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No CDS checked #574

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hongphuc265 opened this issue Jan 1, 2025 · 0 comments
Open

No CDS checked #574

hongphuc265 opened this issue Jan 1, 2025 · 0 comments

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@hongphuc265
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Describe the issue
A clear and concise description of what the issue is.
Hello, i'm building database of latest release of GRCh38.p14, also create database of MANE v1.4 from NCBI.
To Reproduce

  1. SnpEff version: 5.2
  2. Genome version: GCF_000001405.40
  3. SnpEff full command line: ./script buildDbNcbi.sh GRCh38.p14.latest (* i have add it into snpEff.config and supply file cds.fa, sequences.fa, genes.gff, protein.fa that i downloaded from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/
    The same problem also occur when i try to create database of MANE v1.4)
  4. Output / Error message: Please include detailed infomration, such as transcript ID, VCF line output, etc.
    FATAL ERROR: No CDS checked. This might be caused by differences in FASTA file transcript IDs respect to database's transcript's IDs.
    Transcript IDs from database (sample):
    'rna-NM_001080383.2'
    'id-IGLV2-11'
    'rna-NR_183126.1'
    'rna-XM_047424472.1'
    'rna-NM_001278292.2'
    'rna-XR_007060357.1'
    'rna-XR_007058166.1'
    'rna-XR_001744432.3'
    'rna-NM_001083591.1'
    'XM_005248274.6'
    'XM_005248275.6'
    'NM_182977.3'
    'NM_001331026.2'
    'XM_006714461.5'
    'XM_011514001.4'
    'NM_012343.4'
    'XM_017009293.3'
    'rna-MIR3156-1'
    'rna-NR_024447.1'
    'rna-XM_047437394.1'
    'NM_014765.3'
    'gene-RN7SL563P'
    Transcript IDs from database (fasta file):
    'lcl|NC_000008.11_prot_XP_047277390.1_58506'
    'lcl|NC_000014.9_prot_XP_005267366.1_92044'
    'lcl|NC_000016.10_prot_NP_071938.1_96958'
    'lcl|NC_000005.10_prot_NP_114172.1_37583'
    'lcl|NC_000010.11_prot_XP_024303815.1_68353'
    'lcl|NC_000019.10_prot_XP_047295528.1_112640'
    'lcl|NC_000019.10_prot_NP_443079.1_112195'
    'lcl|NT_113891.3_prot_XP_054185775.1_140029'
    'lcl|NC_000002.12_prot_XP_047301166.1_17520'
    'lcl|NC_000012.12_prot_XP_024304833.1_83596'
    'lcl|NC_000022.11_prot_NP_996838.1_124172'
    'lcl|NT_167251.2_prot_XP_016885668.1_138732'
    '2_prot_NP_542433'
    '2_prot_NP_542434'
    'lcl|NC_000020.11_prot_XP_047296453.1_120196'
    'lcl|NC_000015.10_prot_XP_011520549.1_95998'
    'lcl|NC_000011.10_prot_NP_001333266.1_73106'
    'lcl|NC_000023.11_prot_XP_047298147.1_128738'
    'lcl|NC_000001.11_prot_NP_004506.2_8031'
    'lcl|NC_000005.10_prot_NP_001243390.1_39337'
    'lcl|NC_000021.9_prot_NP_001001577.1_123226'
    'lcl|NC_000012.12_prot_XP_005253595.1_79826'
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