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  • #1

    [blastp] Warning: CFastaReader: Ignoring invalid residue

    I put the command below. However, the warning messages has been shown. What does this mean and in what cases does this error occur?

    blastp -query trcds.fa -db nr -evalue 0.01 -out blast_to_nr_from_p.out -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore btop" &


    FA FILE

    >Medtr1g005000.1 gene=Medtr1g005000
    MLASPEDHPDARAQTGVHSLHIAGLRPLHAAPVFRRSRVAQLKLNLLFGNTRPGERDISRYCCLSYYFDT
    VVYVKVCTQERCSPPCMTSLSLH.
    >Medtr1g005010.1 gene=Medtr1g005010
    MSGYGQKSICNSFYRENKTHNLSLLGEEHGNLSLLAPESQKFDQLLPSSQAGKLARVVLALRLKAIGFPR
    ERDKEREA.
    >Medtr1g005020.1 gene=Medtr1g005020
    MHSELDCGSTIYRSEEISVVSHPILIISLEGRKTTTETGTKRPPTVTSTPGKAEALLGLRTRKTYFTLAF
    DLEPADLTDGLALPTSMPMDRGPGPTSKESATSGTAPLKKRKKKWKGVFHVKKINWAMFPEVGRLLSGQQ
    SSTSSRLLYDGLPCILGSARSSTLRPSK.


    WARNING MESSAGES

    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 3, position 23
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 6, position 8
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 10, position 28
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 16, position 69
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 23, position 12
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 29, position 54
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 35, position 66
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 38, position 40
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 42, position 42
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 51, position 66
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 55, position 32
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 57, position 55
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 59, position 58
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 64, position 30
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 67, position 5
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 73, position 44
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 76, position 3
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 80, position 0
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 83, position 39
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 85, position 57
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 88, position 6
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 90, position 63
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 94, position 61
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 97, position 26
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 111, position 20
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 115, position 57
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 118, position 58
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 121, position 56
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 126, position 5
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 142, position 5
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 147, position 35
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 150, position 6
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 153, position 6
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 159, position 49
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 162, position 14
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 168, position 55
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 172, position 48
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 175, position 5
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 180, position 23
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 184, position 0
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 186, position 69
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 191, position 23
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 194, position 2
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 198, position 39
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 203, position 40
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 208, position 43
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 212, position 26
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 215, position 30
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 218, position 20
    Warning: (1431.1) CFastaReader: Ignoring invalid residue . at line 225, position 41
    Tags: None
  • #2
    It looks like it doesn't like the periods.

    use sed to get rid of them all.

    Comment

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