ERROR ~ Error executing process > 'vcf:annotate (15)'

Caused by:
  Process `vcf:annotate (15)` terminated with an error exit status (140)


Command executed [/mnt/shared/tools/vip-8.0.0/./modules/vcf/templates/annotate.sh]:

  #!/bin/bash
  set -euo pipefail
  
  capiceOutputPath="GIAB_HG002_chunk_0_capice_output.tsv.gz"
  vcfCapiceAnnotatedPath="GIAB_HG002_chunk_0_capice_annotated.vcf.gz"
  capiceInputPath="GIAB_HG002_chunk_0_capice_input.tsv"
  capiceOutputPath="GIAB_HG002_chunk_0_capice_output.tsv.gz"
  
  annot_sv() {
    local args=()
    args+=("-SVinputFile" "GIAB_HG002_chunk_0_normalized.vcf.gz")
    args+=("-outputDir" ".")
    args+=("-outputFile" "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv")
    args+=("-genomeBuild" "GRCh38")
    args+=("-annotationMode" "full")
    args+=("-annotationsDir" "/mnt/shared/tools/vip-8.0.0/resources/annotsv/v3.3.6")
    if [ -n "" ]; then
      args+=("-hpo" "")
    fi
    ${CMD_ANNOTSV} "${args[@]}"
    
    # AnnotSV potentially exists with the following message without creating a .tsv file
    # ############################################################################
    # No SV to annotate in the SVinputFile - Exit without error.
    # ############################################################################
    
    # write an empty file so that the AnnotSV VEP plugin is always used to ensure an equal number of VEP fields accross chunks
    if [[ ! -f "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv" ]]; then
      echo -e "AnnotSV_ranking_score\tAnnotSV_ranking_criteria\tACMG_class\n" > "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv"
    elif [[ "GRCh38" == "GRCh38" ]]; then
      # workaround for https://github.com/lgmgeo/AnnotSV/issues/152 that might fail for some chromosomes e.g. GRCh37 MT maps to GRCh38 chrM)
      mv "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv" "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv.tmp"
      awk -v FS='\t' -v OFS='\t' 'NR>1 {$2 = "chr"$2} 1' "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv.tmp" > "GIAB_HG002_chunk_0_normalized.vcf.gz.tsv"
    fi
  }
  
  capice() {
    capice_vep
    capice_bcftools
    #only run capice if there a variants with annotations, e.g. <STR> only VCF files do not yield any annotated lines
    if [ "$(wc -l < "${capiceInputPath}")" -gt 1 ]; then
      capice_predict
    fi
  }
  
  capice_vep() {
    local args=()
    args+=("--input_file" "GIAB_HG002_chunk_0_normalized.vcf.gz")
    args+=("--format" "vcf")
    args+=("--output_file" "${vcfCapiceAnnotatedPath}")
    args+=("--vcf")
    args+=("--compress_output" "bgzip")
    args+=("--no_stats")
    args+=("--fasta" "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz")
    args+=("--offline")
    args+=("--cache")
    args+=("--dir_cache" "/mnt/shared/tools/vip-8.0.0/resources/vep/cache")
    args+=("--species" "homo_sapiens")
    args+=("--assembly" "GRCh38")
    args+=("--refseq")
    args+=("--exclude_predicted")
    args+=("--use_given_ref")
    args+=("--symbol")
    args+=("--flag_pick_allele")
    args+=("--sift" "s")
    args+=("--polyphen" "s")
    args+=("--total_length")
    args+=("--shift_3prime" "1")
    args+=("--allele_number")
    args+=("--numbers")
    args+=("--dont_skip")
    args+=("--allow_non_variant")
    args+=("--buffer_size" "1000")
    args+=("--fork" "4")
    args+=("--dir_plugins" "/mnt/shared/tools/vip-8.0.0/resources/vep/plugins")
    args+=("--plugin" "SpliceAI,snv=/mnt/shared/tools/vip-8.0.0/resources/GRCh38/spliceai_scores.masked.snv.hg38.vcf.gz,indel=/mnt/shared/tools/vip-8.0.0/resources/GRCh38/spliceai_scores.masked.indel.hg38.vcf.gz")
    args+=("--plugin" "Grantham")
    args+=("--custom" "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/hg38.phyloP100way.bw,phyloP,bigwig,exact,0")
    args+=("--plugin" "gnomAD,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/gnomad.total.v4.1.sites.stripped.tsv.gz")
  
    ${CMD_VEP} "${args[@]}"
  }
  
  capice_bcftools() {
    local -r format="%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n"
    local -r header="CHROM\tPOS\tREF\tALT\t"
    local -r capiceInputPathHeaderless="${capiceInputPath}.headerless"
  
    local args=()
    args+=("+split-vep")
    args+=("-d")
    args+=("-f" "${format}\n")
    args+=("-A" "tab")
    args+=("-o" "${capiceInputPathHeaderless}")
    args+=("${vcfCapiceAnnotatedPath}")
  
    ${CMD_BCFTOOLS} "${args[@]}"
  
    echo -e "${header}$(${CMD_BCFTOOLS} +split-vep -l "${vcfCapiceAnnotatedPath}" | cut -f 2 | tr '\n' '\t' | sed 's/\t$//')" | cat - "${capiceInputPathHeaderless}" > "${capiceInputPath}"
  }
  
  capice_predict() {
    local args=()
    args+=("predict")
    args+=("--input" "${capiceInputPath}")
    args+=("--output" "${capiceOutputPath}")
    args+=("--model" "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/capice_model_v5.1.2-v3.ubj")
  
    ${CMD_CAPICE} "${args[@]}"
    if [ ! -f "${capiceOutputPath}" ]; then
      echo -e "CAPICE error: failed to produce output" 1>&2
      exit 1
    fi
  }
  
  stranger() {
    local -r vcf="${1}"
    local -r vcfOut="${2}"
  
    local args=()
    args+=("--repeats-file" "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/variant_catalog_grch38_fixed.json")
    args+=("--loglevel" "ERROR")
    args+=("${vcf}")
  
    ${CMD_STRANGER} "${args[@]}" | ${CMD_BCFTOOLS} view --no-version --threads "4" --output-type "z" --output-file "${vcfOut}"
  }
  
  vep_preprocess() {
    local -r vcf="${1}"
    local -r vcfOut="${2}"
  
    # use <CNV:TR> symbolic alleles instead of <STR..> to align with VCF v4.4 section 5.6 and enable VEP annotation
    # 1. add CNV:TR ALT header
    # 2. remove STR[number] ALT headers
    # 3. rename <STR[number]> symbolic alleles to <CNV:TR>
    echo -e '##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance">' > vcf_header_cnv-tr.txt
    ${CMD_BCFTOOLS} annotate --header-lines vcf_header_cnv-tr.txt --no-version --threads "4" "${vcf}" | \
      sed '/^##ALT=<ID=STR[0-9]\+,/d' | \
      sed 's/<STR[0-9]\+>/<CNV:TR>/g' | \
      ${CMD_BCFTOOLS} view --no-version --threads "4" --output-type "z" --output-file "${vcfOut}"
  }
  
  vep() {
    local -r vcf="${1}"
    local -r vcfPreprocessed="preprocessed_${vcf}"
  
    vep_preprocess "${vcf}" "${vcfPreprocessed}"
  
    local args=()
    args+=("--input_file" "${vcfPreprocessed}")
    args+=("--format" "vcf")
    args+=("--output_file" "GIAB_HG002_chunk_0_annotated.vcf.gz")
    args+=("--vcf")
    args+=("--compress_output" "bgzip")
    args+=("--no_stats")
    args+=("--fasta" "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz")
    args+=("--offline")
    args+=("--cache")
    args+=("--dir_cache" "/mnt/shared/tools/vip-8.0.0/resources/vep/cache")
    args+=("--species" "homo_sapiens")
    args+=("--assembly" "GRCh38")
    args+=("--refseq")
    args+=("--exclude_predicted")
    args+=("--use_given_ref")
    args+=("--symbol")
    args+=("--flag_pick_allele")
    args+=("--sift" "s")
    args+=("--polyphen" "s")
    args+=("--total_length")
    args+=("--pubmed")
    args+=("--shift_3prime" "1")
    args+=("--allele_number")
    args+=("--numbers")
    args+=("--dont_skip")
    args+=("--allow_non_variant")
    args+=("--buffer_size" "1000")
    args+=("--fork" "4")
    args+=("--hgvs")
    args+=("--pubmed")
    args+=("--dir_plugins" "/mnt/shared/tools/vip-8.0.0/resources/vep/plugins")
    args+=("--plugin" "Grantham")
    args+=("--plugin" "SpliceAI,snv=/mnt/shared/tools/vip-8.0.0/resources/GRCh38/spliceai_scores.masked.snv.hg38.vcf.gz,indel=/mnt/shared/tools/vip-8.0.0/resources/GRCh38/spliceai_scores.masked.indel.hg38.vcf.gz")
    args+=("--plugin" "Capice,${capiceOutputPath}")
    args+=("--plugin" "UTRannotator,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/uORF_5UTR_PUBLIC.txt")
    args+=("--custom" "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/hg38.phyloP100way.bw,phyloP,bigwig,exact,0")
    args+=("--safe")
  
    if [ -n "" ]; then
      args+=("--plugin" "Hpo,/mnt/shared/tools/vip-8.0.0/resources/hpo_20240404.tsv,")
    fi
    if [ -n "" ]; then
      args+=("--plugin" "GADO,,/mnt/shared/tools/vip-8.0.0/resources/biomart_ensembl_entrez_mapping.txt")
    fi
    args+=("--plugin" "Inheritance,/mnt/shared/tools/vip-8.0.0/resources/inheritance_20240115.tsv")
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/vkgl_consensus_20240701.tsv" ] && [ -n "1" ]; then
      args+=("--plugin" "VKGL,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/vkgl_consensus_20240701.tsv,1")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/gnomad.total.v4.1.sites.stripped.tsv.gz" ]; then
      args+=("--plugin" "gnomAD,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/gnomad.total.v4.1.sites.stripped.tsv.gz")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/clinvar_20241126-stripped.tsv.gz" ]; then
        args+=("--plugin" "ClinVar,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/clinvar_20241126-stripped.tsv.gz")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/annotsv/v3.3.6" ]; then
      # when you change the field also update the empty file header in this file
      args+=("--plugin" "AnnotSV,GIAB_HG002_chunk_0_normalized.vcf.gz.tsv,AnnotSV_ranking_score;AnnotSV_ranking_criteria;ACMG_class")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/AlphScore_final_20230825_stripped_GRCh38.tsv.gz" ]; then
      args+=("--plugin" "AlphScore,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/AlphScore_final_20230825_stripped_GRCh38.tsv.gz")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_ncER_perc.bed.gz" ]; then
      args+=("--plugin" "ncER,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_ncER_perc.bed.gz")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_FATHMM-MKL_NC.tsv.gz" ]; then
      args+=("--plugin" "FATHMM_MKL_NC,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_FATHMM-MKL_NC.tsv.gz")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_ReMM.tsv.gz" ]; then
      args+=("--plugin" "ReMM,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_ReMM.tsv.gz")
    fi
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_GREEN-DB.bed.gz" ] && [ "false" = true  ]; then
      args+=("--plugin" "GREEN_DB,/mnt/shared/tools/vip-8.0.0/resources/GRCh38/GRCh38_GREEN-DB.bed.gz")
    fi
    
    ${CMD_VEP} "${args[@]}"
  }
  
  index () {
    ${CMD_BCFTOOLS} index --csi --output "GIAB_HG002_chunk_0_annotated.vcf.gz.csi" --threads "4" "GIAB_HG002_chunk_0_annotated.vcf.gz"
    ${CMD_BCFTOOLS} index --stats "GIAB_HG002_chunk_0_annotated.vcf.gz" > "GIAB_HG002_chunk_0_annotated.vcf.gz.stats"
  }
  
  main () {
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/annotsv/v3.3.6" ]; then
      annot_sv
    fi
    capice
  
    local vepInputPath=""
    if [ -n "/mnt/shared/tools/vip-8.0.0/resources/GRCh38/variant_catalog_grch38_fixed.json" ]; then
      stranger "GIAB_HG002_chunk_0_normalized.vcf.gz" "stranger_GIAB_HG002_chunk_0_normalized.vcf.gz"
      vepInputPath="stranger_GIAB_HG002_chunk_0_normalized.vcf.gz"
    else
      vepInputPath="GIAB_HG002_chunk_0_normalized.vcf.gz"
    fi
  
    vep "${vepInputPath}"
    index
  }
  
  main "$@"

Command exit status:
  140

Command output:
  	...Breakpoints annotations
  		...GC content annotation
  		...Repeat annotation
  		...Gap annotation
  		...Segmental duplication annotation
  		...ENCODE blacklist annotation
  	...Gene-based annotations
  		...20220617_ACMG.tsv
  		(78 gene identifiers and 1 annotations columns: ACMG)
  		...20220906_ClinGenAnnotations.tsv
  		(1480 gene identifiers and 2 annotations columns: HI, TS)
  		...20200713_HI.tsv.gz
  		(19124 gene identifiers and 1 annotations columns: DDD_HI_percent)
  		...20191219_ExAC.CNV-Zscore.annotations.tsv.gz
  		(15673 gene identifiers and 3 annotations columns: ExAC_delZ, ExAC_dupZ, ExAC_cnvZ)
  		...20201023_GeneIntolerance-Zscore.annotations.tsv.gz
  		(18241 gene identifiers and 2 annotations columns: ExAC_synZ, ExAC_misZ)
  		...20220902_GenCC.tsv
  		(4615 gene identifiers and 4 annotations columns: GenCC_disease, GenCC_moi, GenCC_classification, GenCC_pmid)
  		...20220905_OMIM-1-annotations.tsv.gz
  		(16250 gene identifiers and 1 annotations columns: OMIM_ID)
  		...20220905_OMIM-2-annotations.tsv.gz
  		(16250 gene identifiers and 2 annotations columns: OMIM_phenotype, OMIM_inheritance)
  		...20220905_morbid.tsv.gz
  		(12998 gene identifiers and 1 annotations columns: OMIM_morbid)
  		...20220905_morbidCandidate.tsv.gz
  		(3467 gene identifiers and 1 annotations columns: OMIM_morbid_candidate)
  		...20201106_gnomAD.LOEUF.pLI.annotations.tsv.gz
  		(19451 gene identifiers and 3 annotations columns: LOEUF_bin, GnomAD_pLI, ExAC_pLI)
  
  ...annotation in progress (December 06 2024 - 10:15)
  
  ...writing of ./GIAB_HG002_chunk_0_normalized.vcf.gz.tsv (December 06 2024 - 10:15)
  
  ...output columns annotation (December 06 2024 - 10:15):
  	AnnotSV_ID;SV_chrom;SV_start;SV_end;SV_length;SV_type;Samples_ID;ID;REF;ALT;QUAL;FILTER;INFO;FORMAT;SAMPLE;Annotation_mode;CytoBand;Gene_name;Gene_count;Tx;Tx_start;Tx_end;Overlapped_tx_length;Overlapped_CDS_length;Overlapped_CDS_percent;Frameshift;Exon_count;Location;Location2;Dist_nearest_SS;Nearest_SS_type;Intersect_start;Intersect_end;RE_gene;P_gain_phen;P_gain_hpo;P_gain_source;P_gain_coord;P_loss_phen;P_loss_hpo;P_loss_source;P_loss_coord;P_ins_phen;P_ins_hpo;P_ins_source;P_ins_coord;po_P_gain_phen;po_P_gain_hpo;po_P_gain_source;po_P_gain_coord;po_P_gain_percent;po_P_loss_phen;po_P_loss_hpo;po_P_loss_source;po_P_loss_coord;po_P_loss_percent;P_snvindel_nb;P_snvindel_phen;B_gain_source;B_gain_coord;B_gain_AFmax;B_loss_source;B_loss_coord;B_loss_AFmax;B_ins_source;B_ins_coord;B_ins_AFmax;B_inv_source;B_inv_coord;B_inv_AFmax;po_B_gain_allG_source;po_B_gain_allG_coord;po_B_gain_someG_source;po_B_gain_someG_coord;po_B_loss_allG_source;po_B_loss_allG_coord;po_B_loss_someG_source;po_B_loss_someG_coord;TAD_coordinate;ENCODE_experiment;GC_content_left;GC_content_right;Repeat_coord_left;Repeat_type_left;Repeat_coord_right;Repeat_type_right;Gap_left;Gap_right;SegDup_left;SegDup_right;ENCODE_blacklist_left;ENCODE_blacklist_characteristics_left;ENCODE_blacklist_right;ENCODE_blacklist_characteristics_right;ACMG;HI;TS;DDD_HI_percent;ExAC_delZ;ExAC_dupZ;ExAC_cnvZ;ExAC_synZ;ExAC_misZ;GenCC_disease;GenCC_moi;GenCC_classification;GenCC_pmid;OMIM_ID;OMIM_phenotype;OMIM_inheritance;OMIM_morbid;OMIM_morbid_candidate;LOEUF_bin;GnomAD_pLI;ExAC_pLI;AnnotSV_ranking_score;AnnotSV_ranking_criteria;ACMG_class
  
  
  ...AnnotSV is done with the analysis (December 06 2024 - 10:15)
  2024-12-06 10:15:45 - Fetching regulatory features for plugin: gnomAD
  Successfully exported CAPICE datafile to: %s GIAB_HG002_chunk_0_capice_output.tsv.gz
  2024-12-06 11:16:18 - Fetching regulatory features for plugin: Capice
  2024-12-06 11:16:18 - Fetching regulatory features for plugin: Inheritance
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: VKGL
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: gnomAD
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: ClinVar
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: AnnotSV
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: ncER
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: FATHMM_MKL_NC
  2024-12-06 11:16:20 - Fetching regulatory features for plugin: ReMM

Command error:
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3870261 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3870271 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3870272 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3870278 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3870277 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871243 : WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871241 : WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871244 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871280 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871281 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871268 : WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3871269 : WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: 3872198 : WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ncER' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.
  WARNING: Plugin 'ReMM' went wrong: ERROR: Expecting no more than one score for a position.

Work dir:
  /mnt/flashblade01/scratch/s.wielhouwer/vip_testing/output/.nxf.work/3b/ec09fbf08397b034607f4b0565eebf

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '/mnt/flashblade01/scratch/s.wielhouwer/vip_testing/output/.nxf.log' file for details
ERROR ~ Unexpected error [InvocationTargetException]

 -- Check script '/mnt/shared/tools/vip-8.0.0/./modules/vcf/./utils.nf' at line: 91 or see '/mnt/flashblade01/scratch/s.wielhouwer/vip_testing/output/.nxf.log' file for more details
ERROR ~ Unexpected error [InvocationTargetException]

 -- Check script '/mnt/shared/tools/vip-8.0.0/./modules/vcf/./utils.nf' at line: 91 or see '/mnt/flashblade01/scratch/s.wielhouwer/vip_testing/output/.nxf.log' file for more details
ERROR ~ Unexpected error [InvocationTargetException]

 -- Check script '/mnt/shared/tools/vip-8.0.0/./modules/vcf/./utils.nf' at line: 91 or see '/mnt/flashblade01/scratch/s.wielhouwer/vip_testing/output/.nxf.log' file for more details
ERROR ~ Unexpected error [InvocationTargetException]

 -- Check script '/mnt/shared/tools/vip-8.0.0/./modules/vcf/./utils.nf' at line: 91 or see '/mnt/flashblade01/scratch/s.wielhouwer/vip_testing/output/.nxf.log' file for more details

s.wielhouwer@gs-hpc-login01:/mnt/flashblade01/scratch/s.wielhouwer/vip_testing$ /mnt/shared/tools/vip-8.0.0/vip -w vcf -i samplesheet2.tsv -o output -p slurm