Processing paired-end Bismark output file(s) (SAM format): zr1394_10_s456_trimmed_bismark_bt2.bam zr1394_11_s456_trimmed_bismark_bt2.bam zr1394_12_s456_trimmed_bismark_bt2.bam zr1394_13_s456_trimmed_bismark_bt2.bam zr1394_14_s456_trimmed_bismark_bt2.bam zr1394_15_s456_trimmed_bismark_bt2.bam zr1394_16_s456_trimmed_bismark_bt2.bam zr1394_17_s456_trimmed_bismark_bt2.bam zr1394_18_s456_trimmed_bismark_bt2.bam zr1394_1_s456_trimmed_bismark_bt2.bam zr1394_2_s456_trimmed_bismark_bt2.bam zr1394_3_s456_trimmed_bismark_bt2.bam zr1394_4_s456_trimmed_bismark_bt2.bam zr1394_5_s456_trimmed_bismark_bt2.bam zr1394_6_s456_trimmed_bismark_bt2.bam zr1394_7_s456_trimmed_bismark_bt2.bam zr1394_8_s456_trimmed_bismark_bt2.bam zr1394_9_s456_trimmed_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 >>zr1394_10_s456_trimmed_bismark_bt2.bam<< for signs of file truncation... Now testing Bismark result file zr1394_10_s456_trimmed_bismark_bt2.bam for positional sorting (which would be bad...) The IDs of Read 1 (HWI-C00124:164:C7URDANXX:2:1101:1169:2144_1:N:0:TAGCTT) and Read 2 (HWI-C00124:164:C7URDANXX:2:1101:1312:2151_1:Y:0:TAGCTT) 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) *** Bismark methylation extractor version v0.21.0 *** Trying to determine the type of mapping from the SAM header line of file *deduplicated.bam [FATAL ERROR]: File >>*deduplicated.bam<< did not exist. Please re-specify file names and try again... Found 18 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> zr1394_10_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_11_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_12_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_13_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_14_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_15_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_16_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_17_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_18_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_1_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_2_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_3_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_4_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_5_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_6_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_7_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_8_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr1394_9_s456_trimmed_bismark_bt2_SE_report.html << ============================================================================================================== Using the following alignment report: > zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt < Processing alignment report zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt ... Complete No deduplication report file specified, skipping this step No splitting report file specified, skipping this step No M-bias report file specified, skipping this step No nucleotide coverage report file specified, skipping this step ============================================================================================================== Found Bismark/Bowtie2 single-end files No Bismark/Bowtie2 paired-end BAM files detected No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 18 Bismark BAM file(s)... >> Reading from Bismark report: zr1394_10_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_11_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_12_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_13_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_14_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_15_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_16_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_17_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_18_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_1_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_2_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_3_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_4_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_5_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_6_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_7_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_8_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: zr1394_9_s456_trimmed_bismark_bt2_SE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... Wrote Bismark project summary to >> bismark_summary_report.html << find: ‘*deduplicated.bam’: No such file or directory basename: missing operand Try 'basename --help' for more information. find: ‘*.sorted.bam’: No such file or directory basename: missing operand Try 'basename --help' for more information.