Hi all actually i am running custom blastx with sorghum database with transdecoder longest.orfs query by using following command
blastx -query ~/Transdecoder_out/Rio/longest_orfs.pep -db ~/blastdb/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.pep -num_threads 8 -max_target_seqs 1 -outfmt 6 > Rio.outfmt6
and i am getting error like this
FASTA-Reader: Ignoring invalid residues at position(s): On line 846340: 6-7, 9, 17-18, 22, 24-26, 43, 47, 49 FASTA-Reader: Ignoring invalid residues at position(s): On line 846342: 5-6, 8, 10, 12, 14-15, 18-19, 21, 23-25, 33, 37, 39-40, 44, 47-49 FASTA-Reader: Ignoring invalid residues at position(s): On line 846344: 4, 8, 15, 22-23, 28, 43 FASTA-Reader: Ignoring invalid residues at position(s): On line 846346: 5, 10, 14, 29 FASTA-Reader: Ignoring invalid residues at position(s): On line 846348: 2, 4, 7-8, 16, 22, 25, 27 FASTA-Reader: Ignoring invalid residues at position(s): On line 846350: 3-5, 7-8, 12, 17, 23 FASTA-Reader: Ignoring invalid residues at position(s): On line 846352: 3, 8-9, 17, 20, 25, 27-28, 33, 37, 43-45 FASTA-Reader: Ignoring invalid residues at position(s): On line 846354: 1-2, 7-8, 12, 18, 22 FASTA-Reader: Ignoring invalid residues at position(s): On line 846356: 6, 8-9, 13, 15, 18-19, 21-22 FASTA-Reader: Ignoring invalid residues at position(s): On line 846358: 10, 16-19 FASTA-Reader: Ignoring invalid residues at position(s): On line 846360: 2, 4-5, 8, 12, 14-15, 19 FASTA-Reader: Ignoring invalid residues at position(s): On line 846362: 5, 7, 9-10, 15, 17-18 FASTA-Reader: Ignoring invalid residues at position(s): On line 846364: 3-8, 10, 16-17 FASTA-Reader: Ignoring invalid residues at position(s): On line 846366: 2, 5-6, 9-10, 12, 15-16 FASTA-Reader: Ignoring invalid residues at position(s): On line 846368: 2, 4, 11, 13, 16 FASTA-Reader: Ignoring invalid residues at position(s): On line 846370: 2-5, 8-9, 13-15 FASTA-Reader: Ignoring invalid residues at position(s): On line 846372: 2-3, 5, 9, 14 FASTA-Reader: Ignoring invalid residues at position(s): On line 846374: 1-2, 5, 9-11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846376: 2-3, 7, 10-11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846378: 2-3, 6-8, 10-11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846380: 3, 6, 12-13, 18, 23-24, 29, 34-35, 39, 44, 46, 53, 57, 61, 72, 77, 79 FASTA-Reader: Ignoring invalid residues at position(s): On line 846382: 2, 11, 14-15, 18, 20-21, 23, 25, 29-31, 37, 39 FASTA-Reader: Ignoring invalid residues at position(s): On line 846384: 4, 8, 14-15, 21-22, 26-27, 32 FASTA-Reader: Ignoring invalid residues at position(s): On line 846386: 4, 6-7, 9, 11-13, 15, 18, 21 FASTA-Reader: Ignoring invalid residues at position(s): On line 846388: 2-4, 9, 12, 14-15, 17, 19, 21, 23 FASTA-Reader: Ignoring invalid residues at position(s): On line 846390: 2, 4, 8, 10, 12, 16-17, 22 FASTA-Reader: Ignoring invalid residues at position(s): On line 846392: 1-2, 6-7, 9-10, 12, 14-17 FASTA-Reader: Ignoring invalid residues at position(s): On line 846394: 3, 6, 9-10, 13 FASTA-Reader: Ignoring invalid residues at position(s): On line 846396: 7, 10, 12 FASTA-Reader: Ignoring invalid residues at position(s): On line 846398: 3-4, 8-9, 12, 14, 19, 21, 23, 26, 33, 35-43, 46-47, 49-51, 55-56, 58-59, 62-63, 65, 67, 70, 72, 77, 80, 84, 87, 92-93, 98, 102, 104 FASTA-Reader: Ignoring invalid residues at position(s): On line 846400: 3, 6-8, 12, 16, 26, 32, 38, 41, 45, 49-51, 53-55, 57 FASTA-Reader: Ignoring invalid residues at position(s): On line 846402: 3, 11-13, 15-16, 19, 21, 23, 25-26, 28, 30-32, 34, 36-39 FASTA-Reader: Ignoring invalid residues at position(s): On line 846404: 5, 7, 10, 14-15, 19, 27, 30, 35 FASTA-Reader: Ignoring invalid residues at position(s): On line 846406: 2, 5, 7, 12-13, 16, 18, 21 FASTA-Reader: Ignoring invalid residues at position(s): On line 846408: 6, 11-14, 16 FASTA-Reader: Ignoring invalid residues at position(s): On line 846410: 1-2, 5-6, 8, 10-11, 13-14 FASTA-Reader: Ignoring invalid residues at position(s): On line 846412: 4, 6, 8, 11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846414: 4-5, 10 FASTA-Reader: Ignoring invalid residues at position(s): On line 846416: 1, 3, 5, 7, 11, 15-18, 20, 22, 25, 27, 33-34, 37, 41-42, 46, 56, 58, 63, 68-69, 71, 75, 79, 88, 90, 92, 94-100 FASTA-Reader: Ignoring invalid residues at position(s): On line 846418: 5-7, 10, 14-18, 20, 22, 24, 27, 29-30 FASTA-Reader: Ignoring invalid residues at position(s): On line 846420: 2, 6, 11, 13-14, 16-17, 20-21, 24 FASTA-Reader: Ignoring invalid residues at position(s): On line 846422: 1-3, 5, 7-8, 12, 14, 16, 23-24 FASTA-Reader: Ignoring invalid residues at position(s): On line 846424: 1, 5-6, 9, 12, 16, 21 FASTA-Reader: Ignoring invalid residues at position(s): On line 846426: 5, 9-13, 16, 18, 20 FASTA-Reader: Ignoring invalid residues at position(s): On line 846428: 3, 5, 7, 10-11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846430: 2-3, 5, 10 FASTA-Reader: Ignoring invalid residues at position(s): On line 846432: 9, 12, 14-15, 17, 26-27, 30-32, 35-36, 39, 42, 67, 69-71, 74, 81 FASTA-Reader: Ignoring invalid residues at position(s): On line 846434: 1, 6, 14, 16, 20, 22-23, 35, 41, 45, 48, 51, 54-55, 57, 63, 65, 67, 70, 76 FASTA-Reader: Ignoring invalid residues at position(s): On line 846436: 2-5, 7-8, 12, 14, 18, 21, 23, 35, 37-38, 41, 43-45, 47, 50-54, 58, 60, 62-63, 67 FASTA-Reader: Ignoring invalid residues at position(s): On line 846438: 2-4, 9, 11, 23, 28, 32, 35-36, 38-39 FASTA-Reader: Ignoring invalid residues at position(s): On line 846440: 11, 13, 15, 17-18, 23, 26, 32, 34 FASTA-Reader: Ignoring invalid residues at position(s): On line 846442: 7-8, 10-12 FASTA-Reader: Ignoring invalid residues at position(s): On line 846444: 6, 8, 12 FASTA-Reader: Ignoring invalid residues at position(s): On line 846446: 2, 8-9, 13, 18, 20, 25-26, 30, 32, 39, 41-43, 54, 64, 71, 76, 82-83, 85-86 FASTA-Reader: Ignoring invalid residues at position(s): On line 846448: 1, 3-4, 6-7, 10, 15-16, 19-22, 24, 26-29, 34, 36, 39-41, 43, 47, 49-50, 52, 56, 59-62, 66-68, 70, 73-74, 77, 80-81, 84, 89, 91-92 FASTA-Reader: Ignoring invalid residues at position(s): On line 846450: 1, 6, 9-11, 14, 17, 21, 24-27, 30-31, 33, 38-40, 43 FASTA-Reader: Ignoring invalid residues at position(s): On line 846452: 2, 7, 10-11, 15, 17, 19, 21, 23, 31, 34-35 FASTA-Reader: Ignoring invalid residues at position(s): On line 846454: 2, 7-8, 14, 16, 20 FASTA-Reader: Ignoring invalid residues at position(s): On line 846456: 4-5, 10-11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846458: 5, 7, 10 FASTA-Reader: Ignoring invalid residues at position(s): On line 846460: 5, 8, 10-11, 13, 15-16, 20-21, 23, 25 FASTA-Reader: Ignoring invalid residues at position(s): On line 846462: 3, 13, 18, 22, 24 FASTA-Reader: Ignoring invalid residues at position(s): On line 846464: 4, 6, 15, 18, 20-21, 23 FASTA-Reader: Ignoring invalid residues at position(s): On line 846466: 3-5, 13, 15, 17-18, 20 FASTA-Reader: Ignoring invalid residues at position(s): On line 846468: 1-3, 5, 10-11, 13-15, 18 FASTA-Reader: Ignoring invalid residues at position(s): On line 846470: 2-6, 10-12 FASTA-Reader: Ignoring invalid residues at position(s): On line 846472: 3, 14, 16 FASTA-Reader: Ignoring invalid residues at position(s): On line 846474: 1-3, 5-6, 12-13, 15 FASTA-Reader: Ignoring invalid residues at position(s): On line 846476: 3-6, 8, 10-14 FASTA-Reader: Ignoring invalid residues at position(s): On line 846478: 1-2, 4, 6-9, 11, 13 FASTA-Reader: Ignoring invalid residues at position(s): On line 846480: 3, 6, 13 FASTA-Reader: Ignoring invalid residues at position(s): On line 846482: 1-5, 8, 10-11, 13 FASTA-Reader: Ignoring invalid residues at position(s): On line 846484: 5, 9, 12-13 FASTA-Reader: Ignoring invalid residues at position(s): On line 846486: 3-4, 6, 10-11 FASTA-Reader: Ignoring invalid residues at position(s): On line 846488: 3, 11-12, 18-21, 26, 32, 34, 40, 54, 66, 68, 70, 75, 78-80, 89 FASTA-Reader: Ignoring invalid residues at position(s): On line 846490: 2-3, 10, 14-19, 21, 25-28, 30-32, 34-35, 37, 42-43, 45-46, 48-49, 51, 53-57, 61, 63, 67, 75, 81, 85 FASTA-Reader: Ignoring invalid residues at position(s): On line 846492: 2, 4, 6, 8, 10, 14-15, 28-31, 33-34, 39, 43-44, 49, 51, 54-55 FASTA-Reader: Ignoring invalid residues at position(s): On line 846494: 2-3, 5, 9, 12, 17, 20, 22, 24, 26, 35-36, 42, 45, 50 FASTA-Reader: Ignoring invalid residues at position(s): On line 846496: 2, 8, 15-16, 20, 26, 28, 30-31, 35, 40 FASTA-Reader: Ignoring invalid residues at position(s): On line 846498: 1, 4, 12, 16, 22, 26 FASTA-Reader: Ignoring invalid residues at position(s): On line 846500: 5, 11-12 FASTA-Reader: Ignoring invalid residues at position(s): On line 846502: 2, 6-7, 11, 13, 20, 22, 29, 31, 33, 38, 40, 44, 46, 49-51, 53, 55, 61-67, 69 FASTA-Reader: Ignoring invalid residues at position(s): On line 846504: 3, 6, 9, 11, 13-15, 17, 20, 22, 26-27, 31, 35, 37, 46, 53, 55-56, 58, 62, 64, 69 FASTA-Reader: Ignoring invalid residues at position(s): On line 846506: 3, 7-8, 11, 15, 17, 19-20, 23, 27, 30-32, 34-35, 37 FASTA-Reader: Ignoring invalid residues at position(s): On line 846508: 4, 6-7, 9, 13, 16-18, 20 FASTA-Reader: Ignoring invalid residues at position(s): On line 846510: 3, 9-10, 12, 15 FASTA-Reader: Ignoring invalid residues at position(s): On line 846512: 4, 6, 8, 12, 14, 16, 24-25, 28-30 FASTA-Reader: Ignoring invalid residues at position(s): On line 846514: 2, 4, 17, 19, 28 FASTA-Reader: Ignoring invalid residues at position(s): On line 846516: 6, 8, 10-11, 16, 18, 20, 22 FASTA-Reader: Ignoring invalid residues at position(s): On line 846518: 8, 14, 16, 18, 21-24 FASTA-Reader: Ignoring invalid residues at position(s): On line 846520: 5, 7, 9, 11-13
Before I had run the same command with swissprot.pep DB, there was no error like this why i am getting this error with sorghum custom DB
someone please guide me
If you have peptide queries you should not be using
blastx. Useblastpfor protein-protein searches.