Help with JASPAR enrichment - I'm probably missing something to add to the enichment

[T B]

Hello!

So I have a list of differentially expressed transcripts with ensembl_trasncript_ids from the same data I collected transcript ids for the non-DE genes AND the DE genes. Using the UCSC table browser I made a BED file with 2kb of sequence upstream of the TSS (from UCSC). the universe file and the userset look like this.

#chrom  chromStart      chromEnd        name    score   strand  GeneName
chr1    192807038       192814275       ENST00000235382.7       0       +       RGS2
chr1    93446130        93556659        ENST00000260506.12      0       +       FNBP1L
chr1    150280553       150289093       ENST00000290363.6       0       +       CIART
chr1    236833615       236902418       ENST00000366576.3       0       +       MTR

One has about 100 transcripts and the universe has about 30k

I run the script like this,

JASPAR_enrich.sh oneSetBg /dataVol/data/Murry/LOLA_DB/JASPAR2020_LOLA_hg38/ CBP_txPlus2k.bed Universe_txPlus2k.bed ./output jaspar.elixir.no/api/v1/matrix/ 1

I ran with one core.

in the outputs file I get this:

allEnrichments_swarm.pdf      Batch_11  Batch_16  Batch_5  JASPAR_enrichment_beeswarmplot.png
allEnrichments_swarm.pdf.png  Batch_12  Batch_17  Batch_6  success
allEnrichments.tsv            Batch_13  Batch_2   Batch_7
Batch_1                       Batch_14  Batch_3   Batch_8
Batch_10                      Batch_15  Batch_4   Batch_9

The "allenrichments_swarm.pdf" has some data but it is listed as "N.S." (attached)

When I run the script I get this error right away,

Error in fisher.test(matrix(c(support, b, c, d), 2, 2), alternative = fisherAlternative) :
  all entries of 'x' must be nonnegative and finite
Calls: runLOLA -> [ -> [.data.table -> fisher.test
Execution halted

I only get this error once and the script still runs.

Loading required package: IRanges
Loading required package: Seqinfo
Converting GRanges to GRangesList.
Calculating unit set overlaps...
Calculating universe set overlaps...
Calculating Fisher scores...
./output/Batch_5/col_MA0601.1.tsv
./output/Batch_5/col_MA0602.1.tsv
./output/Batch_5/col_MA0603.1.tsv

Finally before dying I get this error

Error in `geom_beeswarm()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error:
! Aesthetics are not valid data columns.
✖ The following aesthetics are invalid:
• `x = family`
• `colour = family`
• `angle = class`

No beeswarm plot is made

The output file AllEnrichments.tsv looks like this:

 userSet oddsRatio       matrixID        pValueLog       rnkPV   TF_name dataSource
1       Inf     MA0732.1        0.380777804281658       1       EGR3    jaspar
1       Inf     MA0659.3        0.269311300593277       1       Mafg    jaspar
1       Inf     MA1712.1        0.265336572341969       1       ZNF454  jaspar
1       Inf     MA0163.1        0.261362272015915       1       PLAG1   jaspar
1       Inf     MA0024.3        0.197831589544242       1       E2F1    jaspar

So my questions are. Do I need to add any annotation to get decent plots.  I am including 2kb upstream of  "+" strand and "-" strand.

I've not used these tools before. i guess I could download the example dataset to check its formatting, but I figured I would ask here to see if I am doing something crazy. Any information or advice is greatly apprecaited.

TIA

Matt