Processing paired-end Bismark output file(s) (SAM format): 105M_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 >>105M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.bam: 4864 Total number duplicated alignments removed: 290 (5.96%) Duplicated alignments were found at: 264 different position(s) Total count of deduplicated leftover sequences: 4574 (94.04% of total) Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.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 >>105M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.deduplicated.bam: 4574 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4574 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.deduplicated.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 >>105M_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.deduplicated.deduplicated.bam: 4574 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4574 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.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 >>105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 105M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam: 4574 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4574 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 106M_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 >>106M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 106M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 106M_1_bismark_bt2_pe.bam: 4749 Total number duplicated alignments removed: 374 (7.88%) Duplicated alignments were found at: 336 different position(s) Total count of deduplicated leftover sequences: 4375 (92.12% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_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 >>107M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 107M_1_bismark_bt2_pe.bam: 4683 Total number duplicated alignments removed: 330 (7.05%) Duplicated alignments were found at: 300 different position(s) Total count of deduplicated leftover sequences: 4353 (92.95% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.deduplicated.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 >>107M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in 107M_1_bismark_bt2_pe.deduplicated.bam: 4353 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4353 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.deduplicated.deduplicated.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 >>107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 107M_1_bismark_bt2_pe.deduplicated.deduplicated.bam: 4353 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4353 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.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 >>107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.deduplicated.bam Total number of alignments analysed in 107M_1_bismark_bt2_pe.deduplicated.deduplicated.deduplicated.bam: 4353 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4353 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 239M_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 >>239M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 239M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 239M_1_bismark_bt2_pe.bam: 4744 Total number duplicated alignments removed: 315 (6.64%) Duplicated alignments were found at: 284 different position(s) Total count of deduplicated leftover sequences: 4429 (93.36% of total) Processing paired-end Bismark output file(s) (SAM format): 239M_1_bismark_bt2_pe.deduplicated.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 >>239M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 239M_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in 239M_1_bismark_bt2_pe.deduplicated.bam: 4429 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4429 (100.00% of total) Processing paired-end Bismark output file(s) (SAM format): 270M_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 >>270M_1_bismark_bt2_pe.bam<< for signs of file truncation... ...passed! Output file is: 270M_1_bismark_bt2_pe.deduplicated.bam Total number of alignments analysed in 270M_1_bismark_bt2_pe.bam: 4693 Total number duplicated alignments removed: 355 (7.56%) Duplicated alignments were found at: 326 different position(s) Total count of deduplicated leftover sequences: 4338 (92.44% of total) Processing paired-end Bismark output file(s) (SAM format): 270M_1_bismark_bt2_pe.deduplicated.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 >>270M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... ...passed! Output file is: 270M_1_bismark_bt2_pe.deduplicated.deduplicated.bam Total number of alignments analysed in 270M_1_bismark_bt2_pe.deduplicated.bam: 4338 Total number duplicated alignments removed: 0 (0.00%) Duplicated alignments were found at: 0 different position(s) Total count of deduplicated leftover sequences: 4338 (100.00% of total) *** Bismark methylation extractor version v0.24.2 *** Trying to determine the type of mapping from the SAM header line of file 105M_1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28) Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 28 Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated Merge CHG and CHH context to non-CpG context specified Output will be written to the current directory ('/mmfs1/gscratch/scrubbed/sr320/github/project-mytilus-methylation/output/04-bismark-pipeline') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>105M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Captured error message: '[main_samview] fail to read the header from "105M_1_bismark_bt2_pe.deduplicated.bam".' [ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...