Diffatac error

[kopardev]

Activating singularity image /data/CCBR_Pipeliner/SIFs/f1377d9e7c36f023245c48c6243ba596.simg
WARNING: While bind mounting '/data/CCBR_Pipeliner:/data/CCBR_Pipeliner': destination is already in the mount point list
+ TMPDIR=/lscratch/57710933
+ '[' '!' -d /lscratch/57710933 ']'
++ dirname /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/DiffATAC/tn5sites/degs.done
+ outdir=/vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/DiffATAC/tn5sites
+ '[' '!' -d /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/DiffATAC/tn5sites ']'
+ cd /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/DiffATAC/tn5sites
+ echo 'Contrast file:'
+ cat /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/contrasts.tsv
+ '[' '!' -s /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/contrasts.tsv ']'
+ mapfile -t lines
+ '[' 1 -eq 0 ']'
+ for line in "${lines[@]}"
+ IFS=' '
+ read -r g1 g2
+ '[' -z DMS273LM ']'
+ '[' -z DMS273P ']'
+ echo 'Processing contrast: g1=DMS273LM, g2=DMS273P'
+ Rscript /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/scripts/DESeq2_runner.R --countsmatrix /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/fixed_width/counts/ROI.genrich.tn5sites_counts.tsv --genome mm10 --coldata /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/sampleinfo.txt --contrastnumerator DMS273LM --contrastdenominator DMS273P --foldchange 2 --fdr 0.05 --indexcols Geneid --excludecols Chr,Start,End,Strand,Length --outdir /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/DiffATAC/tn5sites --tmpdir /lscratch/57710933 --scriptsdir /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/scripts


processing file: DESeq2.Rmd

genome=mm10
TRUE

Quitting from lines 255-260 [updown] (DESeq2.Rmd)
Error in `.rowNamesDF<-`:
! invalid 'row.names' length
Backtrace:
 1. base::`rownames<-`(`*tmp*`, value = `<chr>`)
 2. base::`rownames<-`(`*tmp*`, value = `<chr>`)
 4. base::`row.names<-.data.frame`(`*tmp*`, value = value)
 5. base::`.rowNamesDF<-`(x, value = value)
Execution halted
[Mon May 19 19:48:02 2025]
Error in rule diffatac:
    jobid: 0
    input: /vf/users/SCLC_scRNA/ccbr1418/ATACseq/aspen/results/peaks/genrich/fixed_width/counts/ROI.genrich.tn5sites_counts.tsv

[kopardev]

• if FDR and FC cutoffs are too strict (FC > 2 and FDR < 0.05 can be strict in ATACseq)
• up_roi and/or down_roi can be zeros. Hence table x can have < 2 rows and 2 rownames