Output will be written into the directory: /gscratch/scrubbed/strigg/analyses/20190814_Calig/
Processing paired-end Bismark output file(s) (SAM format):
/gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.bam	/gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_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/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F1_S20_R1_001_val_1_bismark_bt2_pe.bam:	63327608
Total number duplicated alignments removed:	23521989 (37.14%)
Duplicated alignments were found at:	12771810 different position(s)

Total count of deduplicated leftover sequences: 39805619 (62.86% of total)

Checking file >>/gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.bam<< for signs of file truncation...


...passed!
Output file is: Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.deduplicated.bam


Total number of alignments analysed in /gscratch/scrubbed/strigg/analyses/20190814_Calig/Sealice_F2_S22_R1_001_val_1_bismark_bt2_pe.bam:	35458887
Total number duplicated alignments removed:	8834707 (24.92%)
Duplicated alignments were found at:	5486581 different position(s)

Total count of deduplicated leftover sequences: 26624180 (75.08% of total)