User specifified dedup report: output/13-wgbs-hapa/dedup/Pum1_pe.deduplication_report.txt A specific output filename was specified: Pum1_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Pum1_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Pum1_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Pum1_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Pum1_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Pum1_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Pum1_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Pum1_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Pum1_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Pum1_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Pum1_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Pum1_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Qui1_pe.deduplication_report.txt A specific output filename was specified: Qui1_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Qui1_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Qui1_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Qui1_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Qui1_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Qui1_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Qui1_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Qui1_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Qui1_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Qui1_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Qui1_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Qui1_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Qui2_pe.deduplication_report.txt A specific output filename was specified: Qui2_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Qui2_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Qui2_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Qui2_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Qui2_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Qui2_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Qui2_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Qui2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Qui2_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Qui2_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Qui2_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Qui2_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Qui3_pe.deduplication_report.txt A specific output filename was specified: Qui3_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Qui3_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Qui3_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Qui3_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Qui3_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Qui3_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Qui3_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Qui3_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Qui3_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Qui3_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Qui3_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Qui3_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Qui4_pe.deduplication_report.txt A specific output filename was specified: Qui4_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Qui4_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Qui4_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Qui4_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Qui4_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Qui4_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Qui4_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Qui4_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Qui4_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Qui4_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Qui4_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Qui4_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Rio1_pe.deduplication_report.txt A specific output filename was specified: Rio1_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Rio1_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Rio1_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Rio1_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Rio1_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Rio1_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Rio1_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Rio1_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Rio1_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Rio1_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Rio1_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Rio1_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Rio2_pe.deduplication_report.txt A specific output filename was specified: Rio2_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Rio2_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Rio2_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Rio2_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Rio2_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Rio2_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Rio2_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Rio2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Rio2_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Rio2_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Rio2_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Rio2_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Rio3_pe.deduplication_report.txt A specific output filename was specified: Rio3_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Rio3_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Rio3_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Rio3_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Rio3_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Rio3_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Rio3_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Rio3_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Rio3_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Rio3_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Rio3_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Rio3_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== User specifified dedup report: output/13-wgbs-hapa/dedup/Rio4_pe.deduplication_report.txt A specific output filename was specified: Rio4_bismark_report.html. Using that one instead of deriving the filename Writing Bismark HTML report to >> output/13-wgbs-hapa/reports/Rio4_bismark_report.html << ============================================================================================================== Using the following alignment report: > output/13-wgbs-hapa/bismark/Rio4_PE_report.txt < Processing alignment report output/13-wgbs-hapa/bismark/Rio4_PE_report.txt ... Complete Using the following deduplication report: > output/13-wgbs-hapa/dedup/Rio4_pe.deduplication_report.txt < Processing deduplication report output/13-wgbs-hapa/dedup/Rio4_pe.deduplication_report.txt ... Complete Using the following splitting report: > output/13-wgbs-hapa/methylation/Rio4_pe.deduplicated_splitting_report.txt < Processing splitting report output/13-wgbs-hapa/methylation/Rio4_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > output/13-wgbs-hapa/methylation/Rio4_pe.deduplicated.M-bias.txt < Processing M-bias report output/13-wgbs-hapa/methylation/Rio4_pe.deduplicated.M-bias.txt ... Complete Using the following nucleotide coverage report: > output/13-wgbs-hapa/dedup/Rio4_pe.deduplicated.nucleotide_stats.txt < Processing nucleotide coverage report 'output/13-wgbs-hapa/dedup/Rio4_pe.deduplicated.nucleotide_stats.txt' ... Complete ============================================================================================================== Generating Bismark summary report from 9 Bismark BAM file(s)... >> Reading from Bismark report: Pum1_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Qui1_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Qui2_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Qui3_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Qui4_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Rio1_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Rio2_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Rio3_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... >> Reading from Bismark report: Rio4_PE_report.txt No deduplication report present, skipping... No methylation extractor report present, skipping... Wrote Bismark project summary to >> ../reports/bismark_summary_report.html << /// MultiQC v1.30 version_check | MultiQC Version v1.35 now available! file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs-hapa/fastp file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs-hapa/bismark file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs-hapa/dedup file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs-hapa/methylation bismark | Found 9 alignment reports bismark | Found 9 dedup reports bismark | Found 9 methextract reports bismark | Found 9 bismark bam2nuc reports fastp | Found 9 reports write_results | Data : output/13-wgbs-hapa/reports/multiqc_13-wgbs_data write_results | Report : output/13-wgbs-hapa/reports/multiqc_13-wgbs.html multiqc | MultiQC complete sample pairs_analysed mapping_pct dup_pct CpG_meth_pct CHG_meth_pct CHH_meth_pct Pum1 38376265 65.7 7.01 19.8 0.6 0.6 Qui1 38720614 67.2 7.01 19.2 0.8 0.8 Qui2 36627727 66.9 6.40 22.0 0.7 0.8 Qui3 41446330 67.4 7.12 20.9 0.7 0.8 Qui4 34443887 67.3 5.30 19.6 0.7 0.7 Rio1 41519830 68.5 6.40 20.6 0.6 0.7 Rio2 35781535 67.5 6.18 20.4 0.7 0.7 Rio3 32773197 67.9 4.81 21.5 0.8 0.8 Rio4 39972937 68.2 4.99 20.8 0.7 0.8