User specifified dedup report: output/13-wgbs/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/reports/Pum1_bismark_report.html <<

==============================================================================================================
Using the following alignment report:		> output/13-wgbs/bismark/Pum1_PE_report.txt <
Processing alignment report output/13-wgbs/bismark/Pum1_PE_report.txt ...
Complete

Using the following deduplication report:	> output/13-wgbs/dedup/Pum1_pe.deduplication_report.txt <
Processing deduplication report output/13-wgbs/dedup/Pum1_pe.deduplication_report.txt ...
Complete

Using the following splitting report:		> output/13-wgbs/methylation/Pum1_pe.deduplicated_splitting_report.txt <
Processing splitting report output/13-wgbs/methylation/Pum1_pe.deduplicated_splitting_report.txt ...
Complete

Using the following M-bias report:		> output/13-wgbs/methylation/Pum1_pe.deduplicated.M-bias.txt <
Processing M-bias report output/13-wgbs/methylation/Pum1_pe.deduplicated.M-bias.txt ...
Complete

Using the following nucleotide coverage report:	> output/13-wgbs/dedup/Pum1_pe.deduplicated.nucleotide_stats.txt <
Processing nucleotide coverage report 'output/13-wgbs/dedup/Pum1_pe.deduplicated.nucleotide_stats.txt' ...
Complete

==============================================================================================================


No Bismark/Bowtie2 single-end BAM files detected
Found Bismark/Bowtie2 paired-end files
No Bismark/HISAT2 single-end BAM files detected
No Bismark/HISAT2 paired-end BAM files detected

Generating Bismark summary report from 1 Bismark BAM file(s)...
>> Reading from Bismark report: Pum1_R1_bismark_bt2_PE_report.txt
No deduplication report present, skipping...
No methylation extractor report present, skipping...
Excluding sample >Pum1_R1_bismark_bt2_pe.bam< for plotting as there were no calls in CpG context

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/fastp
       file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/bismark
       file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/dedup
       file_search | Search path: /mmfs1/gscratch/scrubbed/sr320/github/project-ostrea-chil/output/13-wgbs/methylation
           bismark | Error calculating percentage for Pum1_R1_bismark_bt2_PE_report.txt - ignoring sample.
           bismark | Found 1 alignment reports
           bismark | Found 1 dedup reports
           bismark | Found 1 methextract reports
           bismark | Found 1 bismark bam2nuc reports
             fastp | Found 1 reports
     write_results | Data        : output/13-wgbs/reports/multiqc_13-wgbs_data
     write_results | Report      : output/13-wgbs/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        56.0         6.99     19.5