Runtime delta score error about spliceai HOT 8 CLOSED

Could you let me know what the variant under consideration is? (the first variant that has not been annotated by SpliceAI, i.e., INFO field doesn't contain the key SpliceAI)

from spliceai.

I'm running this with ClinVar data's vcf format. Here's the first few lines:

##fileDate=2019-02-11
##source=ClinVar
##reference=GRCh37
##ID=<Description="ClinVar Variation ID">
##INFO=<ID=AF_ESP,Number=1,Type=Float,Description="allele frequencies from GO-ESP">
##INFO=<ID=AF_EXAC,Number=1,Type=Float,Description="allele frequencies from ExAC">
##INFO=<ID=AF_TGP,Number=1,Type=Float,Description="allele frequencies from TGP">
##INFO=<ID=ALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB">
##INFO=<ID=CLNDNINCL,Number=.,Type=String,Description="For included Variant : ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN">
##INFO=<ID=CLNDISDBINCL,Number=.,Type=String,Description="For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.">
##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar review status for the Variation ID">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant">
##INFO=<ID=CLNSIGCONF,Number=.,Type=String,Description="Conflicting clinical significance for this single variant">
##INFO=<ID=CLNSIGINCL,Number=.,Type=String,Description="Clinical significance for a haplotype or genotype that includes this variant. Reported as pairs of VariationID:clinical significance.">
##INFO=<ID=CLNVC,Number=1,Type=String,Description="Variant type">
##INFO=<ID=CLNVCSO,Number=1,Type=String,Description="Sequence Ontology id for variant type">
##INFO=<ID=CLNVI,Number=.,Type=String,Description="the variant's clinical sources reported as tag-value pairs of database and variant identifier">
##INFO=<ID=DBVARID,Number=.,Type=String,Description="nsv accessions from dbVar for the variant">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Gene(s) for the variant reported as gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
##INFO=<ID=MC,Number=.,Type=String,Description="comma separated list of molecular consequence in the form of Sequence Ontology ID|molecular_consequence">
##INFO=<ID=ORIGIN,Number=.,Type=String,Description="Allele origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 -
 uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other">
##INFO=<ID=RS,Number=.,Type=String,Description="dbSNP ID (i.e. rs number)">
##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes. One or more of the following values may be added: 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       949422  475283  G       A       .       .       AF_ESP=0.00546;AF_EXAC=0.00165;AF_TGP=0.00619;ALLELEID=446939;CLNDISDB=MedGen:C4015293,OMIM:616126,Orphanet:ORPHA319563;CLNDN=Immunodeficiency_38_with_basal_ganglia_calcification;CL
NHGVS=NC_000001.10:g.949422G>A;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=ISG15:9636;MC=SO:0001583|missense_variant;ORIGIN=1;RS=143888043
1       949502  542074  C       T       .       .       AF_ESP=0.00015;AF_EXAC=0.00010;ALLELEID=514926;CLNDISDB=MedGen:C4015293,OMIM:616126,Orphanet:ORPHA319563;CLNDN=Immunodeficiency_38_with_basal_ganglia_calcification;CLNHGVS=NC_000001
.10:g.949502C>T;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=ISG15:9636;MC=SO:0001583|missense_variant;ORIGIN=1;RS=150861311```

from spliceai.

Did SpliceAI annotate a few variants before producing this error, or was the error produced right away? You can get the answer to this in the output file.

from spliceai.

Ah I found the error. This is the line that it stopped on.
1 7682000 599309 CGTCTTCTCTGGGTGACCTCGTGTGACCTTGCAATCCCGTCAAGTCTTTGGTTCTGCAGAAACAACTGTCAGATCGGGAGTTAGTCACCTCCAAAGACAGAAACCAAAAACCAAAACAGTGACCTTGTTCTTTCTGTTCATGACCCTGGAGGTATGGGGGGAGGAGGAGGAAGCGGAGATTGGTTTTGCTCGTTAACTCATTATCAGTGACTGAGCGGCTACTCATGGCTGGGAACTTGTTGGGTGCCCTCCATTACACTTCCCTTAATCCTCTCAATGGCTTTTGATATCCTCAGGTAGATGGGAGGATCCCCATTTTACCTGGGAGGGATACAAGGCCAAGAGGGGTTAAGTAACTTGCCCAAGATCACACAGCGTTTGAAGTGGCCAAGGTGAAATTTGATCTAACTTCCACTTGGATGTGTGATTCCACTCCACATCCAAGTTCTTTCCATCATCTGGCTGCAGGCAAGATAACAGATTGGTGTATTCTTTCTATCTTATTTGAATTCCAAAGTTAGTATCCGCTATTGAAAACAGCTGACTTCATTATAACCCATCATTGACTCCTTTCTTTAACAAATAACCAGCAAAACAGAGCGTTCTTTCGGAGTAAGCCTTCCACCACCTGAACTTTGACAACTTTCTCCCTAATGGGTTTCTCCCTGTGAGTATTTGATCTTGGCCACCAGCATGAGCCTATCCTGGTGATCTCAAAATGCTGAGGTTTTTCTTCTGTTAAGAGATTGAATCTTCTGTTCCATGTGGAGGCTTATTCAACATTAAAGCGTTCCTGAACCATTTCATTTATTCAACAAATATTTTCCAAGCCCAGCTCTGGGCCAGATGCCAGGCTCAAGGCTTAGCAAGCCAGACAGATGTGGAGCCGCCATCATGGAACTCGGCCCTCACAGGCCATTGTCCTTGGCTTTCCAGACTGAACCTCTGTGCTTTCTTGTTTCACGGCTGTTTTCCTGAATGCTCCCTGTGAGCCCGAGTCTGTCCTGAGGTCTTCGTCCCTATTCCCTGTGCCTGAATCCTTTCCTCTCCCAGAGCTCCCCACAGCTGGCTTCTTTTTATCATCTCAGATACAGCTGAAGGTTCCATCCTCAGAGGCCTTCTCAAGCTCGCTGGCTAAATTCTCCACCCACCCCCATTTTTTATGCTCATACCACTTCATGCCATCCAGAACCACCTTATTCTTTATTCCAATGTTTATAGCTCGTCTCTTCCATGCTCTTTGAGGGCAGAGTCTTAGACTTGGTCACAGTAGACCCCAAATGTAGGCCAGTCCCTGGTATCTTGTGGTTCTTGAGAGCTAATCTGTTGAATGAATGAATGAATGAATGAATGAGGGAATTAATGAACACCCTGCAAAGCAAGTGCCACAGTTACCCCTACTCTATAGAAGAGGCAGCTGTTCCTCTAAAAGGCTGAGAATCCCACCTCAGAGCTACCTGCAGGAGAGTGGGTGAGCTGGGACCCCAGTCATTTCAGGTTAACTGAAGGGAAAGCCTGACTTCCCATCAGCTCCACACACTGAGTCCTTTCTCCTAGAAATGAAGGAAACACAAAGAAGTCACTAAGAAGGCACCTCGCCCTCAAGCATCTGAAACCCTCAGTTGGAAATTTGACTGCAACCTCTGCCTCCTGGGTTCAAGGGATTCTCCTGCCTCAGCCCCCCAAGTAGCTGGGACTACAGGCATGCGCCACCACACCCAGCTAATTCTGTATTTTCAGGAGAGATGGGATTTCACCATGTTGGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGTTCCGCCCGCCTCGGCCTCCCGAGGTGCTGGGATTACAGAAGCTCTTTTTCAACATTGCCTTTTAGATCCCCTTTCCCATCAGCTTCCTCCAAAGGAGCTGCTGGCTTGATTTACCTGCAGCCACCGCAATTAATTGCTGTCCCCTGGTAGCTAACATCTCTTAACAGCTCCATAGCAACAGTGGTTTCCAAATGCCAGAAAGTGTTTTTTCCAAGGGGACTCTATCCTCGACGCAAAATAGAACATTTTGAGTGAAATTTAAACACAGTTTTTGAACGGTGCTGTTCTGATTTCTTCACACTTCACAAATGCTTTCTTTGCAAACATGGGTGTCCCAGTTACCCTGGGCTGGTGCCAAGGCCCTCAGCCCAGCTTCTGTTTTCTCAGCTTCAAGGCAGCCGTGGTAAGACCTAAAAACAAACAGGGAGCGAGTGCTGTGGGTCTCCCCGCTAAGGGGTTGCCTTGCGCCTGTGCAGAGATGAGGACCACAGTTTGTCTCCCACACCAGCTGTGATCAATTGGTGATGACAACGCAGAACCCTGCCTATGCGATTTCTGGGACCCCATCTGAGCTTAGTGGGAAAGAGTGCCATCCGCCATGGTTCCAGTGCAGAATTCCAAGGGCCAAGATGGGGAGTAGGGATTTGTGTATGAGTGGTTGGTTGGAACAAATCATCCTGGTATACCACTGCTCCCACAGGTGGAAACAGAGAAACTGGGTTAAAATGAAGACTCCAGTAAATTCGCATGCAGAAGTACCCAGAAAGGCCCTTGCCATGTCCTTCACTCTGCCTTGGTGAAGGTGGAAGAGATGAAGGGAGAGGGTGATGGGTGGGTGGTGGGTGTGCTGGCCACCGACTGGCACAGCCCCCAGCACAGGGGCTGTCTCTAGTGACCGATCCAGGATGAGTGTCCCCATTCAGATGCAGTCAACCCACCACTGATTCAACCAACACTTGCTGACTGCCTATCAGGGAATACATTTCCTTCTGATGCACACTCTGCTCTCAGGAAGTCTGGGGTCCAGAGAGGGAATGGAGGTGCCAGCCAGCCTGAAGATCAGTGGAAAGAGTGAGGCTGGCTGATGCTGCAGGAGAGACACAGAGGACTGTCAGGGGAGTCCCAAAGGGAATGAAATTATTTTGGTTGGAAGGATAAAGGGAGGCTGGAAGGACAGTGTGACGTTGGATCTGGGTCTTGACA C . . ALLELEID=590571;CLNDISDB=MedGen:C3553661,OMIM:614756,Orphanet:ORPHA314647;CLNDN=Cerebellar_ataxia,_nonprogressive,_with_mental_retardation;CLNHGVS=NC_000001.10:g.7682001_7685000del;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Pathogenic;CLNVC=Deletion;CLNVCSO=SO:0000159;GENEINFO=CAMTA1:23261;ORIGIN=32

from spliceai.

This makes sense. It turns out that the software cannot handle deletions larger than 500. Thank you for bringing this to our attention, we will fix this in the next commit. For now, if you could just delete such variants, you should be fine.

from spliceai.

Another issue

  File "/home/ubuntu/anaconda3/envs/tensorflow_p36/bin/spliceai", line 11, in <module>
    sys.exit(main())
  File "/home/ubuntu/anaconda3/envs/tensorflow_p36/lib/python3.6/site-packages/spliceai/__main__.py", line 53, in main
    scores = get_delta_scores(record, ann)
  File "/home/ubuntu/anaconda3/envs/tensorflow_p36/lib/python3.6/site-packages/spliceai/utils.py", line 72, in get_delta_scores
    for j in range(len(record.alts)):
TypeError: object of type 'NoneType' has no len()

The value:

1 11854442 187893 C . . . AF_ESP=8e-05;AF_EXAC=2e-05;ALLELEID=185770;CLNDISDB=MedGen:C1856058,OMIM:236250;CLNDN=Homocysteinemia_due_to_MTHFR_deficiency;CLNHGVS=NC_000001.10:g.11854442C>T;CLNREVSTAT=no_assertion_criteria_provided;CLNSIG=Pathogenic;CLNVC=single_nucleotide_variant;CLNVCSO=SO:0001483;GENEINFO=MTHFR:4524;MC=SO:0001819|synonymous_variant;ORIGIN=1;RS=367585605;

from spliceai.

I am not entirely sure what this variant is. As earlier, please delete this variant (and others which have a "." in the ALT column) in the input file before running the software. Do let us know if you run into more edge cases like these, and we will incorporate them into the annotation software so that it skips such variants automatically instead of crashing.

from spliceai.

The current release (v1.2) should ignore these edge cases automatically.

from spliceai.