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sanger-pathogens / ariba

Antimicrobial Resistance Identification By Assembly
http://sanger-pathogens.github.io/ariba/
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Error running --test with CD-HIT and SPAdes #95

Closed ramarquezo closed 8 years ago

ramarquezo commented 8 years ago

Hi, I'm trying to install your software but I have a lot of problems. When I run "python3 setup.py test" there are some problems to find SPAdes and CD-HIT, I have those programs added to the path and working properly... but test is no able to find them, in "external_progs.py" CD-HIT is called "cd-hit-est", but when I installed CD-HIT this is called "cdhit-est". About SPAdes, I don't understand why, if I have v3.8.0, in the log output, test called the address like '/foo/bar/SPAdes-3.6.0-Linux/bin/spades'.... I really got lost, I don't know what to do, I'll be very grateful if you can help me!

genetica@UBGENETICA:~/Documentos/Software/ariba-master$ python3 setup.py test test_check_coding_seq (aln_to_metadata_test.TestAlnToMetadata) test _check_coding_seq ... ok test_check_insertion_coords (aln_to_metadata_test.TestAlnToMetadata) test _check_insertion_coords ... ok test_check_seq_lengths_same (aln_to_metadata_test.TestAlnToMetadata) test _check_seq_lengths_same ... ok test_check_sequences_coding (aln_to_metadata_test.TestAlnToMetadata) test _check_sequences with coding seqs ... ok test_check_sequences_non_coding (aln_to_metadata_test.TestAlnToMetadata) test _check_sequences with noncoding seqs ... ok test_check_variants_match_sequences (aln_to_metadata_test.TestAlnToMetadata) test _check_variants_match_sequences ... ok test_insertion_coords (aln_to_metadata_test.TestAlnToMetadata) test _insertion_coords ... ok test_load_aln_file (aln_to_metadata_test.TestAlnToMetadata) test _load_aln_file ... ok test_load_vars_bad_files (aln_to_metadata_test.TestAlnToMetadata) test _load_vars_file bad input files ... ok test_load_vars_file_good_file (aln_to_metadata_test.TestAlnToMetadata) test _load_vars_file good input file ... ok test_make_cluster_file (aln_to_metadata_test.TestAlnToMetadata) test _make_cluster_file ... ok test_make_unpadded_insertion_coords (aln_to_metadata_test.TestAlnToMetadata) test _make_unpadded_insertion_coords ... ok test_make_unpadded_seqs (aln_to_metadata_test.TestAlnToMetadata) test _make_unpadded_seqs ... ok test_padded_to_unpadded_nt_position (aln_to_metadata_test.TestAlnToMetadata) test _padded_to_unpadded_nt_position ... ok test_run_coding (aln_to_metadata_test.TestAlnToMetadata) test run coding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 ok test_run_noncoding (aln_to_metadata_test.TestAlnToMetadata) test run noncoding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ok test_unpadded_to_padded_nt_position (aln_to_metadata_test.TestAlnToMetadata) test _unpadded_to_padded_nt_position ... ok test_variant_ids_are_unique (aln_to_metadata_test.TestAlnToMetadata) test variant_ids_are_unique ... ok test_variants_to_tsv_lines_coding (aln_to_metadata_test.TestAlnToMetadata) test _variants_to_tsv_lines coding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 ok test_variants_to_tsv_lines_noncoding (aln_to_metadata_test.TestAlnToMetadata) test _variants_to_tsv_lines noncoding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ok test_find_next_stop_codon (assembly_compare_test.TestAssemblyCompare) test _find_next_stop_codon ... ok test_find_previous_start_codon (assembly_compare_test.TestAssemblyCompare) test _find_previous_start_codon ... ok test_gene_from_nucmer_match (assembly_compare_test.TestAssemblyCompare) test _gene_from_nucmer_match ... ok test_get_assembled_reference_sequences (assembly_compare_test.TestAssemblyCompare) test _get_assembled_reference_sequences ... ok test_get_gene_matching_ref (assembly_compare_test.TestAssemblyCompare) test _get_gene_matching_ref ... ok test_longest_nucmer_hit_in_ref (assembly_compare_test.TestAssemblyCompare) test _longest_nucmer_hit_in_ref ... ok test_nucmer_hit_containing_reference_position (assembly_compare_test.TestAssemblyCompare) test nucmer_hit_containing_reference_position ... ok test_nucmer_hits_to_assembly_coords (assembly_compare_test.TestAssemblyCompare) test _nucmer_hits_to_assembly_coords ... ok test_nucmer_hits_to_percent_identity (assembly_compare_test.TestAssemblyCompare) test _nucmer_hits_to_percent_identity ... ok test_nucmer_hits_to_ref_coords (assembly_compare_test.TestAssemblyCompare) test nucmer_hits_to_ref_coords ... ok test_parse_nucmer_coords_file (assembly_compare_test.TestAssemblyCompare) test _parse_nucmer_coords_file ... ok test_ref_cov_per_contig (assembly_compare_test.TestAssemblyCompare) test ref_cov_per_contig ... ok test_ref_covered_by_at_least_one_full_length_contig (assembly_compare_test.TestAssemblyCompare) test _ref_covered_by_at_least_one_full_length_contig ... ok test_ref_has_region_assembled_twice (assembly_compare_test.TestAssemblyCompare) test _ref_has_region_assembled_twice ... ok test_whole_gene_covered_by_nucmer_hits (assembly_compare_test.TestAssemblyCompare) test _whole_gene_covered_by_nucmer_hits ... ok test_assemble_with_spades (assembly_test.TestAssembly) test _assemble_with_spades ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR test_assemble_with_spades_fail (assembly_test.TestAssembly) test _assemble_with_spades handles spades fail ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR test_check_spades_log_file (assembly_test.TestAssembly) test _check_spades_log_file ... Error running SPAdes. Cannot continue. This is the error from the log file /home/genetica/Documentos/Software/ariba-master/ariba/tests/data/assembly_test_check_spades_log_file.log.bad ... == Error == system call for: "['/foo/bar/SPAdes-3.6.0-Linux/bin/spades', '/spam/eggs/K21/configs/config.info']" finished abnormally, err code: -7

ok test_fix_contig_orientation (assembly_test.TestAssembly) test _fix_contig_orientation ... ok test_gap_fill_with_gapfiller_no_gaps (assembly_test.TestAssembly) test _gap_fill_with_gapfiller no gaps ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR test_gap_fill_with_gapfiller_with_gaps (assembly_test.TestAssembly) test _gap_fill_with_gapfiller with gaps ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR test_get_assembly_kmer (assembly_test.TestAssembly) test _get_assembly_kmer ... ok test_has_gaps_to_fill (assembly_test.TestAssembly) test _has_gaps_to_fill ... ok test_parse_bam (assembly_test.TestAssembly) test _parse_bam ... ok test_rename_scaffolds (assembly_test.TestAssembly) test _rename_scaffolds ... ok test_scaffold_with_sspace (assembly_test.TestAssembly) test _scaffold_with_sspace ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR test_filter_mummer_variants (assembly_variants_test.TestAssemblyVariants) test filter_mummer_variants ... ok test_get_codon_start (assembly_variants_test.TestAssemblyVariants) test _get_codon_start ... ok test_get_mummer_variants_has_variants (assembly_variants_test.TestAssemblyVariants) test _get_mummer_variants when there are variants ... ok test_get_mummer_variants_no_variants (assembly_variants_test.TestAssemblyVariants) test _get_mummer_variants when no variants ... ok test_get_one_variant_for_one_contig_coding (assembly_variants_test.TestAssemblyVariants) test _get_one_variant_for_one_contig_coding ... ok test_get_one_variant_for_one_contig_non_coding (assembly_variants_test.TestAssemblyVariants) test _get_one_variant_for_one_contig_non_coding ... ok test_get_remaining_known_ref_variants_amino_acids (assembly_variants_test.TestAssemblyVariants) test _get_remaining_known_ref_variants with amino acids ... ok test_get_remaining_known_ref_variants_nucleotides (assembly_variants_test.TestAssemblyVariants) test _get_remaining_known_ref_variants with nucleotides ... ok test_get_variant_effect (assembly_variants_test.TestAssemblyVariants) test _get_variant_effect ... ok test_get_variants_presence_absence (assembly_variants_test.TestAssemblyVariants) test get_variants presence absence genes ... ok test_get_variants_variants_only (assembly_variants_test.TestAssemblyVariants) test get_variants variants only ... ok test_parse (bam_parse_test.TestBamParse) test parse ... ok test_sam_to_soft_clipped (bam_parse_test.TestBamParse) test _sam_to_soft_clipped ... ok test_update_soft_clipped_from_sam (bam_parse_test.TestBamParse) test _update_soft_clipped_from_sam ... ok test_update_unmapped_mates_from_sam (bam_parse_test.TestBamParse) test _update_unmapped_mates_from_sam ... ok test_write_soft_clipped_to_file (bam_parse_test.TestBamParse) test _write_soft_clipped_to_file ... ok test_write_unmapped_mates_to_file (bam_parse_test.TestBamParse) test _write_unmapped_mates_to_file ... ok WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) Failure: Error (Dependency error(s). Cannot continue) ... ERROR test_ARO_accession (card_record_test.TestCardRecord) test _ARO_accession ... ok test_ARO_description (card_record_test.TestCardRecord) test _ARO_description ... ok test_ARO_id (card_record_test.TestCardRecord) test _ARO_id ... ok test_ARO_name (card_record_test.TestCardRecord) test _ARO_name ... ok test_ARO_name_to_fasta_name (card_record_test.TestCardRecord) test _ARO_name_to_fasta_name ... ok test_dna_seqs_and_genbank_ids (card_record_test.TestCardRecord) test _dna_seqs_and_genbank_ids ... Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo ok test_get_data (card_record_test.TestCardRecord) ... ok test_snps (card_record_test.TestCardRecord) test snps ... ok WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) Failure: Error (Dependency error(s). Cannot continue) ... ERROR test_full_run_assembly_fail (cluster_test.TestCluster) test complete run of cluster when assembly fails ... ERROR test_full_run_choose_ref_fail (cluster_test.TestCluster) test complete run of cluster when choosing ref seq fails ... ERROR test_full_run_ok_non_coding (cluster_test.TestCluster) test complete run of cluster on a noncoding sequence ... ERROR test_full_run_ok_presence_absence (cluster_test.TestCluster) test complete run of cluster on a presence absence gene ... ERROR test_full_run_ok_variants_only_variant_is_present (cluster_test.TestCluster) test complete run of cluster on a variants only gene when variant is present ... ERROR test_full_run_ok_variants_only_variant_not_present (cluster_test.TestCluster) test complete run of cluster on a variants only gene when variant not present ... ERROR test_full_run_ok_variants_only_variant_not_present_always_report (cluster_test.TestCluster) test complete run of cluster on a variants only gene when variant not present but always report variant ... ERROR test_init_fail_files_missing (cluster_test.TestCluster) test init_fail_files_missing ... ok test_make_reads_for_assembly_proper_sample (cluster_test.TestCluster) Test _make_reads_for_assembly when sampling from reads ... ok test_make_reads_for_assembly_symlinks (cluster_test.TestCluster) Test _make_reads_for_assembly when just makes symlinks ... ok test_number_of_reads_for_assembly (cluster_test.TestCluster) Test _number_of_reads_for_assembly ... ok WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) Failure: Error (Dependency error(s). Cannot continue) ... ERROR test_cat_files (common_test.TestCommon) test cat_files ... ok test_external_progs_ok (external_progs_test.TestExternalProgs) Test that external programs are found ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) Failure: Error (Dependency error(s). Cannot continue) ... ERROR test_add (flag_test.TestFlag) Test add ... ok test_has (flag_test.TestFlag) Test has ... ok test_init_and_to_number (flag_test.TestFlag) Test init and to_number ... ok test_set_flag (flag_test.TestFlag) Test set_flag ... ok test_str (flag_test.TestFlag) Test str ... ok test_to_long_str (flag_test.TestFlag) Test to_long_str ... ok test_add (histogram_test.TestCluster) Test add ... ok test_len (histogram_test.TestCluster) Test len ... ok test_stats (histogram_test.TestCluster) Test stats ... ok test_to_bin (histogram_test.TestCluster) Test _to_bin ... ok test_distance_to_contig_end (link_test.TestLink) test _distance_to_contig_end ... ok test_distance_to_contig_ends (link_test.TestLink) test _distance_to_contig_ends ... ok test_init_no_links (link_test.TestLink) test link init no links made ... ok test_init_with_link (link_test.TestLink) test link init link made ... ok test_insert_size (link_test.TestLink) test insert_size ... ok test_lt (link_test.TestLink) test lt ... ok test_merge (link_test.TestLink) test merge ... ok test_sort (link_test.TestLink) test sort ... ok test_swap (link_test.TestLink) test _swap ... ok WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) Failure: Error (Dependency error(s). Cannot continue) ... ERROR test_clean (read_store_test.TestReadStore) Test clean ... ok test_compress_and_index_file (read_store_test.TestReadStore) Test _compress_and_index_file ... ok test_get_reads (read_store_test.TestReadStore) Test get_reads ... ok test_sort_file (read_store_test.TestReadStore) test _sort_file ... ok test_get_ref_files_naming_each_file (ref_preparer_test.TestRefPreparer) ... ok test_get_ref_files_ref_prefix (ref_preparer_test.TestRefPreparer) test _get_ref_files using ref_prefix ... ok test_write_info_file (ref_preparer_test.TestRefPreparer) test _write_info_file ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ERROR test_all_non_wild_type_variants (reference_data_test.TestReferenceData) Test all_non_wild_type_variants ... ok test_cluster_with_cdhit (reference_data_test.TestReferenceData) Test cluster_with_cd_hit ... The following command failed with exit code 127 cd-hit-est -i /home/genetica/Documentos/Software/ariba-master/ariba/tests/data/reference_data_test_cluster_with_cdhit.presence_absence.fa -o /home/genetica/Documentos/Software/ariba-master/tmp.run_cd-hit.dj970f6i/cdhit -c 0.9 -T 1 -s 0.9 -d 0 -bak 1

The output was:

/bin/sh: 1: cd-hit-est: not found

ERROR test_cluster_with_cdhit_clusters_in_file (reference_data_test.TestReferenceData) Test cluster_with_cd_hit clusters from file ... ok test_dict_keys_intersection (reference_data_test.TestReferenceData) Test dict_keys_intersection ... ok test_filter_bad_variant_data (reference_data_test.TestReferenceData) Test _filter_bad_variant_data ... ok test_find_gene_in_seqs (reference_data_test.TestReferenceData) Test _find_gene_in_seqs ... ok test_get_filename (reference_data_test.TestReferenceData) Test _get_filename ... ok test_init_fails (reference_data_test.TestReferenceData) Test init fails when it should ... ok test_init_ok (reference_data_test.TestReferenceData) Test init with good input ... ok test_load_fasta_file (reference_data_test.TestReferenceData) Test _load_fasta_file ... ok test_load_metadata_tsv (reference_data_test.TestReferenceData) Test _load_metadata_tsv ... ok test_make_catted_fasta (reference_data_test.TestReferenceData) Test make_catted_fasta ... ok test_new_seq_name (reference_data_test.TestReferenceData) Test _new_seq_name ... ok test_remove_bad_genes (reference_data_test.TestReferenceData) Test _remove_bad_genes ... ok test_rename_metadata_set (reference_data_test.TestReferenceData) Test _rename_metadata_set ... ok test_rename_names_in_metadata (reference_data_test.TestReferenceData) Test _rename_names_in_metadata ... ok test_rename_names_in_seq_dicts (reference_data_test.TestReferenceData) Test _rename_names_in_seq_dicts ... ok test_rename_sequences (reference_data_test.TestReferenceData) Test rename_sequences ... Had to rename some sequences. See tmp.test_rename_sequences.out for old -> new names ok test_seq_names_to_rename_dict (reference_data_test.TestReferenceData) Test _seq_names_to_rename_dict ... ok test_sequence (reference_data_test.TestReferenceData) Test sequence ... ok test_sequence_length (reference_data_test.TestReferenceData) Test sequence_length ... ok test_sequence_type (reference_data_test.TestReferenceData) Test sequence_type ... ok test_try_to_get_gene_seq (reference_data_test.TestReferenceData) Test _try_to_get_gene_seq ... ok test_write_cluster_allocation_file (reference_data_test.TestReferenceData) Test write_cluster_allocation_file ... ok test_write_dict_of_sequences (reference_data_test.TestReferenceData) Test _write_dict_of_sequences ... ok test_write_metadata_tsv (reference_data_test.TestReferenceData) Test _write_metadata_tsv ... ok test_write_seqs_to_fasta (reference_data_test.TestReferenceData) Test write_seqs_to_fasta ... ok test_dict_to_report_line (report_filter_test.TestReportFilter) Test _dict_to_report_line ... ok test_filter_dicts (report_filter_test.TestReportFilter) Test _filter_dicts ... ok test_filter_list_of_dicts_all_fail (report_filter_test.TestReportFilter) Test _filter_list_of_dicts where all fail ... ok test_filter_list_of_dicts_with_essential (report_filter_test.TestReportFilter) Test _filter_list_of_dicts with an essential line but all others fail ... ok test_filter_list_of_dicts_with_pass (report_filter_test.TestReportFilter) Test _filter_list_of_dicts with a line that passes ... ok test_flag_passes_filter (report_filter_test.TestReportFilter) Test _flag_passes_filter ... ok test_init_bad_file (report_filter_test.TestReportFilter) test init on bad input file ... ok test_init_good_file (report_filter_test.TestReportFilter) test init on good input file ... ok test_load_report (report_filter_test.TestReportFilter) ... ok test_remove_all_after_first_frameshift (report_filter_test.TestReportFilter) Test _remove_all_after_first_frameshift ... ok test_report_dict_passes_essential_filters (report_filter_test.TestReportFilter) Test _report_dict_passes_essential_filters ... ok test_report_dict_passes_non_essential_filters_known_vars (report_filter_test.TestReportFilter) Test _report_dict_passes_non_essential_filters with known vars ... ok test_report_dict_passes_non_essential_filters_synonymous (report_filter_test.TestReportFilter) Test _report_dict_passes_non_essential_filters with synonymous AA changes ... ok test_report_line_to_dict (report_filter_test.TestReportFilter) ... ok test_run (report_filter_test.TestReportFilter) Test run ... ok test_write_report_tsv (report_filter_test.TestReportFilter) Test write_report_tsv ... ok WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) Failure: Error (Dependency error(s). Cannot continue) ... ERROR test_contig_graph_is_consistent (scaffold_graph_test.TestScaffoldGraph) test _contig_graph_is_consistent ... ok test_make_graph (scaffold_graph_test.TestScaffoldGraph) test _make_graph ... ok test_remove_low_cov_links (scaffold_graph_test.TestScaffoldGraph) test _remove_low_cov_links ... ok test_update_from_sam (scaffold_graph_test.TestScaffoldGraph) test update_from_sam ... ok test_write_all_links_to_file (scaffold_graph_test.TestScaffoldGraph) test write_all_links_to_file ... ok test_has_variant (sequence_metadata_test.TestSequenceMetadata) test has_variant ... ok test_init_fails_on_bad_lines (sequence_metadata_test.TestSequenceMetadata) Test init fails on bad lines ... ok test_init_on_good_input (sequence_metadata_test.TestSequenceMetadata) test init ok on good input ... ok test_str (sequence_metadata_test.TestSequenceMetadata) test str ... ok test_to_string (sequence_metadata_test.TestSequenceMetadata) test to_string ... ok test_has_variant (sequence_variant_test.TestSequenceVariant) test has_variant ... ok test_init_fails_on_bad_variant_strings (sequence_variant_test.TestSequenceVariant) Test init fails on bad variant strings ... ok test_init_ok (sequence_variant_test.TestSequenceVariant) Test init ok ... ok test_init_str (sequence_variant_test.TestSequenceVariant) Test init ok and str ... ok test_nucleotide_range (sequence_variant_test.TestSequenceVariant) test nucleotide_range ... ok test_sanity_check_against_seq_no_translate (sequence_variant_test.TestSequenceVariant) test sanity_check_against_seq with translate False ... ok test_sanity_check_against_seq_translate (sequence_variant_test.TestSequenceVariant) test sanity_check_against_seq with translate True ... ok test_add_data_dict (summary_cluster_test.TestSummaryCluster) Test add_data_dict ... ok test_column_summary_data (summary_cluster_test.TestSummaryCluster) Test column_summary_data ... ok test_get_nonsynonymous_var (summary_cluster_test.TestSummaryCluster) Test _get_nonsynonymous_var ... ok test_has_any_known_variant (summary_cluster_test.TestSummaryCluster) ... ok test_has_any_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _has_any_nonsynonymous ... ok test_has_any_novel_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _has_any_novel_nonsynonymous ... ok test_has_known_variant (summary_cluster_test.TestSummaryCluster) Test _has_known_variant ... ok test_has_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _has_nonsynonymous ... ok test_has_novel_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _has_novel_nonsynonymous ... ok test_has_resistance (summary_cluster_test.TestSummaryCluster) Test _has_resistance ... ok test_has_var_groups (summary_cluster_test.TestSummaryCluster) Test has_var_groups ... ok test_line2dict (summary_cluster_test.TestSummaryCluster) Test _line2dict ... ok test_non_synon_variants (summary_cluster_test.TestSummaryCluster) Test non_synon_variants ... ok test_pc_id_of_longest (summary_cluster_test.TestSummaryCluster) Test pc_id_of_longest ... ok test_to_cluster_summary_has_known_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _to_cluster_summary_has_known_nonsynonymous ... ok test_to_cluster_summary_has_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _to_cluster_summary_has_nonsynonymous ... ok test_to_cluster_summary_has_novel_nonsynonymous (summary_cluster_test.TestSummaryCluster) Test _to_cluster_summary_has_novel_nonsynonymous ... ok test_to_cluster_summary_number (summary_cluster_test.TestSummaryCluster) Test _to_cluster_summary_assembled ... ok test_column_summary_data (summary_sample_test.TestSummarySample) Test _column_summary_data ... ok test_load_file (summary_sample_test.TestSummarySample) Test _load_file ... ok test_var_groups (summary_sample_test.TestSummarySample) test _var_groups ... ok test_variant_column_names_tuples (summary_sample_test.TestSummarySample) Test _variant_column_names_tuples ... ok test_add_phandango_colour_columns (summary_test.TestSummary) Test _add_phandango_colour_columns ... ok test_determine_cluster_cols (summary_test.TestSummary) ... ok test_determine_var_cols (summary_test.TestSummary) ... ok test_distance_score_between_lists (summary_test.TestSummary) Test _distance_score_between_lists ... ok test_distance_score_bewteen_values (summary_test.TestSummary) Test _distance_score_bewteen_values ... ok test_filter_matrix_columns (summary_test.TestSummary) Test _filter_matrix_columns ... ok test_filter_matrix_rows (summary_test.TestSummary) Test _filter_matrix_rows ... ok test_gather_output_rows (summary_test.TestSummary) Test _gather_output_rows ... ok test_get_all_cluster_names (summary_test.TestSummary) Test _get_all_cluster_names ... ok test_get_all_var_groups (summary_test.TestSummary) test _get_all_var_groups ... ok test_get_all_variant_columns (summary_test.TestSummary) Test _get_all_variant_columns ... ok test_init (summary_test.TestSummary) Test init ... ok test_load_input_files (summary_test.TestSummary) Test _load_input_files ... ok test_matrix_to_csv (summary_test.TestSummary) Test _matrix_to_csv ... ok test_newick_from_dist_matrix (summary_test.TestSummary) Test _newick_from_dist_matrix ... ok test_to_matrix (summary_test.TestSummary) Test _to_matrix ... ok test_write_distance_matrix (summary_test.TestSummary) Test _write_distance_matrix ... ok test_get_all_versions (versions_test.TestVersions) Test get_all_versions ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ERROR: cdhit not found in path. Looked for cd-hit-est

Something wrong with at least one dependency. Please see the above error message(s) ok test_fa_header_to_name_and_metadata (vfdb_parser_test.TestVfdbParser) test _fa_header_to_name_and_metadata ... ok test_fa_header_to_name_pieces (vfdb_parser_test.TestVfdbParser) test _fa_header_to_name_pieces ... ok test_run (vfdb_parser_test.TestVfdbParser) test run ... ok

ERROR: test_assemble_with_spades (assembly_test.TestAssembly)

test _assemble_with_spades

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py", line 39, in test_assemble_with_spades a = assembly.Assembly(reads1, reads2, ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) File "/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py", line 61, in init self.extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_assemble_with_spades_fail (assembly_test.TestAssembly)

test _assemble_with_spades handles spades fail

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py", line 51, in test_assemble_with_spades_fail a = assembly.Assembly(reads1, reads2, ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) File "/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py", line 61, in init self.extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_gap_fill_with_gapfiller_no_gaps (assembly_test.TestAssembly)

test _gap_fill_with_gapfiller no gaps

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py", line 93, in test_gap_fill_with_gapfiller_no_gaps a = assembly.Assembly(reads1, reads2, 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) File "/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py", line 61, in init self.extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_gap_fill_with_gapfiller_with_gaps (assembly_test.TestAssembly)

test _gap_fill_with_gapfiller with gaps

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py", line 105, in test_gap_fill_with_gapfiller_with_gaps a = assembly.Assembly(reads1, reads2, 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) File "/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py", line 61, in init self.extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_scaffold_with_sspace (assembly_test.TestAssembly)

test _scaffold_with_sspace

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py", line 63, in test_scaffold_with_sspace a = assembly.Assembly(reads1, reads2, ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) File "/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py", line 61, in init self.extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: Failure: Error (Dependency error(s). Cannot continue)

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 235, in load_module return load_source(name, filename, file) File "/usr/lib/python3.4/imp.py", line 171, in load_source module = methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/best_seq_chooser_test.py", line 9, in extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: Failure: Error (Dependency error(s). Cannot continue)

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 235, in load_module return load_source(name, filename, file) File "/usr/lib/python3.4/imp.py", line 171, in load_source module = methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cdhit_test.py", line 8, in extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_full_run_assembly_fail (cluster_test.TestCluster)

test complete run of cluster when assembly fails

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 128, in test_full_run_assembly_fail shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_assembly_fail'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.test_full_run_assembly_fail'

ERROR: test_full_run_choose_ref_fail (cluster_test.TestCluster)

test complete run of cluster when choosing ref seq fails

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 110, in test_full_run_choose_ref_fail shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_choose_ref_fail'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.test_full_run_choose_ref_fail'

ERROR: test_full_run_ok_non_coding (cluster_test.TestCluster)

test complete run of cluster on a noncoding sequence

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 148, in test_full_run_ok_non_coding shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_non_coding'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.test_full_run_ok_non_coding'

ERROR: test_full_run_ok_presence_absence (cluster_test.TestCluster)

test complete run of cluster on a presence absence gene

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 174, in test_full_run_ok_presence_absence shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_presence_absence'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_presence_absence'

ERROR: test_full_run_ok_variants_only_variant_is_present (cluster_test.TestCluster)

test complete run of cluster on a variants only gene when variant is present

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 238, in test_full_run_ok_variants_only_variant_is_present shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_variants_only.present'

ERROR: test_full_run_ok_variants_only_variant_not_present (cluster_test.TestCluster)

test complete run of cluster on a variants only gene when variant not present

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 200, in test_full_run_ok_variants_only_variant_not_present shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_variants_only.not_present'

ERROR: test_full_run_ok_variants_only_variant_not_present_always_report (cluster_test.TestCluster)

test complete run of cluster on a variants only gene when variant not present but always report variant

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py", line 219, in test_full_run_ok_variants_only_variant_not_present_always_report shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir) File "/usr/lib/python3.4/shutil.py", line 303, in copytree os.makedirs(dst) File "/usr/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode) FileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_variants_only.not_present.always_report'

ERROR: Failure: Error (Dependency error(s). Cannot continue)

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 235, in load_module return load_source(name, filename, file) File "/usr/lib/python3.4/imp.py", line 171, in load_source module = methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/clusters_test.py", line 12, in extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_external_progs_ok (external_progs_test.TestExternalProgs)

Test that external programs are found

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/external_progs_test.py", line 8, in test_external_progs_ok progs = external_progs.ExternalProgs(verbose=True) File "/home/genetica/Documentos/Software/ariba-master/ariba/externalprogs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') nose.proxy.Error: Dependency error(s). Cannot continue -------------------- >> begin captured stdout << --------------------- __ Checking dependencies and their versions __ bcftools 1.3.1 /usr/local/bin/bcftools bowtie2 2.2.5 /usr/bin/bowtie2 cdhit NA NOT_FOUND gapfiller NA NOT_FOUND nucmer 3.1 /usr/bin/nucmer r 3.3.0 /usr/bin/Rscript samtools 1.3.1 /usr/local/bin/samtools spades .8.0 python2 /home/genetica/Documentos/Software/SPAdes-3.8.0-Linux/bin/spades.py sspace NA NOT_FOUND

--------------------- >> end captured stdout << ----------------------

ERROR: Failure: Error (Dependency error(s). Cannot continue)

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 235, in load_module return load_source(name, filename, file) File "/usr/lib/python3.4/imp.py", line 171, in load_source module = methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/faidx_test.py", line 8, in extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: Failure: Error (Dependency error(s). Cannot continue)

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 235, in load_module return load_source(name, filename, file) File "/usr/lib/python3.4/imp.py", line 171, in load_source module = methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/mapping_test.py", line 10, in extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_write_info_file (ref_preparer_test.TestRefPreparer)

test _write_info_file

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/ref_preparer_test.py", line 109, in test_write_info_file extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

ERROR: test_cluster_with_cdhit (reference_data_test.TestReferenceData)

Test cluster_with_cd_hit

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/reference_data_test.py", line 557, in test_cluster_with_cdhit got = refdata.cluster_with_cdhit(inprefix, outprefix) File "/home/genetica/Documentos/Software/ariba-master/ariba/reference_data.py", line 486, in cluster_with_cdhit new_clusters = cdhit_runner.run() File "/home/genetica/Documentos/Software/ariba-master/ariba/cdhit.py", line 190, in run common.syscall(cmd, verbose=self.verbose) File "/home/genetica/Documentos/Software/ariba-master/ariba/common.py", line 22, in syscall sys.exit(1) nose.proxy.SystemExit: 1

ERROR: Failure: Error (Dependency error(s). Cannot continue)

Traceback (most recent call last): File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 235, in load_module return load_source(name, filename, file) File "/usr/lib/python3.4/imp.py", line 171, in load_source module = methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/home/genetica/Documentos/Software/ariba-master/ariba/tests/samtools_variants_test.py", line 9, in extern_progs = external_progs.ExternalProgs() File "/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py", line 115, in init raise Error('Dependency error(s). Cannot continue') ariba.external_progs.Error: Dependency error(s). Cannot continue

Ran 219 tests in 3.644s

FAILED (errors=21)

martinghunt commented 8 years ago

Hi,

The names of cd hit executables are not consistent depending on the platform/install method. You can change the name ariba looks for like this:

export ARIBA_CDHIT=cdhit-est

As for SPAdes, I don't think there is a problem. It's using 3.8.0. There is a test to look for a specific type of error in the spades log file, which is what the '/foo/bar/SPAdes-3.6.0-Linux/bin/spades' is referring to. That's normal.

Before you run the tests again, can you run

rm -rf tmp.*

in the directory where you ran the tests, to make sure the temporary files from the failed tests are cleaned up.

ramarquezo commented 8 years ago

Thanks martinghunt!!!!!!! The test ran perfectly!!

Ran 249 tests in 37.167s

OK

ramarquezo commented 8 years ago

Hi again martinghunt. Ariba is already running!! I just have a silly question, is there any way to run the program with a finished assembly? it means without reads libraries?

Thanks in advance!!

martinghunt commented 8 years ago

Glad it's working.

There's no way to run it without reads. The whole method is based on local assemblies of the reads, instead of trusting an assembly.