[Debian-med-packaging] Bug#951944: ariba: FTBFS: dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.7 returned exit code 13
Lucas Nussbaum
lucas at debian.org
Sun Feb 23 06:54:59 GMT 2020
Source: ariba
Version: 2.14.4+ds-2
Severity: serious
Justification: FTBFS on amd64
Tags: buster sid
Usertags: ftbfs-20200222 ftbfs-buster
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules build
> dh build --with python3 --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:217: python3.7 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:217: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/assembly_compare.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/versions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/link.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/aln_to_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/megares_zip_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/summary_cluster_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/mapping.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/summary_cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/mic_plotter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/reference_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/histogram.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/vfdb_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/report_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/clusters.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/samtools_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/faidx.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/mlst_reporter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/ref_seq_chooser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/mlst_profile.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/bam_parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/pubmlst_ref_preparer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/pubmlst_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/sequence_variant.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/sequence_metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/card_record.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/common.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/read_store.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/assembly_variants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/ref_genes_getter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/cluster.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/cdhit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/external_progs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/assembly.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/report_flag_expander.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/megares_data_finder.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/scaffold_graph.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/summary_sample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> copying ariba/read_filter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/megares_zip_parser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/flag_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/assembly_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/faidx_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/versions_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/megares_data_finder_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/aln_to_metadata_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/sequence_metadata_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/summary_cluster_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/summary_sample_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/histogram_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/scaffold_graph_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/assembly_compare_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/mic_plotter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/samtools_variants_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/ref_genes_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/ncbi_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/pubmlst_ref_preparer_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/mlst_reporter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/read_filter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/report_flag_expander_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/mapping_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/ref_preparer_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/pubmlst_getter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/cdhit_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/common_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/link_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/external_progs_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/report_filter_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/read_store_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/sequence_variant_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/vfdb_parser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/bam_parse_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/cluster_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/ref_seq_chooser_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/assembly_variants_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/tb_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/card_record_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/clusters_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/summary_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/test_refdata_query.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/summary_cluster_variant_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/mlst_profile_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> copying ariba/tests/reference_data_test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/getref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/reportfilter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/refquery.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/flag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/pubmlstget.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/test.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/prepareref.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/aln2meta.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/expandflag.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/summary.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/prepareref_tb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/pubmlstspecies.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> copying ariba/tasks/micplot.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tasks
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
> copying ariba/test_run_data/ref_seqs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
> copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
> copying ariba/test_run_data/metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
> copying ariba/test_run_data/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
> copying ariba/test_run_data/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/test_run_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/panel.20181221.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/NC_000962.3.gb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/panel.20181115.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/panel.20190102.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/NC_000962.3.fa.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/panel.20181221.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/panel.20190102.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> copying ariba/tb_data/panel.20181115.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tb_data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_run.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_sequence.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_fails.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_dummy_db.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_fix_out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_report.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_flag_expander.run.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_ok.params.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_fix_in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/pubmlst_getter.dbases.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_to_matrix.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/graph_test_update_from_sam.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_check_too_short.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_load_fofn -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_count_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_sequence_type.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_fix_out.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_rename_file.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.no_link.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_sort_file.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_run_fermilite.expected.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_init_good.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_parse.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_run.expected.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_data_info_file -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run.in.read_store -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/test_common_cat_files.in.1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/test_common_cat_files.in.3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_ok.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_rename_sequences.out -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_whole_run.out.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_rename_sequences.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.make_link.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/dummy.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_profile_test.profile.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_fasta_file.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_dummy_db.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_init_refdata.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refdata_query_prepareref.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/test_common_cat_files.in.2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_init_refdata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_to_matrix.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_fails.empty.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_ok.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_init_bad.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_filter_test_write_report.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_clean.in -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_run.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/report_flag_expander.run.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_init.fofn -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_sequence.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_test_count_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/read_store_test_sort_file.out -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_check_too_long.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_fix_out.rename -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/refcheck_test_check_ok.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> copying ariba/tests/data/test_common_cat_files.out -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/refdata_query_prepareref
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
> copying ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
> copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
> copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
> copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
> copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
> copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run.out
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_run_with_tb.ref
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
> copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
> copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
> copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
> copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
> copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
> copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
> copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
> copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
> copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
> copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
> copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
> copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
> copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
> copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
> copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
> copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
> copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
> copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
> copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
> copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
> copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
> copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
> copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
> copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
> copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
> copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
> copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
> copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
> copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/megares_zip_parser_write_files
> copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/megares_zip_parser_write_files
> copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/megares_zip_parser_write_files
> copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/megares_zip_parser_write_files
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
> copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
> copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
> copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
> copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
> copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
> copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
> copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
> copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
> copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
> copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
> copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
> copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
> copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
> copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
> copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
> copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
> copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
> copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
> copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
> copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
> copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
> copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
> copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
> copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
> copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene
> running build_ext
> building 'minimap_ariba' extension
> creating build
> creating build/temp.linux-amd64-3.7
> creating build/temp.linux-amd64-3.7/ariba
> creating build/temp.linux-amd64-3.7/ariba/ext
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.7m -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-amd64-3.7/ariba/ext/minimap_ariba.o
> ariba/ext/minimap_ariba.cpp: In function ‘bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)’:
> ariba/ext/minimap_ariba.cpp:371:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
> 371 | if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l))
> | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ariba/ext/minimap_ariba.cpp:381:26: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
> 381 | startOk = (r->qs < endTolerance || refLength - r->re < endTolerance);
> | ~~~~~~^~~~~~~~~~~~~~
> ariba/ext/minimap_ariba.cpp:382:60: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
> 382 | endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance);
> | ~~~~~~^~~~~~~~~~~~~~
> ariba/ext/minimap_ariba.cpp:386:26: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
> 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance);
> | ~~~~~~^~~~~~~~~~~~~~
> ariba/ext/minimap_ariba.cpp:386:50: warning: comparison of integer expressions of different signedness: ‘const int32_t’ {aka ‘const int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare]
> 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance);
> | ~~~~~~^~~~~~~~~~~~~~
> x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/ariba/ext/minimap_ariba.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/minimap_ariba.cpython-37m-x86_64-linux-gnu.so -lz -lminimap
> building 'fermilite_ariba' extension
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-amd64-3.7/ariba/ext/fml-asm_ariba.o
> x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/ariba/ext/fml-asm_ariba.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/fermilite_ariba.cpython-37m-x86_64-linux-gnu.so -lz -lfml
> building 'vcfcall_ariba' extension
> x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.7m -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-amd64-3.7/ariba/ext/vcfcall_ariba.o
> x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/ariba/ext/vcfcall_ariba.o -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/vcfcall_ariba.cpython-37m-x86_64-linux-gnu.so
> running build_scripts
> creating build/scripts-3.7
> copying and adjusting scripts/ariba -> build/scripts-3.7
> changing mode of build/scripts-3.7/ariba from 644 to 755
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build; python3.7 -m nose -v
> WARNING: spades not found in path. Looked for spades.py
> test _check_coding_seq ... ok
> test _check_insertion_coords ... ok
> test _check_seq_lengths_same ... ok
> test _check_sequences with coding seqs ... ok
> test _check_sequences with noncoding seqs ... ok
> test _check_variants_match_sequences ... ok
> test _insertion_coords ... ok
> test _load_aln_file ... ok
> test _load_vars_file bad input files ... ok
> test _load_vars_file good input file ... ok
> test _make_cluster_file ... ok
> test _make_unpadded_insertion_coords ... ok
> test _make_unpadded_seqs ... ok
> test _padded_to_unpadded_nt_position ... ok
> 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 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 ... ok
> test variant_ids_are_unique ... ok
> 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 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 ... ok
> test _find_previous_start_codon ... ok
> test _gene_from_nucmer_match ... ok
> test _get_assembled_reference_sequences ... ok
> test _get_gene_matching_ref ... ok
> test _longest_nucmer_hit_in_ref ... ok
> test nucmer_hit_containing_reference_position ... ok
> test _nucmer_hits_to_assembly_coords ... ok
> test _nucmer_hits_to_percent_identity ... ok
> test _nucmer_hits_to_ref_and_qry_coords ... ok
> test nucmer_hits_to_ref_coords ... ok
> test _parse_nucmer_coords_file ... ok
> test ref_cov_per_contig ... ok
> test _ref_covered_by_at_least_one_full_length_contig ... ok
> test _ref_has_region_assembled_twice ... ok
> test _whole_gene_covered_by_nucmer_hits ... ok
> test _assemble_with_fermilite ... FAIL
> test _assemble_with_fermilite fails ... ok
> test _assemble_with_spades ... SKIP: Spades assembler is optional and is not configured
> test _assemble_with_spades handles spades fail ... SKIP: Spades assembler is optional and is not configured
> test _check_spades_log_file ... Error running SPAdes. Cannot continue. This is the error from the log file /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/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 ... ok
> test _parse_bam ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam'
> ok
> test _run_fermilite ... FAIL
> test _run_fermilite when it fails ... ok
> test filter_mummer_variants ... ok
> test _get_codon_start ... ok
> test _get_mummer_variants when there are variants ... ok
> test _get_mummer_variants when no variants ... ok
> test _get_remaining_known_ref_variants with amino acids ... ok
> test _get_remaining_known_ref_variants with nucleotides ... ok
> test _get_variant_effect ... ok
> test get_variants presence absence genes ... ok
> test get_variants variants only ... ok
> test _get_one_variant_for_one_contig_coding ... ok
> test _get_one_variant_for_one_contig_non_coding ... ok
> test parse ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_parse.bam'
> ok
> test _sam_to_soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam'
> [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam'
> ok
> test _update_soft_clipped_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam'
> [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam'
> ok
> test _update_unmapped_mates_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam'
> [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam'
> ok
> test _write_soft_clipped_to_file ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/dummy.bam'
> ok
> test _write_unmapped_mates_to_file ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/dummy.bam'
> ok
> test _ARO_accession ... ok
> test _ARO_description ... ok
> test _ARO_id ... ok
> test _ARO_name ... ok
> test _ARO_name_to_fasta_name ... ok
> 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 (ariba.tests.card_record_test.TestCardRecord) ... ok
> test snps ... ok
> test fake_run ... ok
> test fake_run min_cluster 42 ... ok
> test fake_run with non-unique names ... ok
> test _get_clusters_from_bak_file ... ok
> test_get_run_cmd_with_default_memory ... ok
> test_get_run_cmd_with_non_default_memory ... ok
> test_get_run_cmd_with_unlimited_memory ... ok
> test init_fail_infile_missing ... ok
> test_init_fail_invalid_memory ... ok
> test _load_user_clusters_file with bad input files ... ok
> test _load_user_clusters_file with good input file ... WARNING: ignoring sequence seq6 from clusters file because not in fasta file. This probably means it failed sanity checks - see the log files 01.filter.check_genes.log, 01.filter.check_metadata.log.
> ok
> test _load_user_clusters_file with good input file with some renamed ... ok
> test run ... ok
> test run_get_clusters_from_file ... ok
> test run_get_clusters_from_file with renaming ... ok
> test run with min_cluster_number 42 ... ok
> test complete run of cluster when assembly fails ... ok
> test complete run of cluster when choosing ref seq fails ... FAIL
> test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var ... FAIL
> Test complete run where there is a deleted codon ... FAIL
> Test complete run where there is a inserted codon ... FAIL
> test complete run where samtools calls a snp at a known snp location in a presence/absence gene ... FAIL
> test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding ... FAIL
> Test complete run where there is a codon with a SNP and an indel ... FAIL
> test complete run of cluster when filtering removes all reads ... ok
> test complete run where gene extended because too different at end for full nucmer match ... FAIL
> test complete run of cluster on a noncoding sequence ... FAIL
> test complete run of cluster on a presence absence gene ... FAIL
> test complete run of cluster on a variants only gene when variant is present ... FAIL
> test complete run of cluster on a variants only gene when variant not present ... FAIL
> test complete run of cluster on a variants only gene when variant not present but always report variant ... FAIL
> Test complete run where only part of the ref gene is present in the reads ... FAIL
> test complete run of cluster when nearest ref is outside cluster ... FAIL
> test complete run where samtools calls a snp in a presence/absence noncoding sequence at a known snp position ... FAIL
> test complete run where samtools calls a snp in a presence/absence gene ... FAIL
> test complete run where samtools calls a snp in a presence/absence noncoding sequence ... FAIL
> test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant ... FAIL
> test complete run where samtools calls a snp in a variant only gene ... FAIL
> test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant ... FAIL
> test complete run where samtools calls a snp in a presence/absence noncoding sequence ... FAIL
> test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var ... FAIL
> test init_fail_files_missing ... ok
> Test _make_reads_for_assembly when sampling from reads ... ok
> Test _make_reads_for_assembly when just makes symlinks ... ok
> Test _number_of_reads_for_assembly ... ok
> test _write_catted_genes_matching_refs_fasta ... ok
> test _load_minimap_files ... ok
> test _load_minimap_insert_histogram ... ok
> test _load_minimap_out_cluster2representative ... ok
> test _load_minimap_out_cluster_counts ... ok
> test _load_minimap_proper_pairs ... ok
> test _load_reference_data_from_dir ... ok
> test _load_reference_data_info_file ... ok
> test test_minimap_reads_to_all_ref_seqs ... ok
> test complete run with TB amr calling ... FAIL
> test _set_insert_size_data ... ok
> test _write_catted_assembled_seqs_fasta ... ok
> test _write_catted_assemblies_fasta ... ok
> test _write_mlst_reports ... ok
> test_write_report (ariba.tests.clusters_test.TestClusters) ... ok
> test _write_tb_resistance_calls_json ... ok
> test cat_files ... ok
> test rmtree ... ok
> Test that external programs are found ... ok
> test write_fa_subset ... ok
> Test add ... ok
> Test has ... ok
> Test __init__ and to_number ... ok
> Test set_flag ... ok
> Test __str__ ... ok
> Test to_comma_separated_string ... ok
> Test to_long_str ... ok
> Test add ... ok
> Test __len__ ... ok
> Test stats ... ok
> Test _to_bin ... ok
> test _distance_to_contig_end ... ok
> test _distance_to_contig_ends ... ok
> test link __init__ no links made ... ok
> test link __init__ link made ... ok
> test insert_size ... ok
> test __lt__ ... ok
> test merge ... ok
> test sort ... ok
> test _swap ... ok
> test bowtie2_index ... ok
> Test get_total_alignment_score ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam'
> ok
> Test run_bowtie2 unsorted ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam'
> [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bowtie2.bam'
> ok
> Test run_bowtie2 sorted ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam'
> ok
> Test run_bowtie2 unsorted remove both unmapped ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam'
> [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bowtie2_remove_both_unmapped.bam'
> ok
> test sam_pair_to_insert ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam'
> ok
> test sam_to_fastq ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam'
> ok
> test _get_url_for_version ... ok
> test _zips_from_index_page_string ... ok
> test _extract_files when all ok ... ok
> test _extract_files when one missing ... ok
> test _load_annotations_file ... ok
> test _load_header_mappings_file ... ok
> test _write_files ... WARNING: sequence "Only_in_fasta_file" has no record in annotations file
> WARNING: sequence "Only_in_fasta_file" has no record in header mappings file
> ok
> test _bottom_scatter_data ... ok
> test _filter_top_plot_data ... ok
> test _get_colours ... ok
> Test _get_top_plot_data ... ok
> Test _load_mic_file ... ok
> Test _load_summary_file ... ok
> Test _mic_string_to_float ... ok
> test _ordered_bottom_plot_rows ... ok
> test _ordered_colunns ... ok
> test _top_plot_scatter_counts ... ok
> test _top_plot_scatter_data ... ok
> test _top_plot_violin_data ... ok
> test _top_plot_y_ticks ... ok
> Test get_sequence_type ... ok
> Test has_gene ... ok
> test init ... WARNING: Same profile found twice in input file, but two different STs. Going to use the ST with the smaller number (2)
> ... STs are 2 3 and alleles are nusA:1, rpoB:26, eno:2, gltB:4, lepA:59, nuoL:2, nrdA:5
> ok
> test init ... ok
> test when all alleles 100% there no variants ... ok
> test when one gene has a het snp ... ok
> test when one gene has two het snps ... ok
> test when allele combination is new ... ok
> test when one gene missing ... ok
> test _get_profile_and_fasta_urls ... ok
> test _get_species_list ... ok
> test _rename_seqs_in_fasta ... ok
> test _filter_seq_dict ... WARNING: Median sequence length is 5 but seq1 has length 1 which is too long or short. Removing.
> WARNING: Median sequence length is 5 but seq5 has length 14 which is too long or short. Removing.
> ok
> test _load_fasta_files_and_write_clusters_file ... WARNING: spades not found in path. Looked for spades.py
> ok
> test _cdhit_clstr_to_reads ... ok
> Test clean ... ok
> Test _compress_and_index_file ... ok
> Test get_reads fasta pair ... ok
> Test get_reads fastq interleaved ... ok
> Test get_reads fastq pair ... ok
> Test get_reads subset ... ok
> test _sort_file ... ok
> test _fix_virulencefinder_fasta_file ... WARNING: found line with ">" not at the start! Fixing. Line:AC>seq3 in file /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa
> WARNING: found line with ">" at the end! Fixing. Line:AACGT> in file /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa
> ok
> test _fasta_to_metadata ... ok
> test _rename_clusters ... ok
> test run ... WARNING. 1 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them:
> grep REMOVE tmp.ref_preparer_test_run/01.filter.check_genes.log
> cat tmp.ref_preparer_test_run/01.filter.check_noncoding.log
> WARNING. Problem with at least one variant. Problem variants are removed. Please see the file tmp.ref_preparer_test_run/01.filter.check_metadata.log for details.
> ok
> test run with no metadata input, all sequences are noncoding ... ok
> test run with noncoding sequences that are outside of the allowed size range ... WARNING. 5 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them:
> grep REMOVE tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_genes.log
> cat tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_noncoding.log
> WARNING. Problem with at least one variant. Problem variants are removed. Please see the file tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_metadata.log for details.
> ok
> test _make_matching_contig_pieces_fasta ... ok
> Test full run where the best match is in the cluster ... ok
> Test full run where there is a match in cluster, but better match to seq not in cluster ... ok
> Test full run where ref seq completely contains another seq outside cluster ... ok
> Test full run where amount of flanking seq varies ... ok
> Test full run when nearest match is not in the cluster ... ok
> Test full run when there is nearest match in cluster, but no nucmer matches ... ok
> Test all_non_wild_type_variants ... ok
> Test _check_noncoding_seq ... ok
> Test cluster_with_cd_hit clusters from file ... ok
> Test cluster_with_cd_hit do not run cdhit ... ok
> Test cluster_with_cd_hit ... ok
> Test _filter_bad_variant_data ... WARNING: sequence "non_coding_not_in_fasta" found in metadata, but not in fasta file. Ignoring it.
> WARNING: sequence "presence_absence_not_in_fasta" found in metadata, but not in fasta file. Ignoring it.
> WARNING: sequence "variants_only_not_in_fasta" found in metadata, but not in fasta file. Ignoring it.
> ok
> Test __init__ fails when it should ... ok
> Test init with good input ... ok
> Test _load_all_fasta_files ... ok
> Test _load_all_metadata_tsvs ... ok
> Test _load_fasta_file ... ok
> Test _load_input_files_and_check_seq_names with bad input ... ok
> Test _load_input_files_and_check_seq_names with good input ... WARNING: sequence "seq3" found in metadata, but not in fasta file. Ignoring it.
> ok
> Test _load_metadata_tsv ... ok
> Test _load_rename_file ... ok
> Test _new_seq_name ... ok
> Test _remove_bad_genes ... ok
> Test _remove_bad_noncoding_seqs ... ok
> Test _rename_metadata_set ... ok
> Test _rename_names_in_metadata ... ok
> Test _rename_names_in_seq_dict ... ok
> Test rename_sequences ... ok
> Test _seq_names_to_rename_dict ... ok
> Test sequence ... ok
> Test sequence_type ... ok
> Test _try_to_get_gene_seq ... ok
> Test write_cluster_allocation_file ... ok
> Test _write_metadata_tsv ... ok
> Test write_seqs_to_fasta ... ok
> Test _write_sequences_to_files ... ok
> Test _dict_to_report_line ... ok
> Test _filter_dicts ... ok
> Test _filter_list_of_dicts where all fail ... ok
> Test _filter_list_of_dicts with an essential line but all others fail ... ok
> Test _filter_list_of_dicts with a line that passes ... ok
> Test _flag_passes_filter ... ok
> test __init__ on bad input file ... ok
> test __init__ on good input file ... ok
> test_load_report (ariba.tests.report_filter_test.TestReportFilter) ... ok
> Test _remove_all_after_first_frameshift ... ok
> Test _remove_all_after_first_frameshift when gene is complete ... ok
> Test _report_dict_passes_essential_filters ... ok
> Test _report_dict_passes_non_essential_filters with known vars ... ok
> Test _report_dict_passes_non_essential_filters with synonymous AA changes ... ok
> test_report_line_to_dict (ariba.tests.report_filter_test.TestReportFilter) ... ok
> Test run ... ok
> Test write_report_tsv ... ok
> test run ... ok
> test get_depths_at_position ... ok
> test _get_read_depths ... ok
> test _get_variant_positions_from_vcf ... ok
> test _get_variants ... ok
> test _make_vcf_and_read_depths_files ... ok
> test total_depth_per_contig ... ok
> test variants_in_coords ... ok
> test _contig_graph_is_consistent ... ok
> test _make_graph ... ok
> test _remove_low_cov_links ... ok
> test update_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam'
> ok
> test write_all_links_to_file ... ok
> test has_variant ... ok
> Test init fails on bad lines ... ok
> test init ok on good input ... ok
> test __str__ ... ok
> test to_string ... ok
> test has_variant ... ok
> Test init fails on bad variant strings ... ok
> Test init ok ... ok
> Test init ok and str ... ok
> test nucleotide_range ... ok
> test sanity_check_against_seq with translate False ... ok
> test sanity_check_against_seq with translate True ... ok
> Test add_data_dict ... ok
> Test column_summary_data ... ok
> test gather_data ... ok
> test _get_all_nonsynon_variants_set ... ok
> Test _get_known_noncoding_het_snp ... ok
> Test _get_nonsynonymous_var ... ok
> test_has_any_known_variant (ariba.tests.summary_cluster_test.TestSummaryCluster) ... ok
> Test _has_any_nonsynonymous ... ok
> Test _has_any_novel_nonsynonymous ... ok
> Test _has_any_part_of_ref_assembled ... ok
> Test _has_known_variant ... ok
> Test _has_match ... ok
> Test _has_nonsynonymous ... ok
> Test _has_novel_nonsynonymous ... ok
> Test has_var_groups ... ok
> test known_noncoding_het_snps ... ok
> Test _line2dict ... ok
> Test non_synon_variants ... ok
> Test _pc_id_and_read_depth_of_longest ... ok
> Test _to_cluster_summary_has_known_nonsynonymous ... ok
> Test _to_cluster_summary_has_nonsynonymous ... ok
> Test _to_cluster_summary_has_novel_nonsynonymous ... ok
> Test _to_cluster_summary_assembled ... ok
> test _filter_depths ... ok
> test _get_is_het_and_percent ... ok
> Test _has_nonsynonymous ... ok
> test __init__ ... ok
> Test _column_summary_data ... ok
> Test _load_file ... ok
> test _var_groups ... ok
> Test _variant_column_names_tuples_and_het_snps ... ok
> Test _add_phandango_colour_columns ... ok
> test_determine_cluster_cols (ariba.tests.summary_test.TestSummary) ... ok
> Test _distance_score_between_lists ... ok
> Test _distance_score_bewteen_values ... ok
> Test _filter_matrix_columns ... ok
> Test _filter_matrix_rows ... ok
> test gather_unfiltered_output_data ... ok
> Test init ... ok
> Test _load_fofn ... ok
> Test _load_input_files ... ok
> Test _matrix_to_csv ... ok
> Test _matrix_to_csv with remove_nas ... ok
> Test _newick_from_dist_matrix ... ok
> Test _to_matrix all columns ... ok
> Test _to_matrix with assembled column only ... ok
> Test _to_matrix with cluster columns only ... ok
> Test _to_matrix with groups ... ok
> Test _to_matrix with vars ... ok
> Test whole run to check csv ok (skip making tree) ... ok
> Test _write_distance_matrix ... ok
> test genbank_to_gene_coords ... ok
> test load_mutations ... ok
> test make_prepareref_dir ... ok
> test make_prepareref_files ... ok
> test report_to_resistance_dict ... ok
> test write_prepareref_fasta_file ... ok
> test write_prepareref_metadata_file ... ok
> test _cluster2seqs ... ok
> test _load_clusters ... ok
> test query with unknown query ... ok
> test _seq2cluster ... ok
> test _seqinfo ... ok
> Test get_all_versions ... WARNING: spades not found in path. Looked for spades.py
> ok
> test _fa_header_to_name_and_metadata ... ok
> test _fa_header_to_name_pieces ... ok
> test run ... ok
>
> ======================================================================
> FAIL: test _assemble_with_fermilite
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/assembly_test.py", line 53, in test_assemble_with_fermilite
> self.assertTrue(a.assembled_ok)
> AssertionError: False is not true
>
> ======================================================================
> FAIL: test _run_fermilite
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/assembly_test.py", line 21, in test_run_fermilite
> self.assertEqual(0, got)
> AssertionError: 0 != 1
>
> ======================================================================
> FAIL: test complete run of cluster when choosing ref seq fails
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 130, in test_full_run_choose_ref_fail
> self.assertEqual([expected], c.report_lines)
> AssertionError: Lists differ: ['.\t.\t.\t.\t1024\t2\tcluster_name\t.\t.\t.\t.\t.\t.\t[49 chars]\t.'] != ['.\t.\t.\t.\t64\t2\tcluster_name\t.\t.\t.\t.\t.\t.\t.\[47 chars]\t.']
>
> First differing element 0:
> '.\t.\t.\t.\t1024\t2\tcluster_name\t.\t.\t.\t.\t.\t.\t[48 chars].\t.'
> '.\t.\t.\t.\t64\t2\tcluster_name\t.\t.\t.\t.\t.\t.\t.\[46 chars].\t.'
>
> - ['.\t.\t.\t.\t1024\t2\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> ? ^^^
>
> + ['.\t.\t.\t.\t64\t2\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> ? ^
>
> '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 500, in test_full_run_cluster_test_full_run_smtls_snp_varonly_nonc
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_seq\tref_seq\t0\t1\t147\t148\tcluster[169 chars]\t.'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_seq\tref_seq\t0\t1\t147\t148\tcluster[168 chars]p\t.'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_seq\tref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tn\tA18G\t1\t.\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\tref_seq:0:1:A18G:.:Description of A18G snp\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: Test complete run where there is a deleted codon
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 555, in test_full_run_delete_codon
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['presence_absence1\tpresence_absence1\t1\t[191 chars]ce1'] != ['.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'presence_absence1\tpresence_absence1\t1\t[190 chars]nce1'
> '.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t117\t'
> - '117\t92.31\tcluster_name.l15.c30.ctg.1\t1104\t20.0\t0\t.\tp\t.\t0\t'
> - 'R25_A26del\tDEL\t73\t73\tA\t553\t553\tA\t27\tA\t27\t.\tGeneric description '
> - 'of presence_absence1']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: Test complete run where there is a inserted codon
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 573, in test_full_run_insert_codon
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['presence_absence1\tpresence_absence1\t1\t[194 chars]ce1'] != ['.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'presence_absence1\tpresence_absence1\t1\t[193 chars]nce1'
> '.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t108\t'
> - '108\t92.31\tcluster_name.l15.c30.ctg.1\t1115\t19.9\t0\t.\tp\t.\t0\t'
> - 'S25_M26insELI\tINS\t73\t73\tA\t554\t554\tG\t24\tG\t24\t.\tGeneric '
> - 'description of presence_absence1']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp at a known snp location in a presence/absence gene
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 349, in test_full_run_known_smtls_snp_presabs_gene
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_gene\tref_gene\t1\t0\t155\t148\tclust[189 chars]\t.'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_gene\tref_gene\t1\t0\t155\t148\tclust[188 chars]p\t.'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_gene\tref_gene\t1\t0\t155\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tp\tM6I\t0\t.\t.\t16\t18\tATG\t'
> - '135\t137\tATG\t65;64;63\tA;T;G,A\t65;64;32,31\t'
> - 'ref_gene:1:0:M6I:.:Description of M6I snp\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 460, in test_full_run_known_smtls_snp_presabs_nonc
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_seq\tref_seq\t0\t0\t147\t148\tcluster[169 chars]\t.'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_seq\tref_seq\t0\t0\t147\t148\tcluster[168 chars]p\t.'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_seq\tref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tn\tG18A\t0\t.\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\tref_seq:0:0:G18A:.:Description of G18A snp\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: Test complete run where there is a codon with a SNP and an indel
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 537, in test_full_run_multiple_vars_in_codon
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['presence_absence1\tpresence_absence1\t1\t[439 chars]ce1'] != ['.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'presence_absence1\tpresence_absence1\t1\t[203 chars]nce1'
> '.\t.\t.\t.\t64\t292\tcluster_name\t.\t.\t[60 chars].\t.'
>
> First list contains 1 additional elements.
> First extra element 1:
> 'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t96\t96\t96.91\tcluster_name.l15.c30.ctg.1\t1074\t20.4\t0\t.\tp\t.\t0\tA10fs\tFSHIFT\t28\t28\tG\t491\t491\tG\t26\tG\t26\t.\tGeneric description of presence_absence1'
>
> Diff is 647 characters long. Set self.maxDiff to None to see it.
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where gene extended because too different at end for full nucmer match
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 293, in test_full_run_ok_gene_start_mismatch
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['gene\tgene\t1\t0\t27\t112\tcluster_name\t[128 chars]ene'] != ['.\t.\t.\t.\t64\t112\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'gene\tgene\t1\t0\t27\t112\tcluster_name\t[127 chars]gene'
> '.\t.\t.\t.\t64\t112\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t112\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['gene\tgene\t1\t0\t27\t112\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l6.c30.ctg.1\t362\t27.8\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> - '.\t.\t.\t.\tGeneric description of gene']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run of cluster on a noncoding sequence
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 197, in test_full_run_ok_non_coding
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['noncoding1\tnoncoding1\t0\t0\t531\t72\tcl[1389 chars]ng1'] != ['.\t.\t.\t.\t64\t72\tcluster_name\t.\t.\t.[60 chars]\t.']
>
> First differing element 0:
> 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcl[238 chars]ing1'
> '.\t.\t.\t.\t64\t72\tcluster_name\t.\t.\t.[59 chars].\t.'
>
> First list contains 5 additional elements.
> First extra element 1:
> 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\tcluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\tG61T\tSNP\t61\t61\tG\t121\t121\tT\t24\tT\t24\t.\tgeneric description of noncoding1'
>
> + ['.\t.\t.\t.\t64\t72\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\t'
> - 'cluster_name.l15.c30.ctg.1\t234\t15.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t14\t'
> - '14\tA\t74\t74\tT\t19\tT\t19\tnoncoding1:0:0:A14T:.:ref has wild type, reads '
> - 'has variant so should report\tgeneric description of noncoding1',
> - 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\t'
> - 'cluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\tG61T\tSNP\t61\t61\tG\t'
> - '121\t121\tT\t24\tT\t24\t.\tgeneric description of noncoding1',
> - 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\t'
> - 'cluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\t.82C\tINS\t82\t82\tA\t'
> - '143\t143\tC\t23\tC\t23\t.\tgeneric description of noncoding1',
> - 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\t'
> - 'cluster_name.l15.c30.ctg.1\t234\t15.4\t0\t.\tn\t.\t0\tT108.\tDEL\t108\t108\t'
> - 'T\t168\t168\tC\t17\tC\t17\t.\tgeneric description of noncoding1',
> - 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\t'
> - 'cluster_name.l15.c30.ctg.1\t234\t15.4\t1\tSNP\tn\tA6G\t1\t.\t.\t6\t6\tG\t66\t'
> - '66\tG\t19\tG\t19\tnoncoding1:0:0:A6G:.:variant in ref and reads so should '
> - 'report\tgeneric description of noncoding1',
> - 'noncoding1\tnoncoding1\t0\t0\t531\t72\tcluster_name\t120\t120\t95.87\t'
> - 'cluster_name.l15.c30.ctg.1\t234\t15.4\t1\tSNP\tn\tG9T\t0\t.\t.\t9\t9\tG\t69\t'
> - '69\tG\t19\tG\t19\tnoncoding1:0:0:G9T:.:wild type in ref and reads\tgeneric '
> - 'description of noncoding1']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run of cluster on a presence absence gene
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 220, in test_full_run_ok_presence_absence
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['presence_absence1\tpresence_absence1\t1\t[1134 chars]ce1'] != ['.\t.\t.\t.\t64\t64\tcluster_name\t.\t.\t.[60 chars]\t.']
>
> First differing element 0:
> 'presence_absence1\tpresence_absence1\t1\t[276 chars]nce1'
> '.\t.\t.\t.\t64\t64\tcluster_name\t.\t.\t.[59 chars].\t.'
>
> First list contains 3 additional elements.
> First extra element 1:
> 'presence_absence1\tpresence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.l15.c30.ctg.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t52\t54\tATT\t107\t109\tATC\t31;31;32\tA;T;C\t31;31;32\t.\tGeneric description of presence_absence1'
>
> Diff is 1395 characters long. Set self.maxDiff to None to see it.
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run of cluster on a variants only gene when variant is present
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 276, in test_full_run_ok_variants_only_variant_is_present
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['variants_only1\tvariants_only1\t1\t1\t27\[537 chars]ly1'] != ['.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.[60 chars]\t.']
>
> First differing element 0:
> 'variants_only1\tvariants_only1\t1\t1\t27\[240 chars]nly1'
> '.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.[59 chars].\t.'
>
> First list contains 1 additional elements.
> First extra element 1:
> 'variants_only1\tvariants_only1\t1\t1\t27\t66\tcluster_name\t96\t96\t100.0\tcluster_name.l15.c30.ctg.1\t215\t15.3\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tGCG\t71\t73\tGCG\t17;17;17\tG;C;G\t17;17;17\tvariants_only1:1:1:I5A:.:Ref and reads have variant so report\tGeneric description of variants_only1'
>
> Diff is 744 characters long. Set self.maxDiff to None to see it.
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run of cluster on a variants only gene when variant not present
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 238, in test_full_run_ok_variants_only_variant_not_present
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['variants_only1\tvariants_only1\t1\t1\t27\[259 chars]ly1'] != ['.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.[60 chars]\t.']
>
> First differing element 0:
> 'variants_only1\tvariants_only1\t1\t1\t27\[258 chars]nly1'
> '.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.[59 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['variants_only1\tvariants_only1\t1\t1\t27\t66\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t215\t15.3\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tCGC\t'
> - '65\t67\tCGC\t18;18;19\tC;G;C\t18;18;19\tvariants_only1:1:1:R3S:.:Ref and '
> - 'assembly have wild type, so do not report\tGeneric description of '
> - 'variants_only1']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run of cluster on a variants only gene when variant not present but always report variant
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 256, in test_full_run_ok_variants_only_variant_not_present_always_report
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['variants_only1\tvariants_only1\t1\t1\t27\[267 chars]ly1'] != ['.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.[60 chars]\t.']
>
> First differing element 0:
> 'variants_only1\tvariants_only1\t1\t1\t27\[266 chars]nly1'
> '.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.[59 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t66\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['variants_only1\tvariants_only1\t1\t1\t27\t66\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t215\t15.3\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tCGC\t'
> - '65\t67\tCGC\t18;18;19\tC;G;C\t18;18;19\tvariants_only1:1:1:R3S:.:Ref and '
> - 'assembly have wild type, but always report anyway\tGeneric description of '
> - 'variants_only1']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: Test complete run where only part of the ref gene is present in the reads
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 518, in test_full_run_partial_assembly
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['presence_absence1\tpresence_absence1\t1\t[168 chars]ce1'] != ['.\t.\t.\t.\t64\t278\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'presence_absence1\tpresence_absence1\t1\t[167 chars]nce1'
> '.\t.\t.\t.\t64\t278\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t278\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['presence_absence1\tpresence_absence1\t1\t0\t19\t278\tcluster_name\t96\t77\t'
> - '100.0\tcluster_name.l15.c17.ctg.1\t949\t20.5\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> - '.\t.\t.\t.\t.\t.\t.\tGeneric description of presence_absence1']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run of cluster when nearest ref is outside cluster
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 150, in test_full_run_ref_not_in_cluster
> self.assertEqual([expected], c.report_lines)
> AssertionError: Lists differ: ['.\t.\t.\t.\t1024\t72\tcluster_name\t.\t.\t.\t.\t.\t.\[50 chars]\t.'] != ['.\t.\t.\t.\t64\t72\tcluster_name\t.\t.\t.\t.\t.\t.\t.[48 chars]\t.']
>
> First differing element 0:
> '.\t.\t.\t.\t1024\t72\tcluster_name\t.\t.\t.\t.\t.\t.\[49 chars].\t.'
> '.\t.\t.\t.\t64\t72\tcluster_name\t.\t.\t.\t.\t.\t.\t.[47 chars].\t.'
>
> - ['.\t.\t.\t.\t1024\t72\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> ? ^^^
>
> + ['.\t.\t.\t.\t64\t72\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> ? ^ +++
>
> - '.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> ? ---
>
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp in a presence/absence noncoding sequence at a known snp position
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 423, in test_full_run_smtls_known_snp_presabs_nonc
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_seq\tref_seq\t0\t0\t147\t148\tcluster[194 chars]seq'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_seq\tref_seq\t0\t0\t147\t148\tcluster[193 chars]_seq'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_seq\tref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tn\tG18A\t0\t.\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\tref_seq:0:0:G18A:.:Description of G18A\tGeneric '
> - 'description of ref_seq']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp in a presence/absence gene
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 310, in test_full_run_smtls_snp_presabs_gene
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_gene\tref_gene\t1\t0\t155\t148\tclust[160 chars]ene'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_gene\tref_gene\t1\t0\t155\t148\tclust[159 chars]gene'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_gene\tref_gene\t1\t0\t155\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\t.\tGeneric description of ref_gene']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp in a presence/absence noncoding sequence
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 406, in test_full_run_smtls_snp_presabs_nonc
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_seq\tref_seq\t0\t0\t147\t148\tcluster[157 chars]seq'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_seq\tref_seq\t0\t0\t147\t148\tcluster[156 chars]_seq'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_seq\tref_seq\t0\t0\t147\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\t.\tGeneric description of ref_seq']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 389, in test_full_run_smtls_snp_varonly_gene
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_gene\tref_gene\t1\t1\t155\t148\tclust[189 chars]\t.'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_gene\tref_gene\t1\t1\t155\t148\tclust[188 chars]p\t.'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_gene\tref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tp\tI6M\t1\t.\t.\t16\t18\tATG\t'
> - '135\t137\tATG\t65;64;63\tA;T;G,A\t65;64;32,31\t'
> - 'ref_gene:1:1:I6M:.:Description of I6M snp\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp in a variant only gene
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 329, in test_full_run_smtls_snp_varonly_gene_2
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_gene\tref_gene\t1\t1\t155\t148\tclust[160 chars]ene'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_gene\tref_gene\t1\t1\t155\t148\tclust[159 chars]gene'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_gene\tref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\t.\tGeneric description of ref_gene']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 369, in test_full_run_smtls_snp_varonly_gene_no_snp
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_gene\tref_gene\t1\t1\t155\t148\tclust[189 chars]\t.'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_gene\tref_gene\t1\t1\t155\t148\tclust[188 chars]p\t.'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_gene\tref_gene\t1\t1\t155\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tp\tM6I\t0\t.\t.\t16\t18\tATG\t'
> - '135\t137\tATG\t65;64;63\tA;T;G,A\t65;64;32,31\t'
> - 'ref_gene:1:1:M6I:.:Description of M6I snp\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp in a presence/absence noncoding sequence
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 440, in test_full_run_smtls_snp_varonly_nonc
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_seq\tref_seq\t0\t1\t147\t148\tcluster[157 chars]seq'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_seq\tref_seq\t0\t1\t147\t148\tcluster[156 chars]_seq'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_seq\tref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t0\tHET\t.\t.\t.\tG18A\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\t.\tGeneric description of ref_seq']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/cluster_test.py", line 480, in test_full_run_smtls_snp_varonly_nonc_no_snp
> self.assertEqual(expected, c.report_lines)
> AssertionError: Lists differ: ['ref_seq\tref_seq\t0\t1\t147\t148\tcluster[169 chars]\t.'] != ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[61 chars]\t.']
>
> First differing element 0:
> 'ref_seq\tref_seq\t0\t1\t147\t148\tcluster[168 chars]p\t.'
> '.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t[60 chars].\t.'
>
> + ['.\t.\t.\t.\t64\t148\tcluster_name\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t.\t'
> + '.\t.\t.\t.\t.\t.\t.\t.\t.\t.']
> - ['ref_seq\tref_seq\t0\t1\t147\t148\tcluster_name\t96\t96\t100.0\t'
> - 'cluster_name.l15.c30.ctg.1\t335\t39.8\t1\tSNP\tn\tG18A\t0\t.\t.\t18\t18\tG\t'
> - '137\t137\tG\t63\tG,A\t32,31\tref_seq:0:1:G18A:.:Description of G18A snp\t.']
> -------------------- >> begin captured stdout << ---------------------
> cluster_name detected 1 threads available to it
>
> --------------------- >> end captured stdout << ----------------------
>
> ======================================================================
> FAIL: test complete run with TB amr calling
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build/ariba/tests/clusters_test.py", line 349, in test_run_with_tb
> self.assertEqual(expect_json, got_json)
> AssertionError: {'Pyrazinamide': [['pncA', 'A3E']]} != {}
> - {'Pyrazinamide': [['pncA', 'A3E']]}
> + {}
> -------------------- >> begin captured stdout << ---------------------
> cluster detected 1 threads available to it
> cluster reported completion
> cluster_1 detected 1 threads available to it
> cluster_1 reported completion
>
> --------------------- >> end captured stdout << ----------------------
>
> ----------------------------------------------------------------------
> Ran 356 tests in 40.055s
>
> FAILED (SKIP=2, failures=26)
> E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_ariba/build; python3.7 -m nose -v
> dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.7 returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2020/02/22/ariba_2.14.4+ds-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
More information about the Debian-med-packaging
mailing list