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...
Captured error message: '[main_samview] fail to read the header from "105M_1_bismark_bt2_pe.bam".'

[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...

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):
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...
Captured error message: '[main_samview] fail to read the header from "239M_1_bismark_bt2_pe.bam".'

[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...


 *** Bismark methylation extractor version v0.24.2 ***

Trying to determine the type of mapping from the SAM header line of file 107M_1_bismark_bt2_pe.deduplicated.bam
[main_samview] fail to read the header from "107M_1_bismark_bt2_pe.deduplicated.bam".
Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28)

Summarising Bismark methylation extractor parameters:
===============================================================
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:	<Chromosome> <Start Position> <End Position> <Methylation Percentage>
coverage format:	<Chromosome> <Start Position> <End Position> <Methylation Percentage> <count methylated> <count non-methylated>

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 >>107M_1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation...
Captured error message: '[main_samview] fail to read the header from "107M_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...