Hello group,
i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic genome, i am running the command
tblastn -query sequence.fa -out output.txt -subject ref_protein.fa -evalue 1e-5 -outfmt 7 -max_target_seqs 5 -best_hit_score_edge 0.05 -best_hit_overhang 0.25
but getting following error
Warning: lcl|Query_20167 contig20167: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options.
i used dustmasker also for filtering and masking and then run with masked genome, but still got the same error. i ahve also run by keeping filtering turn off with the following command
tblastn -query sequence.fa -out output.txt -F T -subject ref_protein.fa -evalue 1e-5 -outfmt 7 -max_target_seqs 5 -best_hit_score_edge 0.05 -best_hit_overhang 0.25
but got the following error
USAGE
tblastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-entrez_query entrez_query]
[-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
[-subject subject_input_file] [-subject_loc range] [-query input_file]
[-out output_file] [-evalue evalue] [-word_size int_value]
[-gapopen open_penalty] [-gapextend extend_penalty]
...
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