ADD_MOST_SEVERE_CSQ error when using Sniffles1 as SV-caller

[fellen31]

Description of the bug

Perhaps because there's a variant without CSQ:

##VEP-command-line='vep --appris --assembly GRCh38 --biotype --buffer_size 500 --cache --cache_version 110 --canonical --ccds --compress_output bgzip --database 0 --dir_cache [PATH]/vep_cache --dir_plugins . --distance 5000 --domains --exclude_predicted --fasta GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta --force_overwrite --fork --format vcf --hgvs --humdiv --input_file NIST_query.vcf --max_sv_size 248387328 --merged --no_progress --no_stats --numbers --offline --output_file NIST_svs_cnvs_merged_annotated.vcf.gz --per_gene --plugin pLI,grch38_vep_112_pli_values_-v1.0-.txt --polyphen p --protein --regulatory --sift p --symbol --tsl --uniprot --vcf' #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002 HG003 HG004 chr1 257667 8 N <INV> . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr1;END=248935507;ZMW=3;STD_quant_start=2.3094;STD_quant_stop=4.6188;Kurtosis_quant_start=0;Kurtosis_quant_stop=0;SVTYPE=INV;SUPTYPE=SR;SVLEN=248677840;STRANDS=--;STRANDS2=0,3,3,0;RE=3;REF_strand=25,28;Strandbias_pval=0.24513;AF=0.0566038;FOUND_IN=sniffles;set=HG003_sniffles_svs;FOUNDBY=1;HG003_sniffles_svs_CHROM=8|chr1;HG003_sniffles_svs_POS=8|257667;HG003_sniffles_svs_QUAL=8|.;HG003_sniffles_svs_FILTERS=8|PASS;HG003_sniffles_svs_SAMPLE=8|HG003|GT:0/1|DR:50|DV:3;HG003_sniffles_svs_INFO=8|PRECISE|SVMETHOD:Snifflesv1.0.12|CHR2:chr1|END:248935507|ZMW:3|STD_quant_start:2.3094|STD_quant_stop:4.6188|Kurtosis_quant_start:0|Kurtosis_quant_stop:0|SVTYPE:INV|SUPTYPE:SR|SVLEN:248677840|STRANDS:--|STRANDS2:0:3:3:0|RE:3|REF_strand:25:28|Strandbias_pval:0.24513|AF:0.0566038|FOUND_IN:sniffles;svdb_origin=HG003_sniffles_svs;SUPP_VEC=010;set=svs;FOUNDBY=1;svs_CHROM=8|chr1;svs_POS=8|257667;svs_QUAL=8|.;svs_FILTERS=8|PASS;svs_SAMPLE=8|HG002|GT:./.|DR:.|DV:.|HG003|GT:0/1|DR:50|DV:3|HG004|GT:./.|DR:.|DV:.;svs_INFO=8|PRECISE|SVMETHOD:Snifflesv1.0.12|CHR2:chr1|END:248935507|ZMW:3|STD_quant_start:2.3094|STD_quant_stop:4.6188|Kurtosis_quant_start:0|Kurtosis_quant_stop:0|SVTYPE:INV|SUPTYPE:SR|SVLEN:248677840|STRANDS:--|STRANDS2:0:3:3:0|RE:3|REF_strand:25:28|Strandbias_pval:0.24513|AF:0.0566038|FOUND_IN:sniffles|set:HG003_sniffles_svs|FOUNDBY:1|svdb_origin:HG003_sniffles_svs|SUPP_VEC:010;svdb_origin=svs;SUPP_VEC=01 GT:DR:DV ./.:.:. 0/1:50:3 ./.:.:.

Command used and terminal output

INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
  Traceback (most recent call last):
    File "/vulpes/proj/ugc/ngi2016002/workflows/nallo/workflow/fellen31-skierfe_fix-trio-repeats/fix_trio_repeats/bin/add_most_severe_consequence.py", line 192, in <module>
      sys.exit(main())
    File "/vulpes/proj/ugc/ngi2016002/workflows/nallo/workflow/fellen31-skierfe_fix-trio-repeats/fix_trio_repeats/bin/add_most_severe_consequence.py", line 188, in main
      write_csq_annotated_vcf(in_vcf, out_vcf, var_csq)
    File "/vulpes/proj/ugc/ngi2016002/workflows/nallo/workflow/fellen31-skierfe_fix-trio-repeats/fix_trio_repeats/bin/add_most_severe_consequence.py", line 142, in write_csq_annotated_vcf
      mscsq = construct_most_severe_consequence_info(line, allele_ind, csq_ind, hgnc_ind, var_csq)
    File "/vulpes/proj/ugc/ngi2016002/workflows/nallo/workflow/fellen31-skierfe_fix-trio-repeats/fix_trio_repeats/bin/add_most_severe_consequence.py", line 75, in construct_most_severe_consequence_info
      transcripts, allele_ind, csq_ind, hgnc_ind, var_csq
  UnboundLocalError: local variable 'transcripts' referenced before assignment

Relevant files

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System information

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