Splicing part error when running own data

[liffcardio]

Hi, I set an environment by using the DROP_1.2.2.yaml, then run the demo in the environment. It worked well. Then I use the same environment to run my own data. The expression part worked. But when I run the splicing part using

snakemake -c2 aberrantSplicing

the error came and the log is attached. the yaml file for my data is also attached. Any help is much appreciated. Do you have a clue about this? Thank you very much.

2022-11-15T104746.086646.snakemake.log

projectTitle: "DROP: Detection of RNA Outliers" root: /droptest/Output # root directory of all output objects and tables htmlOutputPath: /droptest/Output/html # path for HTML rendered reports indexWithFolderName: true # whether the root base name should be part of the index name

hpoFile: null # if null, downloads it from webserver sampleAnnotation: /droptest/Data/sample_annotation.tsv # path to sample annotation (see documentation on how to create it)

root: /droptest/Output sampleAnnotation: /droptest/Data/sample_annotation.tsv geneAnnotation: v29: /droptest/Data/gencode.v42.chr_patch_hapl_scaff.annotation.gtf genomeAssembly: hg38 genome: gencode: /droptest/Data/GRCh38.p13.genome.fa

hpoFile: null #relation between genes and phenotypes encoded as HPO term(necessary?)

exportCounts:

specify which gene annotations to include and which

# groups to exclude when exporting counts
geneAnnotations:
    - v29
excludeGroups: null

genome: # path to reference genome sequence in fasta format.

You can define multiple reference genomes in yaml format, ncbi: path/to/ncbi, ucsc: path/to/ucsc

# the keywords that define the path should be in the GENOME column of the sample annotation table
gencode: /droptest/Data/GRCh38.p13.genome.fa 

aberrantExpression: run: true groups:

• cardio fpkmCutoff: 1 implementation: autoencoder padjCutoff: 0.05 zScoreCutoff: 0 maxTestedDimensionProportion: 3 dassie: tssWindow: 500 pasWindow: 1000

aberrantSplicing: run: true groups:

• cardio recount: false longRead: false keepNonStandardChrs: false filter: true minExpressionInOneSample: 20 minDeltaPsi: 0.05 implementation: PCA padjCutoff: 0.1 zScoreCutoff: 0 deltaPsiCutoff : 0.3 maxTestedDimensionProportion: 6

mae: run: true groups:

• cardio gatkIgnoreHeaderCheck: true padjCutoff: 0.05 allelicRatioCutoff: 0.7 addAF: true maxAF: .001 maxVarFreqCohort: 0.05

  VCF-BAM matching

  qcVcf: /droptest/Data/qc_vcf_1000G_hg38.vcf.gz qcGroups:

  • cardio

rnaVariantCalling: run: true groups:

• cardio highQualityVCFs:
• /droptest/Data/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
• /droptest/Data/Homo_sapiens_assembly38.known_indels.vcf.gz dbSNP: /droptest/Data/00-All.vcf.gz repeat_mask: /droptest/Data/hg38_repeatMasker_sorted.bed createSingleVCF: true addAF: true maxAF: .001 maxVarFreqCohort: 0.05 hcArgs: minAlt: 3

tools: gatkCmd: gatk bcftoolsCmd: bcftools samtoolsCmd: samtools

[vyepez88]

Hi, can you please also attach your sample annotation?

[liffcardio]

Thank you for your reply. I tried to keep running the program and found out my bam file did not have read group tag. I added the read group tag and it seems working well at the moment. Thank you very much.