Question: getting error in runing tblastn
gravatar for inayat45shaikh
5.8 years ago by
inayat45shaikh40 wrote:

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

  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]
    [-xdrop_ungap float_value] [-xdrop_gap float_value]
    [-xdrop_gap_final float_value] [-searchsp int_value]
    [-max_hsps_per_subject int_value] [-db_gencode int_value]
    [-frame_shift_penalty frameshift] [-ungapped] [-max_intron_length length]
    [-seg SEG_options] [-soft_masking soft_masking] [-matrix matrix_name]
    [-threshold float_value] [-culling_limit int_value]
    [-best_hit_overhang float_value] [-best_hit_score_edge float_value]
    [-window_size int_value] [-lcase_masking] [-query_loc range]
    [-parse_deflines] [-outfmt format] [-show_gis]
    [-num_descriptions int_value] [-num_alignments int_value] [-html]
    [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]
    [-comp_based_stats compo] [-use_sw_tback] [-in_pssm psi_chkpt_file]

   Protein Query-Translated Subject BLAST 2.2.26+

Use '-help' to print detailed descriptions of command line arguments
Error: (CArgException::eInvalidArg) Unknown argument: "F"
Error: (CArgException::eInvalidArg) Application's initialization failed


Can anyone give advise on this?


blast • 5.8k views
ADD COMMENTlink modified 4.6 years ago by Ginsea Chen130 • written 5.8 years ago by inayat45shaikh40

as you can see, there is no '-F' option...

ADD REPLYlink written 5.8 years ago by Pierre Lindenbaum126k

Guessing from your file naming, the query is nucl and the DB is protein. You might wanna try swapping the query and subject if that's the case, or use BLASTX/ explore other options.

ADD REPLYlink written 5.8 years ago by RamRS25k
gravatar for Prakki Rama
5.8 years ago by
Prakki Rama2.4k
Prakki Rama2.4k wrote:

The option -F for masking is only in the legacy blast for which one has to run blastall (which is different from blast+). Check the table in this page, a comparison between the masking options of blastall and blast+.

Moreover, as above Ram RS stated, your query should be protein and subject should be nucleotide sequences. If it is other way around, BLASTX is used to fulfill the purpose.

~Prakki Rama.

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 5.8 years ago by Prakki Rama2.4k
gravatar for Ginsea Chen
4.6 years ago by
Ginsea Chen130
Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
Ginsea Chen130 wrote:

You should add -soft_masking true option, then the error was displayed.

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 4.6 years ago by Ginsea Chen130
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