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CCBR / ASPEN

CCBR pipeline for preliminary QC and peak calling from ATACseq datasets 🌲
https://ccbr.github.io/ASPEN/
MIT License
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aggregate error in DiffATAC reported by Krithika #24

Closed kopardev closed 9 months ago

kopardev commented 10 months ago

log files shows:

Activating singularity image /vf/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/.snakemake/singularity/f1377
d9e7c36f023245c48c6243ba596.simg
WARNING: While bind mounting '/data/CCBR_Pipeliner:/data/CCBR_Pipeliner': destination is already in the mount
 point list
+ TMPDIR=/lscratch/16386359
+ '[' '!' -d /lscratch/16386359 ']'
++ dirname /vf/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/results/peaks/genrich/DiffATAC/degs.done
+ outdir=/vf/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/results/peaks/genrich/DiffATAC
+ cd /vf/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/results/peaks/genrich/DiffATAC
+ Rscript /vf/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/scripts/aggregate_results_runner.R --countsmatr
ix /vf/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/results/peaks/genrich/ROI.counts.tsv --diffatacdir /vf
/users/CCRCCDI/analysis/ccrtegs4/atac_test/test2/results/peaks/genrich/DiffATAC --coldata /vf/users/CCRCCDI/a
nalysis/ccrtegs4/atac_test/test2/results/peaks/genrich/DiffATAC/sampleinfo.txt --foldchange 2 --fdr 0.05 --in
dexcols Geneid --excludecols Chr,Start,End,Strand,Length --diffatacdir /vf/users/CCRCCDI/analysis/ccrtegs4/at
ac_test/test2/results/peaks/genrich/DiffATAC --tmpdir /lscratch/16386359 --scriptsdir /vf/users/CCRCCDI/analy
sis/ccrtegs4/atac_test/test2/scripts

processing file: aggregate_results.Rmd

Quitting from lines 72-102 [allsamplepca] (aggregate_results.Rmd)
Error in `vst()`:
! less than 'nsub' rows,
  it is recommended to use varianceStabilizingTransformation directly
Backtrace:
 1. DESeq2::vst(dds1)
Execution halted
kopardev commented 10 months ago

based off of this ... edit code with if-else statement.