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
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:
I have downloaded the demo data from the following script download_data.sh :