ReportingTools does not finish the HTML plot

[hoelzer]

It seems that all the images are created but then the refactoring of the ReportingTools HTML fails:

From running the part of the R script manually:

reportingTools.html(out.sub, dds, deseq2.res, 1.1, l1, l2, annotation_genes)

Invalid response: 400
{"error":"ID 'NANOZOOG1' not found"}
read in 96941 genes.
./refactor_reportingtools_table.rb:162:in `block (2 levels) in refactor_deseq_html_table': undefined method `[]' for nil:NilClass (NoMethodError)

          pos_part = "<td class=\\"\\">#{$id2pos[feature_id][0]}:#{$id2pos[feature_id][1]}-#{$id2pos[feature_id][2]} (#{$id2pos[feature_id][3]})"
                                                          ^^^
    from ./refactor_reportingtools_table.rb:150:in `each'
    from ./refactor_reportingtools_table.rb:150:in `block in refactor_deseq_html_table'
    from ./refactor_reportingtools_table.rb:144:in `each'
    from ./refactor_reportingtools_table.rb:144:in `refactor_deseq_html_table'
    from ./refactor_reportingtools_table.rb:96:in `initialize'
    from ./refactor_reportingtools_table.rb:274:in `new'
    from ./refactor_reportingtools_table.rb:274:in `<main>'

The command I used (I created that branch bc/ I had issues w/ webgestalt):

DIR='/home/martin/tmp/2022-08-10-rnaseq-fungi-slu/2022-1'
nextflow run hoelzer-lab/rnaflow -r webgestalt-empty-input \
     -profile local,docker --cores 8 --max_cores 8 \
     --reads $DIR/reads/prepared-for-analyses/samples-debugging.csv \
     --genome $DIR/execution/SBY92-genome.csv \
     --annotation $DIR/execution/SBY92-annotation.csv \
     --output $DIR/results-SBY92ref-CBS14_P2_vs_SBY92_P3-debugging \
     --featurecounts_additional_params '-t exon -g gene_id -pBP' \
     -resume

I can share the data to test this as well, if needed, via a private link.