Processing paired-end Bismark output file(s) (SAM format):
20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.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 >>20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam<< for signs of file truncation...



Now testing Bismark result file 20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC_bismark_bt2.bam for positional sorting (which would be bad...)	
The IDs of Read 1 (HWI-ST0747:461:C64YUACXX:1:1101:1192:2181_1:N:0:TTAGGC) and Read 2 (HWI-ST0747:461:C64YUACXX:1:1101:1427:2107_1:N:0:TTAGGC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n)

Processing paired-end Bismark output file(s) (SAM format):
20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.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 >>20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam<< for signs of file truncation...



Now testing Bismark result file 20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG_bismark_bt2.bam for positional sorting (which would be bad...)	
The IDs of Read 1 (HWI-ST0747:461:C64YUACXX:1:1101:1393:2105_1:N:0:ATCACG) and Read 2 (HWI-ST0747:461:C64YUACXX:1:1101:1346:2124_1:N:0:ATCACG) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n)

Processing paired-end Bismark output file(s) (SAM format):
20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.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 >>20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam<< for signs of file truncation...



Now testing Bismark result file 20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC_bismark_bt2.bam for positional sorting (which would be bad...)	
The IDs of Read 1 (HWI-ST0747:461:C64YUACXX:1:1101:1464:2079_1:N:0:CAGATC) and Read 2 (HWI-ST0747:461:C64YUACXX:1:1101:1271:2088_1:N:0:CAGATC) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n)

Processing paired-end Bismark output file(s) (SAM format):
20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.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 >>20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.bam<< for signs of file truncation...



Now testing Bismark result file 20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT_bismark_bt2.bam for positional sorting (which would be bad...)	
The IDs of Read 1 (HWI-ST0747:461:C64YUACXX:1:1101:1123:2118_1:N:0:GCCAAT) and Read 2 (HWI-ST0747:461:C64YUACXX:1:1101:1217:2174_1:N:0:GCCAAT) are not the same. This might be a result of sorting the paired-end SAM/BAM files by chromosomal position which is not compatible with correct methylation extraction. Please use an unsorted file instead (e.g. use samtools sort -n)