cct test issue: blast: Error: Unknown argument: "query_gencode"
Hi,
I tried to fix the totally broken autopkgtest in cct (which was never
working - shame on me). Its running now partly but the test is now
stumbling upon:
...
Performing BLAST search for sequence number 1 (_start=1;end=16000;length=16000;source_length=16000).
USAGE
blastn [-h] [-help] [-import_search_strategy filename]
[-export_search_strategy filename] [-task task_name] [-db database_name]
[-dbsize num_letters] [-gilist filename] [-seqidlist filename]
[-negative_gilist filename] [-negative_seqidlist filename]
[-taxids taxids] [-negative_taxids taxids] [-taxidlist filename]
[-negative_taxidlist 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]
[-perc_identity float_value] [-qcov_hsp_perc float_value]
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value]
[-xdrop_gap_final float_value] [-searchsp int_value]
[-sum_stats bool_value] [-penalty penalty] [-reward reward] [-no_greedy]
[-min_raw_gapped_score int_value] [-template_type type]
[-template_length int_value] [-dust DUST_options]
[-filtering_db filtering_database]
[-window_masker_taxid window_masker_taxid]
[-window_masker_db window_masker_db] [-soft_masking soft_masking]
[-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
[-best_hit_score_edge float_value] [-subject_besthit]
[-window_size int_value] [-off_diagonal_range int_value]
[-use_index boolean] [-index_name string] [-lcase_masking]
[-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format]
[-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
[-line_length line_length] [-html] [-sorthits sort_hits]
[-sorthsps sort_hsps] [-max_target_seqs num_sequences]
[-num_threads int_value] [-remote] [-version]
DESCRIPTION
Nucleotide-Nucleotide BLAST 2.10.1+
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Unknown argument: "query_gencode"
Error: (CArgException::eInvalidArg) Unknown argument: "query_gencode"
Program failed, try executing the command manually.
Open ./sample_projects/test_blastn/blast/blast_results_local/two_copies_of_long_ORF_opposite_directions_DNA_vs_match_end_of_orf.fasta_split_DNA_blastn to view the BLAST results.
...
I think this test was working two years ago when I did the test on
the local machine - no idea which blast version.
Any hint how to fix this?
Kind regards
Andreas.
--
http://fam-tille.de
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