{"action":"created","issue":{"url":"https://api.github.com/repos/sanger-pathogens/ariba/issues/95","repository_url":"https://api.github.com/repos/sanger-pathogens/ariba","labels_url":"https://api.github.com/repos/sanger-pathogens/ariba/issues/95/labels{/name}","comments_url":"https://api.github.com/repos/sanger-pathogens/ariba/issues/95/comments","events_url":"https://api.github.com/repos/sanger-pathogens/ariba/issues/95/events","html_url":"https://github.com/sanger-pathogens/ariba/issues/95","id":160001931,"number":95,"title":"Error running --test with CD-HIT and SPAdes","user":{"login":"ramarquezo","id":10735852,"avatar_url":"https://avatars.githubusercontent.com/u/10735852?v=3","gravatar_id":"","url":"https://api.github.com/users/ramarquezo","html_url":"https://github.com/ramarquezo","followers_url":"https://api.github.com/users/ramarquezo/followers","following_url":"https://api.github.com/users/ramarquezo/following{/other_user}","gists_url":"https://api.github.com/users/ramarquezo/gists{/gist_id}","starred_url":"https://api.github.com/users/ramarquezo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramarquezo/subscriptions","organizations_url":"https://api.github.com/users/ramarquezo/orgs","repos_url":"https://api.github.com/users/ramarquezo/repos","events_url":"https://api.github.com/users/ramarquezo/events{/privacy}","received_events_url":"https://api.github.com/users/ramarquezo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-06-13T17:21:47Z","updated_at":"2016-06-14T18:54:41Z","closed_at":null,"body":"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\".\r\nAbout 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'....\r\nI really got lost, I don't know what to do, I'll be very grateful if you can help me! \r\n\r\n\r\ngenetica@UBGENETICA:~/Documentos/Software/ariba-master$ python3 setup.py test\r\ntest_check_coding_seq (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _check_coding_seq ... ok\r\ntest_check_insertion_coords (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _check_insertion_coords ... ok\r\ntest_check_seq_lengths_same (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _check_seq_lengths_same ... ok\r\ntest_check_sequences_coding (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _check_sequences with coding seqs ... ok\r\ntest_check_sequences_non_coding (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _check_sequences with noncoding seqs ... ok\r\ntest_check_variants_match_sequences (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _check_variants_match_sequences ... ok\r\ntest_insertion_coords (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _insertion_coords ... ok\r\ntest_load_aln_file (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _load_aln_file ... ok\r\ntest_load_vars_bad_files (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _load_vars_file bad input files ... ok\r\ntest_load_vars_file_good_file (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _load_vars_file good input file ... ok\r\ntest_make_cluster_file (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _make_cluster_file ... ok\r\ntest_make_unpadded_insertion_coords (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _make_unpadded_insertion_coords ... ok\r\ntest_make_unpadded_seqs (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _make_unpadded_seqs ... ok\r\ntest_padded_to_unpadded_nt_position (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _padded_to_unpadded_nt_position ... ok\r\ntest_run_coding (aln_to_metadata_test.TestAlnToMetadata)\r\ntest run coding sequences ... Warning: position has a gap in sequence  seq3 corresponding to variant A2D (id1) in sequence  seq1 ... Ignoring for seq3\r\nWarning: position has a gap in sequence  seq1 corresponding to variant F2E (id2) in sequence  seq5 ... Ignoring for seq1\r\nWarning: position has a gap in sequence  seq2 corresponding to variant F2E (id2) in sequence  seq5 ... Ignoring for seq2\r\nok\r\ntest_run_noncoding (aln_to_metadata_test.TestAlnToMetadata)\r\ntest run noncoding sequences ... Warning: position has a gap in sequence  seq3 corresponding to variant C5T (id1) in sequence  seq1 ... Ignoring for seq3\r\nWarning: position has a gap in sequence  seq1 corresponding to variant A5T (id2) in sequence  seq5 ... Ignoring for seq1\r\nWarning: position has a gap in sequence  seq2 corresponding to variant A5T (id2) in sequence  seq5 ... Ignoring for seq2\r\nok\r\ntest_unpadded_to_padded_nt_position (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _unpadded_to_padded_nt_position ... ok\r\ntest_variant_ids_are_unique (aln_to_metadata_test.TestAlnToMetadata)\r\ntest variant_ids_are_unique ... ok\r\ntest_variants_to_tsv_lines_coding (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _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\r\nWarning: position has a gap in sequence  seq1 corresponding to variant F2E (id2) in sequence  seq5 ... Ignoring for seq1\r\nWarning: position has a gap in sequence  seq2 corresponding to variant F2E (id2) in sequence  seq5 ... Ignoring for seq2\r\nok\r\ntest_variants_to_tsv_lines_noncoding (aln_to_metadata_test.TestAlnToMetadata)\r\ntest _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\r\nWarning: position has a gap in sequence  seq1 corresponding to variant A5T (id2) in sequence  seq5 ... Ignoring for seq1\r\nWarning: position has a gap in sequence  seq2 corresponding to variant A5T (id2) in sequence  seq5 ... Ignoring for seq2\r\nok\r\ntest_find_next_stop_codon (assembly_compare_test.TestAssemblyCompare)\r\ntest _find_next_stop_codon ... ok\r\ntest_find_previous_start_codon (assembly_compare_test.TestAssemblyCompare)\r\ntest _find_previous_start_codon ... ok\r\ntest_gene_from_nucmer_match (assembly_compare_test.TestAssemblyCompare)\r\ntest _gene_from_nucmer_match ... ok\r\ntest_get_assembled_reference_sequences (assembly_compare_test.TestAssemblyCompare)\r\ntest _get_assembled_reference_sequences ... ok\r\ntest_get_gene_matching_ref (assembly_compare_test.TestAssemblyCompare)\r\ntest _get_gene_matching_ref ... ok\r\ntest_longest_nucmer_hit_in_ref (assembly_compare_test.TestAssemblyCompare)\r\ntest _longest_nucmer_hit_in_ref ... ok\r\ntest_nucmer_hit_containing_reference_position (assembly_compare_test.TestAssemblyCompare)\r\ntest nucmer_hit_containing_reference_position ... ok\r\ntest_nucmer_hits_to_assembly_coords (assembly_compare_test.TestAssemblyCompare)\r\ntest _nucmer_hits_to_assembly_coords ... ok\r\ntest_nucmer_hits_to_percent_identity (assembly_compare_test.TestAssemblyCompare)\r\ntest _nucmer_hits_to_percent_identity ... ok\r\ntest_nucmer_hits_to_ref_coords (assembly_compare_test.TestAssemblyCompare)\r\ntest nucmer_hits_to_ref_coords ... ok\r\ntest_parse_nucmer_coords_file (assembly_compare_test.TestAssemblyCompare)\r\ntest _parse_nucmer_coords_file ... ok\r\ntest_ref_cov_per_contig (assembly_compare_test.TestAssemblyCompare)\r\ntest ref_cov_per_contig ... ok\r\ntest_ref_covered_by_at_least_one_full_length_contig (assembly_compare_test.TestAssemblyCompare)\r\ntest _ref_covered_by_at_least_one_full_length_contig ... ok\r\ntest_ref_has_region_assembled_twice (assembly_compare_test.TestAssemblyCompare)\r\ntest _ref_has_region_assembled_twice ... ok\r\ntest_whole_gene_covered_by_nucmer_hits (assembly_compare_test.TestAssemblyCompare)\r\ntest _whole_gene_covered_by_nucmer_hits ... ok\r\ntest_assemble_with_spades (assembly_test.TestAssembly)\r\ntest _assemble_with_spades ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\ntest_assemble_with_spades_fail (assembly_test.TestAssembly)\r\ntest _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\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\ntest_check_spades_log_file (assembly_test.TestAssembly)\r\ntest _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 ...\r\n== Error ==  system call for: \"['/foo/bar/SPAdes-3.6.0-Linux/bin/spades', '/spam/eggs/K21/configs/config.info']\" finished abnormally, err code: -7\r\n\r\nok\r\ntest_fix_contig_orientation (assembly_test.TestAssembly)\r\ntest _fix_contig_orientation ... ok\r\ntest_gap_fill_with_gapfiller_no_gaps (assembly_test.TestAssembly)\r\ntest _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\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\ntest_gap_fill_with_gapfiller_with_gaps (assembly_test.TestAssembly)\r\ntest _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\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\ntest_get_assembly_kmer (assembly_test.TestAssembly)\r\ntest _get_assembly_kmer ... ok\r\ntest_has_gaps_to_fill (assembly_test.TestAssembly)\r\ntest _has_gaps_to_fill ... ok\r\ntest_parse_bam (assembly_test.TestAssembly)\r\ntest _parse_bam ... ok\r\ntest_rename_scaffolds (assembly_test.TestAssembly)\r\ntest _rename_scaffolds ... ok\r\ntest_scaffold_with_sspace (assembly_test.TestAssembly)\r\ntest _scaffold_with_sspace ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\ntest_filter_mummer_variants (assembly_variants_test.TestAssemblyVariants)\r\ntest filter_mummer_variants ... ok\r\ntest_get_codon_start (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_codon_start ... ok\r\ntest_get_mummer_variants_has_variants (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_mummer_variants when there are variants ... ok\r\ntest_get_mummer_variants_no_variants (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_mummer_variants when no variants ... ok\r\ntest_get_one_variant_for_one_contig_coding (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_one_variant_for_one_contig_coding ... ok\r\ntest_get_one_variant_for_one_contig_non_coding (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_one_variant_for_one_contig_non_coding ... ok\r\ntest_get_remaining_known_ref_variants_amino_acids (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_remaining_known_ref_variants with amino acids ... ok\r\ntest_get_remaining_known_ref_variants_nucleotides (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_remaining_known_ref_variants with nucleotides ... ok\r\ntest_get_variant_effect (assembly_variants_test.TestAssemblyVariants)\r\ntest _get_variant_effect ... ok\r\ntest_get_variants_presence_absence (assembly_variants_test.TestAssemblyVariants)\r\ntest get_variants presence absence genes ... ok\r\ntest_get_variants_variants_only (assembly_variants_test.TestAssemblyVariants)\r\ntest get_variants variants only ... ok\r\ntest_parse (bam_parse_test.TestBamParse)\r\ntest parse ... ok\r\ntest_sam_to_soft_clipped (bam_parse_test.TestBamParse)\r\ntest _sam_to_soft_clipped ... ok\r\ntest_update_soft_clipped_from_sam (bam_parse_test.TestBamParse)\r\ntest _update_soft_clipped_from_sam ... ok\r\ntest_update_unmapped_mates_from_sam (bam_parse_test.TestBamParse)\r\ntest _update_unmapped_mates_from_sam ... ok\r\ntest_write_soft_clipped_to_file (bam_parse_test.TestBamParse)\r\ntest _write_soft_clipped_to_file ... ok\r\ntest_write_unmapped_mates_to_file (bam_parse_test.TestBamParse)\r\ntest _write_unmapped_mates_to_file ... ok\r\nWARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nFailure: Error (Dependency error(s). Cannot continue) ... ERROR\r\ntest_ARO_accession (card_record_test.TestCardRecord)\r\ntest _ARO_accession ... ok\r\ntest_ARO_description (card_record_test.TestCardRecord)\r\ntest _ARO_description ... ok\r\ntest_ARO_id (card_record_test.TestCardRecord)\r\ntest _ARO_id ... ok\r\ntest_ARO_name (card_record_test.TestCardRecord)\r\ntest _ARO_name ... ok\r\ntest_ARO_name_to_fasta_name (card_record_test.TestCardRecord)\r\ntest _ARO_name_to_fasta_name ... ok\r\ntest_dna_seqs_and_genbank_ids (card_record_test.TestCardRecord)\r\ntest _dna_seqs_and_genbank_ids ... Missing data from foo\r\nMissing data from foo\r\nMissing data from foo\r\nMissing data from foo\r\nMissing data from foo\r\nMissing data from foo\r\nMissing data from foo\r\nok\r\ntest_get_data (card_record_test.TestCardRecord) ... ok\r\ntest_snps (card_record_test.TestCardRecord)\r\ntest snps ... ok\r\nWARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nFailure: Error (Dependency error(s). Cannot continue) ... ERROR\r\ntest_full_run_assembly_fail (cluster_test.TestCluster)\r\ntest complete run of cluster when assembly fails ... ERROR\r\ntest_full_run_choose_ref_fail (cluster_test.TestCluster)\r\ntest complete run of cluster when choosing ref seq fails ... ERROR\r\ntest_full_run_ok_non_coding (cluster_test.TestCluster)\r\ntest complete run of cluster on a noncoding sequence ... ERROR\r\ntest_full_run_ok_presence_absence (cluster_test.TestCluster)\r\ntest complete run of cluster on a presence absence gene ... ERROR\r\ntest_full_run_ok_variants_only_variant_is_present (cluster_test.TestCluster)\r\ntest complete run of cluster on a variants only gene when variant is present ... ERROR\r\ntest_full_run_ok_variants_only_variant_not_present (cluster_test.TestCluster)\r\ntest complete run of cluster on a variants only gene when variant not present ... ERROR\r\ntest_full_run_ok_variants_only_variant_not_present_always_report (cluster_test.TestCluster)\r\ntest complete run of cluster on a variants only gene when variant not present but always report variant ... ERROR\r\ntest_init_fail_files_missing (cluster_test.TestCluster)\r\ntest init_fail_files_missing ... ok\r\ntest_make_reads_for_assembly_proper_sample (cluster_test.TestCluster)\r\nTest _make_reads_for_assembly when sampling from reads ... ok\r\ntest_make_reads_for_assembly_symlinks (cluster_test.TestCluster)\r\nTest _make_reads_for_assembly when just makes symlinks ... ok\r\ntest_number_of_reads_for_assembly (cluster_test.TestCluster)\r\nTest _number_of_reads_for_assembly ... ok\r\nWARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nFailure: Error (Dependency error(s). Cannot continue) ... ERROR\r\ntest_cat_files (common_test.TestCommon)\r\ntest cat_files ... ok\r\ntest_external_progs_ok (external_progs_test.TestExternalProgs)\r\nTest 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\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\nWARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nFailure: Error (Dependency error(s). Cannot continue) ... ERROR\r\ntest_add (flag_test.TestFlag)\r\nTest add ... ok\r\ntest_has (flag_test.TestFlag)\r\nTest has ... ok\r\ntest_init_and_to_number (flag_test.TestFlag)\r\nTest __init__ and to_number ... ok\r\ntest_set_flag (flag_test.TestFlag)\r\nTest set_flag ... ok\r\ntest_str (flag_test.TestFlag)\r\nTest __str__ ... ok\r\ntest_to_long_str (flag_test.TestFlag)\r\nTest to_long_str ... ok\r\ntest_add (histogram_test.TestCluster)\r\nTest add ... ok\r\ntest_len (histogram_test.TestCluster)\r\nTest __len__ ... ok\r\ntest_stats (histogram_test.TestCluster)\r\nTest stats ... ok\r\ntest_to_bin (histogram_test.TestCluster)\r\nTest _to_bin ... ok\r\ntest_distance_to_contig_end (link_test.TestLink)\r\ntest _distance_to_contig_end ... ok\r\ntest_distance_to_contig_ends (link_test.TestLink)\r\ntest _distance_to_contig_ends ... ok\r\ntest_init_no_links (link_test.TestLink)\r\ntest link __init__ no links made ... ok\r\ntest_init_with_link (link_test.TestLink)\r\ntest link __init__ link made ... ok\r\ntest_insert_size (link_test.TestLink)\r\ntest insert_size ... ok\r\ntest_lt (link_test.TestLink)\r\ntest __lt__ ... ok\r\ntest_merge (link_test.TestLink)\r\ntest merge ... ok\r\ntest_sort (link_test.TestLink)\r\ntest sort ... ok\r\ntest_swap (link_test.TestLink)\r\ntest _swap ... ok\r\nWARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nFailure: Error (Dependency error(s). Cannot continue) ... ERROR\r\ntest_clean (read_store_test.TestReadStore)\r\nTest clean ... ok\r\ntest_compress_and_index_file (read_store_test.TestReadStore)\r\nTest _compress_and_index_file ... ok\r\ntest_get_reads (read_store_test.TestReadStore)\r\nTest get_reads ... ok\r\ntest_sort_file (read_store_test.TestReadStore)\r\ntest _sort_file ... ok\r\ntest_get_ref_files_naming_each_file (ref_preparer_test.TestRefPreparer) ... ok\r\ntest_get_ref_files_ref_prefix (ref_preparer_test.TestRefPreparer)\r\ntest _get_ref_files using ref_prefix ... ok\r\ntest_write_info_file (ref_preparer_test.TestRefPreparer)\r\ntest _write_info_file ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nERROR\r\ntest_all_non_wild_type_variants (reference_data_test.TestReferenceData)\r\nTest all_non_wild_type_variants ... ok\r\ntest_cluster_with_cdhit (reference_data_test.TestReferenceData)\r\nTest cluster_with_cd_hit ... The following command failed with exit code 127\r\ncd-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\r\n\r\nThe output was:\r\n\r\n/bin/sh: 1: cd-hit-est: not found\r\n\r\nERROR\r\ntest_cluster_with_cdhit_clusters_in_file (reference_data_test.TestReferenceData)\r\nTest cluster_with_cd_hit clusters from file ... ok\r\ntest_dict_keys_intersection (reference_data_test.TestReferenceData)\r\nTest dict_keys_intersection ... ok\r\ntest_filter_bad_variant_data (reference_data_test.TestReferenceData)\r\nTest _filter_bad_variant_data ... ok\r\ntest_find_gene_in_seqs (reference_data_test.TestReferenceData)\r\nTest _find_gene_in_seqs ... ok\r\ntest_get_filename (reference_data_test.TestReferenceData)\r\nTest _get_filename ... ok\r\ntest_init_fails (reference_data_test.TestReferenceData)\r\nTest __init__ fails when it should ... ok\r\ntest_init_ok (reference_data_test.TestReferenceData)\r\nTest init with good input ... ok\r\ntest_load_fasta_file (reference_data_test.TestReferenceData)\r\nTest _load_fasta_file ... ok\r\ntest_load_metadata_tsv (reference_data_test.TestReferenceData)\r\nTest _load_metadata_tsv ... ok\r\ntest_make_catted_fasta (reference_data_test.TestReferenceData)\r\nTest make_catted_fasta ... ok\r\ntest_new_seq_name (reference_data_test.TestReferenceData)\r\nTest _new_seq_name ... ok\r\ntest_remove_bad_genes (reference_data_test.TestReferenceData)\r\nTest _remove_bad_genes ... ok\r\ntest_rename_metadata_set (reference_data_test.TestReferenceData)\r\nTest _rename_metadata_set ... ok\r\ntest_rename_names_in_metadata (reference_data_test.TestReferenceData)\r\nTest _rename_names_in_metadata ... ok\r\ntest_rename_names_in_seq_dicts (reference_data_test.TestReferenceData)\r\nTest _rename_names_in_seq_dicts ... ok\r\ntest_rename_sequences (reference_data_test.TestReferenceData)\r\nTest rename_sequences ... Had to rename some sequences. See tmp.test_rename_sequences.out for old -> new names\r\nok\r\ntest_seq_names_to_rename_dict (reference_data_test.TestReferenceData)\r\nTest _seq_names_to_rename_dict ... ok\r\ntest_sequence (reference_data_test.TestReferenceData)\r\nTest sequence ... ok\r\ntest_sequence_length (reference_data_test.TestReferenceData)\r\nTest sequence_length ... ok\r\ntest_sequence_type (reference_data_test.TestReferenceData)\r\nTest sequence_type ... ok\r\ntest_try_to_get_gene_seq (reference_data_test.TestReferenceData)\r\nTest _try_to_get_gene_seq ... ok\r\ntest_write_cluster_allocation_file (reference_data_test.TestReferenceData)\r\nTest write_cluster_allocation_file ... ok\r\ntest_write_dict_of_sequences (reference_data_test.TestReferenceData)\r\nTest _write_dict_of_sequences ... ok\r\ntest_write_metadata_tsv (reference_data_test.TestReferenceData)\r\nTest _write_metadata_tsv ... ok\r\ntest_write_seqs_to_fasta (reference_data_test.TestReferenceData)\r\nTest write_seqs_to_fasta ... ok\r\ntest_dict_to_report_line (report_filter_test.TestReportFilter)\r\nTest _dict_to_report_line ... ok\r\ntest_filter_dicts (report_filter_test.TestReportFilter)\r\nTest _filter_dicts ... ok\r\ntest_filter_list_of_dicts_all_fail (report_filter_test.TestReportFilter)\r\nTest _filter_list_of_dicts where all fail ... ok\r\ntest_filter_list_of_dicts_with_essential (report_filter_test.TestReportFilter)\r\nTest _filter_list_of_dicts with an essential line but all others fail ... ok\r\ntest_filter_list_of_dicts_with_pass (report_filter_test.TestReportFilter)\r\nTest _filter_list_of_dicts with a line that passes ... ok\r\ntest_flag_passes_filter (report_filter_test.TestReportFilter)\r\nTest _flag_passes_filter ... ok\r\ntest_init_bad_file (report_filter_test.TestReportFilter)\r\ntest __init__ on bad input file ... ok\r\ntest_init_good_file (report_filter_test.TestReportFilter)\r\ntest __init__ on good input file ... ok\r\ntest_load_report (report_filter_test.TestReportFilter) ... ok\r\ntest_remove_all_after_first_frameshift (report_filter_test.TestReportFilter)\r\nTest _remove_all_after_first_frameshift ... ok\r\ntest_report_dict_passes_essential_filters (report_filter_test.TestReportFilter)\r\nTest _report_dict_passes_essential_filters ... ok\r\ntest_report_dict_passes_non_essential_filters_known_vars (report_filter_test.TestReportFilter)\r\nTest _report_dict_passes_non_essential_filters with known vars ... ok\r\ntest_report_dict_passes_non_essential_filters_synonymous (report_filter_test.TestReportFilter)\r\nTest _report_dict_passes_non_essential_filters with synonymous AA changes ... ok\r\ntest_report_line_to_dict (report_filter_test.TestReportFilter) ... ok\r\ntest_run (report_filter_test.TestReportFilter)\r\nTest run ... ok\r\ntest_write_report_tsv (report_filter_test.TestReportFilter)\r\nTest write_report_tsv ... ok\r\nWARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nFailure: Error (Dependency error(s). Cannot continue) ... ERROR\r\ntest_contig_graph_is_consistent (scaffold_graph_test.TestScaffoldGraph)\r\ntest _contig_graph_is_consistent ... ok\r\ntest_make_graph (scaffold_graph_test.TestScaffoldGraph)\r\ntest _make_graph ... ok\r\ntest_remove_low_cov_links (scaffold_graph_test.TestScaffoldGraph)\r\ntest _remove_low_cov_links ... ok\r\ntest_update_from_sam (scaffold_graph_test.TestScaffoldGraph)\r\ntest update_from_sam ... ok\r\ntest_write_all_links_to_file (scaffold_graph_test.TestScaffoldGraph)\r\ntest write_all_links_to_file ... ok\r\ntest_has_variant (sequence_metadata_test.TestSequenceMetadata)\r\ntest has_variant ... ok\r\ntest_init_fails_on_bad_lines (sequence_metadata_test.TestSequenceMetadata)\r\nTest init fails on bad lines ... ok\r\ntest_init_on_good_input (sequence_metadata_test.TestSequenceMetadata)\r\ntest init ok on good input ... ok\r\ntest_str (sequence_metadata_test.TestSequenceMetadata)\r\ntest __str__ ... ok\r\ntest_to_string (sequence_metadata_test.TestSequenceMetadata)\r\ntest to_string ... ok\r\ntest_has_variant (sequence_variant_test.TestSequenceVariant)\r\ntest has_variant ... ok\r\ntest_init_fails_on_bad_variant_strings (sequence_variant_test.TestSequenceVariant)\r\nTest init fails on bad variant strings ... ok\r\ntest_init_ok (sequence_variant_test.TestSequenceVariant)\r\nTest init ok ... ok\r\ntest_init_str (sequence_variant_test.TestSequenceVariant)\r\nTest init ok and str ... ok\r\ntest_nucleotide_range (sequence_variant_test.TestSequenceVariant)\r\ntest nucleotide_range ... ok\r\ntest_sanity_check_against_seq_no_translate (sequence_variant_test.TestSequenceVariant)\r\ntest sanity_check_against_seq with translate False ... ok\r\ntest_sanity_check_against_seq_translate (sequence_variant_test.TestSequenceVariant)\r\ntest sanity_check_against_seq with translate True ... ok\r\ntest_add_data_dict (summary_cluster_test.TestSummaryCluster)\r\nTest add_data_dict ... ok\r\ntest_column_summary_data (summary_cluster_test.TestSummaryCluster)\r\nTest column_summary_data ... ok\r\ntest_get_nonsynonymous_var (summary_cluster_test.TestSummaryCluster)\r\nTest _get_nonsynonymous_var ... ok\r\ntest_has_any_known_variant (summary_cluster_test.TestSummaryCluster) ... ok\r\ntest_has_any_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _has_any_nonsynonymous ... ok\r\ntest_has_any_novel_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _has_any_novel_nonsynonymous ... ok\r\ntest_has_known_variant (summary_cluster_test.TestSummaryCluster)\r\nTest _has_known_variant ... ok\r\ntest_has_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _has_nonsynonymous ... ok\r\ntest_has_novel_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _has_novel_nonsynonymous ... ok\r\ntest_has_resistance (summary_cluster_test.TestSummaryCluster)\r\nTest _has_resistance ... ok\r\ntest_has_var_groups (summary_cluster_test.TestSummaryCluster)\r\nTest has_var_groups ... ok\r\ntest_line2dict (summary_cluster_test.TestSummaryCluster)\r\nTest _line2dict ... ok\r\ntest_non_synon_variants (summary_cluster_test.TestSummaryCluster)\r\nTest non_synon_variants ... ok\r\ntest_pc_id_of_longest (summary_cluster_test.TestSummaryCluster)\r\nTest pc_id_of_longest ... ok\r\ntest_to_cluster_summary_has_known_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _to_cluster_summary_has_known_nonsynonymous ... ok\r\ntest_to_cluster_summary_has_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _to_cluster_summary_has_nonsynonymous ... ok\r\ntest_to_cluster_summary_has_novel_nonsynonymous (summary_cluster_test.TestSummaryCluster)\r\nTest _to_cluster_summary_has_novel_nonsynonymous ... ok\r\ntest_to_cluster_summary_number (summary_cluster_test.TestSummaryCluster)\r\nTest _to_cluster_summary_assembled ... ok\r\ntest_column_summary_data (summary_sample_test.TestSummarySample)\r\nTest _column_summary_data ... ok\r\ntest_load_file (summary_sample_test.TestSummarySample)\r\nTest _load_file ... ok\r\ntest_var_groups (summary_sample_test.TestSummarySample)\r\ntest _var_groups ... ok\r\ntest_variant_column_names_tuples (summary_sample_test.TestSummarySample)\r\nTest _variant_column_names_tuples ... ok\r\ntest_add_phandango_colour_columns (summary_test.TestSummary)\r\nTest _add_phandango_colour_columns ... ok\r\ntest_determine_cluster_cols (summary_test.TestSummary) ... ok\r\ntest_determine_var_cols (summary_test.TestSummary) ... ok\r\ntest_distance_score_between_lists (summary_test.TestSummary)\r\nTest _distance_score_between_lists ... ok\r\ntest_distance_score_bewteen_values (summary_test.TestSummary)\r\nTest _distance_score_bewteen_values ... ok\r\ntest_filter_matrix_columns (summary_test.TestSummary)\r\nTest _filter_matrix_columns ... ok\r\ntest_filter_matrix_rows (summary_test.TestSummary)\r\nTest _filter_matrix_rows ... ok\r\ntest_gather_output_rows (summary_test.TestSummary)\r\nTest _gather_output_rows ... ok\r\ntest_get_all_cluster_names (summary_test.TestSummary)\r\nTest _get_all_cluster_names ... ok\r\ntest_get_all_var_groups (summary_test.TestSummary)\r\ntest _get_all_var_groups ... ok\r\ntest_get_all_variant_columns (summary_test.TestSummary)\r\nTest _get_all_variant_columns ... ok\r\ntest_init (summary_test.TestSummary)\r\nTest init ... ok\r\ntest_load_input_files (summary_test.TestSummary)\r\nTest _load_input_files ... ok\r\ntest_matrix_to_csv (summary_test.TestSummary)\r\nTest _matrix_to_csv ... ok\r\ntest_newick_from_dist_matrix (summary_test.TestSummary)\r\nTest _newick_from_dist_matrix ... ok\r\ntest_to_matrix (summary_test.TestSummary)\r\nTest _to_matrix ... ok\r\ntest_write_distance_matrix (summary_test.TestSummary)\r\nTest _write_distance_matrix ... ok\r\ntest_get_all_versions (versions_test.TestVersions)\r\nTest get_all_versions ... WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly\r\nWARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly\r\nERROR: cdhit not found in path. Looked for cd-hit-est\r\n\r\nSomething wrong with at least one dependency. Please see the above error message(s)\r\nok\r\ntest_fa_header_to_name_and_metadata (vfdb_parser_test.TestVfdbParser)\r\ntest _fa_header_to_name_and_metadata ... ok\r\ntest_fa_header_to_name_pieces (vfdb_parser_test.TestVfdbParser)\r\ntest _fa_header_to_name_pieces ... ok\r\ntest_run (vfdb_parser_test.TestVfdbParser)\r\ntest run ... ok\r\n\r\n======================================================================\r\nERROR: test_assemble_with_spades (assembly_test.TestAssembly)\r\ntest _assemble_with_spades\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py\", line 39, in test_assemble_with_spades\r\n    a = assembly.Assembly(reads1, reads2, ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py\", line 61, in __init__\r\n    self.extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_assemble_with_spades_fail (assembly_test.TestAssembly)\r\ntest _assemble_with_spades handles spades fail\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py\", line 51, in test_assemble_with_spades_fail\r\n    a = assembly.Assembly(reads1, reads2, ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py\", line 61, in __init__\r\n    self.extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_gap_fill_with_gapfiller_no_gaps (assembly_test.TestAssembly)\r\ntest _gap_fill_with_gapfiller no gaps\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py\", line 93, in test_gap_fill_with_gapfiller_no_gaps\r\n    a = assembly.Assembly(reads1, reads2, 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py\", line 61, in __init__\r\n    self.extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_gap_fill_with_gapfiller_with_gaps (assembly_test.TestAssembly)\r\ntest _gap_fill_with_gapfiller with gaps\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py\", line 105, in test_gap_fill_with_gapfiller_with_gaps\r\n    a = assembly.Assembly(reads1, reads2, 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py\", line 61, in __init__\r\n    self.extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_scaffold_with_sspace (assembly_test.TestAssembly)\r\ntest _scaffold_with_sspace\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/assembly_test.py\", line 63, in test_scaffold_with_sspace\r\n    a = assembly.Assembly(reads1, reads2, ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/assembly.py\", line 61, in __init__\r\n    self.extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: Failure: Error (Dependency error(s). Cannot continue)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py\", line 39, in runTest\r\n    raise self.exc_val.with_traceback(self.tb)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py\", line 418, in loadTestsFromName\r\n    addr.filename, addr.module)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 47, in importFromPath\r\n    return self.importFromDir(dir_path, fqname)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 94, in importFromDir\r\n    mod = load_module(part_fqname, fh, filename, desc)\r\n  File \"/usr/lib/python3.4/imp.py\", line 235, in load_module\r\n    return load_source(name, filename, file)\r\n  File \"/usr/lib/python3.4/imp.py\", line 171, in load_source\r\n    module = methods.load()\r\n  File \"<frozen importlib._bootstrap>\", line 1220, in load\r\n  File \"<frozen importlib._bootstrap>\", line 1200, in _load_unlocked\r\n  File \"<frozen importlib._bootstrap>\", line 1129, in _exec\r\n  File \"<frozen importlib._bootstrap>\", line 1471, in exec_module\r\n  File \"<frozen importlib._bootstrap>\", line 321, in _call_with_frames_removed\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/best_seq_chooser_test.py\", line 9, in <module>\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: Failure: Error (Dependency error(s). Cannot continue)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py\", line 39, in runTest\r\n    raise self.exc_val.with_traceback(self.tb)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py\", line 418, in loadTestsFromName\r\n    addr.filename, addr.module)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 47, in importFromPath\r\n    return self.importFromDir(dir_path, fqname)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 94, in importFromDir\r\n    mod = load_module(part_fqname, fh, filename, desc)\r\n  File \"/usr/lib/python3.4/imp.py\", line 235, in load_module\r\n    return load_source(name, filename, file)\r\n  File \"/usr/lib/python3.4/imp.py\", line 171, in load_source\r\n    module = methods.load()\r\n  File \"<frozen importlib._bootstrap>\", line 1220, in load\r\n  File \"<frozen importlib._bootstrap>\", line 1200, in _load_unlocked\r\n  File \"<frozen importlib._bootstrap>\", line 1129, in _exec\r\n  File \"<frozen importlib._bootstrap>\", line 1471, in exec_module\r\n  File \"<frozen importlib._bootstrap>\", line 321, in _call_with_frames_removed\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cdhit_test.py\", line 8, in <module>\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_full_run_assembly_fail (cluster_test.TestCluster)\r\ntest complete run of cluster when assembly fails\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py\", line 128, in test_full_run_assembly_fail\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_assembly_fail'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.test_full_run_assembly_fail'\r\n\r\n======================================================================\r\nERROR: test_full_run_choose_ref_fail (cluster_test.TestCluster)\r\ntest complete run of cluster when choosing ref seq fails\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py\", line 110, in test_full_run_choose_ref_fail\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_choose_ref_fail'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.test_full_run_choose_ref_fail'\r\n\r\n======================================================================\r\nERROR: test_full_run_ok_non_coding (cluster_test.TestCluster)\r\ntest complete run of cluster on a noncoding sequence\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py\", line 148, in test_full_run_ok_non_coding\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_non_coding'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.test_full_run_ok_non_coding'\r\n\r\n======================================================================\r\nERROR: test_full_run_ok_presence_absence (cluster_test.TestCluster)\r\ntest complete run of cluster on a presence absence gene\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py\", line 174, in test_full_run_ok_presence_absence\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_presence_absence'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_presence_absence'\r\n\r\n======================================================================\r\nERROR: test_full_run_ok_variants_only_variant_is_present (cluster_test.TestCluster)\r\ntest complete run of cluster on a variants only gene when variant is present\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py\", line 238, in test_full_run_ok_variants_only_variant_is_present\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_variants_only.present'\r\n\r\n======================================================================\r\nERROR: test_full_run_ok_variants_only_variant_not_present (cluster_test.TestCluster)\r\ntest complete run of cluster on a variants only gene when variant not present\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/cluster_test.py\", line 200, in test_full_run_ok_variants_only_variant_not_present\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_variants_only.not_present'\r\n\r\n======================================================================\r\nERROR: test_full_run_ok_variants_only_variant_not_present_always_report (cluster_test.TestCluster)\r\ntest complete run of cluster on a variants only gene when variant not present but always report variant\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  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\r\n    shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ok_variants_only'), tmpdir)\r\n  File \"/usr/lib/python3.4/shutil.py\", line 303, in copytree\r\n    os.makedirs(dst)\r\n  File \"/usr/lib/python3.4/os.py\", line 237, in makedirs\r\n    mkdir(name, mode)\r\nFileExistsError: [Errno 17] File exists: 'tmp.cluster_test_full_run_ok_variants_only.not_present.always_report'\r\n\r\n======================================================================\r\nERROR: Failure: Error (Dependency error(s). Cannot continue)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py\", line 39, in runTest\r\n    raise self.exc_val.with_traceback(self.tb)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py\", line 418, in loadTestsFromName\r\n    addr.filename, addr.module)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 47, in importFromPath\r\n    return self.importFromDir(dir_path, fqname)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 94, in importFromDir\r\n    mod = load_module(part_fqname, fh, filename, desc)\r\n  File \"/usr/lib/python3.4/imp.py\", line 235, in load_module\r\n    return load_source(name, filename, file)\r\n  File \"/usr/lib/python3.4/imp.py\", line 171, in load_source\r\n    module = methods.load()\r\n  File \"<frozen importlib._bootstrap>\", line 1220, in load\r\n  File \"<frozen importlib._bootstrap>\", line 1200, in _load_unlocked\r\n  File \"<frozen importlib._bootstrap>\", line 1129, in _exec\r\n  File \"<frozen importlib._bootstrap>\", line 1471, in exec_module\r\n  File \"<frozen importlib._bootstrap>\", line 321, in _call_with_frames_removed\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/clusters_test.py\", line 12, in <module>\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_external_progs_ok (external_progs_test.TestExternalProgs)\r\nTest that external programs are found\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/external_progs_test.py\", line 8, in test_external_progs_ok\r\n    progs = external_progs.ExternalProgs(verbose=True)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nnose.proxy.Error: Dependency error(s). Cannot continue\r\n-------------------- >> begin captured stdout << ---------------------\r\n__________________ Checking dependencies and their versions ___________________\r\nbcftools\t1.3.1\t/usr/local/bin/bcftools\r\nbowtie2\t2.2.5\t/usr/bin/bowtie2\r\ncdhit\tNA\tNOT_FOUND\r\ngapfiller\tNA\tNOT_FOUND\r\nnucmer\t3.1\t/usr/bin/nucmer\r\nr\t3.3.0\t/usr/bin/Rscript\r\nsamtools\t1.3.1\t/usr/local/bin/samtools\r\nspades\t.8.0\tpython2 /home/genetica/Documentos/Software/SPAdes-3.8.0-Linux/bin/spades.py\r\nsspace\tNA\tNOT_FOUND\r\n\r\n\r\n--------------------- >> end captured stdout << ----------------------\r\n\r\n======================================================================\r\nERROR: Failure: Error (Dependency error(s). Cannot continue)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py\", line 39, in runTest\r\n    raise self.exc_val.with_traceback(self.tb)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py\", line 418, in loadTestsFromName\r\n    addr.filename, addr.module)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 47, in importFromPath\r\n    return self.importFromDir(dir_path, fqname)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 94, in importFromDir\r\n    mod = load_module(part_fqname, fh, filename, desc)\r\n  File \"/usr/lib/python3.4/imp.py\", line 235, in load_module\r\n    return load_source(name, filename, file)\r\n  File \"/usr/lib/python3.4/imp.py\", line 171, in load_source\r\n    module = methods.load()\r\n  File \"<frozen importlib._bootstrap>\", line 1220, in load\r\n  File \"<frozen importlib._bootstrap>\", line 1200, in _load_unlocked\r\n  File \"<frozen importlib._bootstrap>\", line 1129, in _exec\r\n  File \"<frozen importlib._bootstrap>\", line 1471, in exec_module\r\n  File \"<frozen importlib._bootstrap>\", line 321, in _call_with_frames_removed\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/faidx_test.py\", line 8, in <module>\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: Failure: Error (Dependency error(s). Cannot continue)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py\", line 39, in runTest\r\n    raise self.exc_val.with_traceback(self.tb)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py\", line 418, in loadTestsFromName\r\n    addr.filename, addr.module)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 47, in importFromPath\r\n    return self.importFromDir(dir_path, fqname)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 94, in importFromDir\r\n    mod = load_module(part_fqname, fh, filename, desc)\r\n  File \"/usr/lib/python3.4/imp.py\", line 235, in load_module\r\n    return load_source(name, filename, file)\r\n  File \"/usr/lib/python3.4/imp.py\", line 171, in load_source\r\n    module = methods.load()\r\n  File \"<frozen importlib._bootstrap>\", line 1220, in load\r\n  File \"<frozen importlib._bootstrap>\", line 1200, in _load_unlocked\r\n  File \"<frozen importlib._bootstrap>\", line 1129, in _exec\r\n  File \"<frozen importlib._bootstrap>\", line 1471, in exec_module\r\n  File \"<frozen importlib._bootstrap>\", line 321, in _call_with_frames_removed\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/mapping_test.py\", line 10, in <module>\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_write_info_file (ref_preparer_test.TestRefPreparer)\r\ntest _write_info_file\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/ref_preparer_test.py\", line 109, in test_write_info_file\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n======================================================================\r\nERROR: test_cluster_with_cdhit (reference_data_test.TestReferenceData)\r\nTest cluster_with_cd_hit\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/reference_data_test.py\", line 557, in test_cluster_with_cdhit\r\n    got = refdata.cluster_with_cdhit(inprefix, outprefix)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/reference_data.py\", line 486, in cluster_with_cdhit\r\n    new_clusters = cdhit_runner.run()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/cdhit.py\", line 190, in run\r\n    common.syscall(cmd, verbose=self.verbose)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/common.py\", line 22, in syscall\r\n    sys.exit(1)\r\nnose.proxy.SystemExit: 1\r\n\r\n======================================================================\r\nERROR: Failure: Error (Dependency error(s). Cannot continue)\r\n----------------------------------------------------------------------\r\nTraceback (most recent call last):\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/failure.py\", line 39, in runTest\r\n    raise self.exc_val.with_traceback(self.tb)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/loader.py\", line 418, in loadTestsFromName\r\n    addr.filename, addr.module)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 47, in importFromPath\r\n    return self.importFromDir(dir_path, fqname)\r\n  File \"/home/genetica/Documentos/Software/ariba-master/.eggs/nose-1.3.7-py3.4.egg/nose/importer.py\", line 94, in importFromDir\r\n    mod = load_module(part_fqname, fh, filename, desc)\r\n  File \"/usr/lib/python3.4/imp.py\", line 235, in load_module\r\n    return load_source(name, filename, file)\r\n  File \"/usr/lib/python3.4/imp.py\", line 171, in load_source\r\n    module = methods.load()\r\n  File \"<frozen importlib._bootstrap>\", line 1220, in load\r\n  File \"<frozen importlib._bootstrap>\", line 1200, in _load_unlocked\r\n  File \"<frozen importlib._bootstrap>\", line 1129, in _exec\r\n  File \"<frozen importlib._bootstrap>\", line 1471, in exec_module\r\n  File \"<frozen importlib._bootstrap>\", line 321, in _call_with_frames_removed\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/tests/samtools_variants_test.py\", line 9, in <module>\r\n    extern_progs = external_progs.ExternalProgs()\r\n  File \"/home/genetica/Documentos/Software/ariba-master/ariba/external_progs.py\", line 115, in __init__\r\n    raise Error('Dependency error(s). Cannot continue')\r\nariba.external_progs.Error: Dependency error(s). Cannot continue\r\n\r\n----------------------------------------------------------------------\r\nRan 219 tests in 3.644s\r\n\r\nFAILED (errors=21)\r\n"},"comment":{"url":"https://api.github.com/repos/sanger-pathogens/ariba/issues/comments/225980896","html_url":"https://github.com/sanger-pathogens/ariba/issues/95#issuecomment-225980896","issue_url":"https://api.github.com/repos/sanger-pathogens/ariba/issues/95","id":225980896,"user":{"login":"ramarquezo","id":10735852,"avatar_url":"https://avatars.githubusercontent.com/u/10735852?v=3","gravatar_id":"","url":"https://api.github.com/users/ramarquezo","html_url":"https://github.com/ramarquezo","followers_url":"https://api.github.com/users/ramarquezo/followers","following_url":"https://api.github.com/users/ramarquezo/following{/other_user}","gists_url":"https://api.github.com/users/ramarquezo/gists{/gist_id}","starred_url":"https://api.github.com/users/ramarquezo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramarquezo/subscriptions","organizations_url":"https://api.github.com/users/ramarquezo/orgs","repos_url":"https://api.github.com/users/ramarquezo/repos","events_url":"https://api.github.com/users/ramarquezo/events{/privacy}","received_events_url":"https://api.github.com/users/ramarquezo/received_events","type":"User","site_admin":false},"created_at":"2016-06-14T18:54:40Z","updated_at":"2016-06-14T18:54:40Z","body":"Hi again martinghunt.\r\nAriba 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?\r\n\r\nThanks in advance!!   \r\n"}}
{"actor":{"display_login":"ramarquezo"}}