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DESEq error on MonoallelicExpression_pipeline_MAE_deseq_mae_R module using demo dataset #601
Description
Hi, I am running the whole DROP pipeline (version-1.4.0) on the test data and I am getting the below error, may I know how can I fix this?
Below is my config file:
projectTitle: Detection of RNA Outlier Pipeline
htmlOutputPath: Output/html
indexWithFolderName: true
root: Output
sampleAnnotation: Data/sample_annotation_relative.tsv
geneAnnotation:
v29: Data/gencode_annotation_trunc.gtf
genomeAssembly: hg19
genome:
ncbi: Data/chr21_ncbi.fa
ucsc: Data/chr21.fa
hpoFile: /projects/pipelines/drop_demo/hpo_genes.tsv.gz
random_seed: true
exportCounts:
geneAnnotations:
- v29
excludeGroups:
- mae
- outrider_external
- fraser_external
aberrantExpression:
run: true
groups:
- outrider
- outrider_external
fpkmCutoff: 1
implementation: autoencoder
padjCutoff: 1
zScoreCutoff: 0
genesToTest: "Data/genes_to_test.yaml"
maxTestedDimensionProportion: 3
yieldSize: 2000000
aberrantSplicing:
run: true
groups:
- fraser
- fraser_external
recount: true
longRead: false
keepNonStandardChrs: false
filter: false
minExpressionInOneSample: 20
quantileMinExpression: 10
quantileForFiltering: 0.95
minDeltaPsi: 0.05
implementation: PCA
padjCutoff: 1
maxTestedDimensionProportion: 6
genesToTest: "Data/genes_to_test.yaml"
### FRASER1 configuration for demo dataset
FRASER_version: "FRASER"
deltaPsiCutoff : 0.05
mae:
run: true
groups:
- mae
gatkIgnoreHeaderCheck: true
padjCutoff: .5
allelicRatioCutoff: 0.7
addAF: false
maxAF: .001
maxVarFreqCohort: 1
# VCF-BAM matching
qcVcf: Data/qc_vcf_1000G.vcf.gz
qcGroups:
- mae
dnaRnaMatchCutoff: 0.85
rnaVariantCalling:
run: true
groups:
- batch_0
- batch_1
highQualityVCFs:
- Data/high_confidence_snps.vcf.gz
- Data/high_confidence_indels.vcf.gz
dbSNP: Data/dbSNP_chr21.vcf.gz
repeat_mask: Data/repeat_mask_chr21.bed
createSingleVCF: true
addAF: false
maxAF: 0.001
maxVarFreqCohort: 1
hcArgs: null
minAlt: 3
yieldSize: 100000
tools:
gatkCmd: gatk
bcftoolsCmd: bcftools
samtoolsCmd: samtools
I have downloaded the demo data from the following script download_data.sh :
#!/bin/bash
set -e
# get data
resource_url="https://github.com/gagneurlab/drop_demo_data/archive/refs/heads/main.zip"
tmpdir="$(dirname "$(mktemp)")"
wget -nc -P $tmpdir $resource_url
# if the directory Data does not exist
if [ ! -d "Data" ]; then
unzip "$tmpdir/main.zip"
mv drop_demo_data-main/Data Data
rm -rf drop_demo_data-main
else
echo "Data directory not empty, is not updated"
fi
# unzip fasta
cd ./Data
if [ ! -f "chr21.fa" ]; then gunzip chr21.fa.gz; fi
Activity
AtaJadidAhari commentedon Mar 25, 2025
Hi, I suspect that running GATK has failed. Can you share the content of
Output/processed_data/mae/allelic_counts/HG00096--HG00096.csv.gz?Roshanshafiha commentedon Mar 26, 2025
Hi , I have attached the output for the file below :
vyepez88 commentedon Apr 4, 2025
Hi, for some reason it seems that the header of the table is twice. Can you pleas manually remove one of the two headers and rerun the pipeline?