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)