: 5542 (98.95% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.bam:	6052
Total number duplicated alignments removed:	78 (1.29%)
Duplicated alignments were found at:	46 different position(s)

Total count of deduplicated leftover sequences: 5974 (98.71% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.bam:	6189
Total number duplicated alignments removed:	110 (1.78%)
Duplicated alignments were found at:	52 different position(s)

Total count of deduplicated leftover sequences: 6079 (98.22% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.bam:	6124
Total number duplicated alignments removed:	72 (1.18%)
Duplicated alignments were found at:	36 different position(s)

Total count of deduplicated leftover sequences: 6052 (98.82% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.bam:	6098
Total number duplicated alignments removed:	73 (1.20%)
Duplicated alignments were found at:	34 different position(s)

Total count of deduplicated leftover sequences: 6025 (98.80% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.bam:	6367
Total number duplicated alignments removed:	64 (1.01%)
Duplicated alignments were found at:	40 different position(s)

Total count of deduplicated leftover sequences: 6303 (98.99% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.bam:	5648
Total number duplicated alignments removed:	53 (0.94%)
Duplicated alignments were found at:	29 different position(s)

Total count of deduplicated leftover sequences: 5595 (99.06% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.bam:	5721
Total number duplicated alignments removed:	51 (0.89%)
Duplicated alignments were found at:	31 different position(s)

Total count of deduplicated leftover sequences: 5670 (99.11% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.bam:	6271
Total number duplicated alignments removed:	34 (0.54%)
Duplicated alignments were found at:	29 different position(s)

Total count of deduplicated leftover sequences: 6237 (99.46% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.bam:	5806
Total number duplicated alignments removed:	25 (0.43%)
Duplicated alignments were found at:	17 different position(s)

Total count of deduplicated leftover sequences: 5781 (99.57% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.bam:	5938
Total number duplicated alignments removed:	38 (0.64%)
Duplicated alignments were found at:	25 different position(s)

Total count of deduplicated leftover sequences: 5900 (99.36% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.bam:	5534
Total number duplicated alignments removed:	52 (0.94%)
Duplicated alignments were found at:	36 different position(s)

Total count of deduplicated leftover sequences: 5482 (99.06% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.bam:	6058
Total number duplicated alignments removed:	33 (0.54%)
Duplicated alignments were found at:	27 different position(s)

Total count of deduplicated leftover sequences: 6025 (99.46% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.bam:	5634
Total number duplicated alignments removed:	83 (1.47%)
Duplicated alignments were found at:	41 different position(s)

Total count of deduplicated leftover sequences: 5551 (98.53% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.bam:	6132
Total number duplicated alignments removed:	47 (0.77%)
Duplicated alignments were found at:	32 different position(s)

Total count of deduplicated leftover sequences: 6085 (99.23% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.bam:	5826
Total number duplicated alignments removed:	61 (1.05%)
Duplicated alignments were found at:	37 different position(s)

Total count of deduplicated leftover sequences: 5765 (98.95% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.bam:	6027
Total number duplicated alignments removed:	43 (0.71%)
Duplicated alignments were found at:	20 different position(s)

Total count of deduplicated leftover sequences: 5984 (99.29% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.bam:	6180
Total number duplicated alignments removed:	66 (1.07%)
Duplicated alignments were found at:	40 different position(s)

Total count of deduplicated leftover sequences: 6114 (98.93% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.bam:	6023
Total number duplicated alignments removed:	38 (0.63%)
Duplicated alignments were found at:	26 different position(s)

Total count of deduplicated leftover sequences: 5985 (99.37% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.bam:	6307
Total number duplicated alignments removed:	70 (1.11%)
Duplicated alignments were found at:	36 different position(s)

Total count of deduplicated leftover sequences: 6237 (98.89% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.bam:	6291
Total number duplicated alignments removed:	38 (0.60%)
Duplicated alignments were found at:	24 different position(s)

Total count of deduplicated leftover sequences: 6253 (99.40% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.bam:	6101
Total number duplicated alignments removed:	40 (0.66%)
Duplicated alignments were found at:	26 different position(s)

Total count of deduplicated leftover sequences: 6061 (99.34% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.bam:	5483
Total number duplicated alignments removed:	46 (0.84%)
Duplicated alignments were found at:	28 different position(s)

Total count of deduplicated leftover sequences: 5437 (99.16% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.bam:	5882
Total number duplicated alignments removed:	31 (0.53%)
Duplicated alignments were found at:	21 different position(s)

Total count of deduplicated leftover sequences: 5851 (99.47% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.bam:	6149
Total number duplicated alignments removed:	22 (0.36%)
Duplicated alignments were found at:	15 different position(s)

Total count of deduplicated leftover sequences: 6127 (99.64% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.bam:	6188
Total number duplicated alignments removed:	15 (0.24%)
Duplicated alignments were found at:	10 different position(s)

Total count of deduplicated leftover sequences: 6173 (99.76% of total)

Checking file >>/gscratch/srlab/strigg/analyses/20181011/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/20181011/EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.bam:	6136
Total number duplicated alignments removed:	17 (0.28%)
Duplicated alignments were found at:	14 different position(s)

Total count of deduplicated leftover sequences: 6119 (99.72% of total)