Use of -e switch gives multifasta file with N's only #132
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One issue thats been reported a few days ago is that the gene names arent being extracted correctly from the gff files which I suspect would cause this bit to go haywire. I'll get a fix out for that in the next day or so, which will then hopefully solve things.... |
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Yea it would be great if you could send them to roary@sanger.ac.uk Thanks a million. |
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Have sent a small dataset (4 genomes) there, made using the don't delete On 1 June 2015 at 09:55, andrewjpage notifications@github.com wrote:
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Hi, then update Roary Regards, On 1 June 2015 at 11:50, dutchscientist notifications@github.com wrote:
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Great, will give that a go :-) |
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Unfortunately I still get a file full of N's, despite installing prank. I test with the set of Prokka 1.11-generated GFF files, which can be downloaded here: I do get the following text when installing via "sudo cpanm Bio::Roary" : Will try manual install as well. |
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Everything else is working, despite the warning, including the addition of the annotation with the query_pan_genome |
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Thanks for sending me the files. On 13 June 2015 at 02:41, dutchscientist notifications@github.com wrote:
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I'd be interested to know what tests are failing when Roary is On 13 June 2015 at 02:41, dutchscientist notifications@github.com wrote:
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Hi Andrew, this is the -v output. --> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK Bio-Roary-3.0.2/ Bio-Roary-3.0.2/AUTHORS Bio-Roary-3.0.2/bin/ Bio-Roary-3.0.2/binaries/ Bio-Roary-3.0.2/contrib/ Bio-Roary-3.0.2/deployment_process Bio-Roary-3.0.2/dist.ini Bio-Roary-3.0.2/GPL-LICENSE Bio-Roary-3.0.2/install_dependencies.sh Bio-Roary-3.0.2/lib/ Bio-Roary-3.0.2/LICENSE Bio-Roary-3.0.2/Makefile.PL Bio-Roary-3.0.2/MANIFEST Bio-Roary-3.0.2/META.yml Bio-Roary-3.0.2/README Bio-Roary-3.0.2/README.md Bio-Roary-3.0.2/t/ Bio-Roary-3.0.2/t/bin/ Bio-Roary-3.0.2/t/Bio/ Bio-Roary-3.0.2/t/data/ Bio-Roary-3.0.2/t/dummy_blastp Bio-Roary-3.0.2/t/dummy_cd-hit Bio-Roary-3.0.2/t/dummy_makeblastdb Bio-Roary-3.0.2/t/lib/ Bio-Roary-3.0.2/t/requires_external.t Bio-Roary-3.0.2/t/lib/TestHelper.pm Bio-Roary-3.0.2/t/data/accessory_graphs/ Bio-Roary-3.0.2/t/data/blast_results Bio-Roary-3.0.2/t/data/clustered_proteins Bio-Roary-3.0.2/t/data/clustered_proteins_pan_genome Bio-Roary-3.0.2/t/data/clustered_proteins_post_analysis Bio-Roary-3.0.2/t/data/clusters_input.fa Bio-Roary-3.0.2/t/data/clusters_to_inflate Bio-Roary-3.0.2/t/data/clusters_to_inflate.mcl Bio-Roary-3.0.2/t/data/clusters_to_inflate_original_input.fa Bio-Roary-3.0.2/t/data/clustersfile Bio-Roary-3.0.2/t/data/core_alignment/ Bio-Roary-3.0.2/t/data/core_alignment.csv Bio-Roary-3.0.2/t/data/core_alignment_core0.66.csv Bio-Roary-3.0.2/t/data/core_group_statistics.csv Bio-Roary-3.0.2/t/data/empty_file Bio-Roary-3.0.2/t/data/example_1.faa Bio-Roary-3.0.2/t/data/example_2.faa Bio-Roary-3.0.2/t/data/example_3.faa Bio-Roary-3.0.2/t/data/example_annotation.gff Bio-Roary-3.0.2/t/data/example_annotation.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/example_annotation_2.gff Bio-Roary-3.0.2/t/data/example_groups Bio-Roary-3.0.2/t/data/example_groups_without_labels Bio-Roary-3.0.2/t/data/exp_qc_report.csv Bio-Roary-3.0.2/t/data/exp_qc_report_real.csv Bio-Roary-3.0.2/t/data/expected_0.seq Bio-Roary-3.0.2/t/data/expected_5.seq Bio-Roary-3.0.2/t/data/expected_clustered_proteins Bio-Roary-3.0.2/t/data/expected_clusters_to_inflate Bio-Roary-3.0.2/t/data/expected_combined_proteome.fa Bio-Roary-3.0.2/t/data/expected_combined_proteome_with_filtering.fa Bio-Roary-3.0.2/t/data/expected_complement_of_groups.gg Bio-Roary-3.0.2/t/data/expected_complement_of_groups_core0.66.gg Bio-Roary-3.0.2/t/data/expected_core_gene_alignment.aln Bio-Roary-3.0.2/t/data/expected_core_gene_alignment_core0.66.aln Bio-Roary-3.0.2/t/data/expected_create_pan_genome.fa Bio-Roary-3.0.2/t/data/expected_example_annotation_1.faa Bio-Roary-3.0.2/t/data/expected_filtered_original_input.fa Bio-Roary-3.0.2/t/data/expected_gff_set_difference_common_set_statistics.csv Bio-Roary-3.0.2/t/data/expected_group_labels Bio-Roary-3.0.2/t/data/expected_group_statitics.csv Bio-Roary-3.0.2/t/data/expected_group_statitics_missing_genes.csv Bio-Roary-3.0.2/t/data/expected_group_statitics_verbose.csv Bio-Roary-3.0.2/t/data/expected_inflated_results Bio-Roary-3.0.2/t/data/expected_intersection_of_groups.gg Bio-Roary-3.0.2/t/data/expected_intersection_of_groups_core0.66.gg Bio-Roary-3.0.2/t/data/expected_nnn_at_end.fa Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.fa.aln Bio-Roary-3.0.2/t/data/expected_nuc_multifasta.faa Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes.tab Bio-Roary-3.0.2/t/data/expected_number_of_conserved_genes_0.6.tab Bio-Roary-3.0.2/t/data/expected_number_of_genes_in_pan_genome.tab Bio-Roary-3.0.2/t/data/expected_number_of_new_genes.tab Bio-Roary-3.0.2/t/data/expected_number_of_unique_genes.tab Bio-Roary-3.0.2/t/data/expected_out_of_order_fasta.fa.sorted.fa Bio-Roary-3.0.2/t/data/expected_output_core_missing_genes.aln Bio-Roary-3.0.2/t/data/expected_output_filtered.fa Bio-Roary-3.0.2/t/data/expected_output_groups Bio-Roary-3.0.2/t/data/expected_output_groups_cdhit Bio-Roary-3.0.2/t/data/expected_output_groups_group_2.fa Bio-Roary-3.0.2/t/data/expected_output_groups_group_2_multi.fa Bio-Roary-3.0.2/t/data/expected_output_groups_group_5.fa Bio-Roary-3.0.2/t/data/expected_output_groups_group_5_multi.fa Bio-Roary-3.0.2/t/data/expected_output_merged.aln Bio-Roary-3.0.2/t/data/expected_output_merged_sparse.aln Bio-Roary-3.0.2/t/data/expected_pan_genome.fa Bio-Roary-3.0.2/t/data/expected_pan_genome_one_gene_per_fasta.fa Bio-Roary-3.0.2/t/data/expected_pan_genome_reference.fa Bio-Roary-3.0.2/t/data/expected_prank_input.fa.aln Bio-Roary-3.0.2/t/data/expected_query_1.fna Bio-Roary-3.0.2/t/data/expected_query_2.fna Bio-Roary-3.0.2/t/data/expected_reannotated_groups_file Bio-Roary-3.0.2/t/data/expected_set_difference_common_set Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_plot.png Bio-Roary-3.0.2/t/data/expected_set_difference_common_set_statistics.csv Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_one_statistics.csv Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_plot.png Bio-Roary-3.0.2/t/data/expected_set_difference_unique_set_two_statistics.csv Bio-Roary-3.0.2/t/data/expected_uneven_sequences.fa Bio-Roary-3.0.2/t/data/expected_union_of_groups.gg Bio-Roary-3.0.2/t/data/genbank_gbff/ Bio-Roary-3.0.2/t/data/group_1.fa.aln Bio-Roary-3.0.2/t/data/group_9.fa Bio-Roary-3.0.2/t/data/kraken_report.txt Bio-Roary-3.0.2/t/data/kraken_test/ Bio-Roary-3.0.2/t/data/locus_tag_gffs/ Bio-Roary-3.0.2/t/data/mcl_file Bio-Roary-3.0.2/t/data/mdoH.fa.aln Bio-Roary-3.0.2/t/data/multfasta1.aln Bio-Roary-3.0.2/t/data/multfasta2.aln Bio-Roary-3.0.2/t/data/multfasta3.aln Bio-Roary-3.0.2/t/data/multfasta4.aln Bio-Roary-3.0.2/t/data/multfasta5.aln Bio-Roary-3.0.2/t/data/nnn_at_end.fa Bio-Roary-3.0.2/t/data/nnn_at_end.fa.sorted.fa Bio-Roary-3.0.2/t/data/nuc_multifasta.fa Bio-Roary-3.0.2/t/data/nuc_to_be_aligned.fa Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa Bio-Roary-3.0.2/t/data/out_of_order_fasta.fa.sorted.fa Bio-Roary-3.0.2/t/data/overall_gene_presence_absence.csv Bio-Roary-3.0.2/t/data/pan_genome_sequences/ Bio-Roary-3.0.2/t/data/post_analysis/ Bio-Roary-3.0.2/t/data/post_analysis_expected/ Bio-Roary-3.0.2/t/data/prank_input.fa Bio-Roary-3.0.2/t/data/proteome_with_and_without_descriptions.faa Bio-Roary-3.0.2/t/data/query_1.fa Bio-Roary-3.0.2/t/data/query_1.gff Bio-Roary-3.0.2/t/data/query_1_alternative_patterns.gff Bio-Roary-3.0.2/t/data/query_2.fa Bio-Roary-3.0.2/t/data/query_2.gff Bio-Roary-3.0.2/t/data/query_3.fa Bio-Roary-3.0.2/t/data/query_3.gff Bio-Roary-3.0.2/t/data/query_4_missing_genes.fa Bio-Roary-3.0.2/t/data/query_4_missing_genes.gff Bio-Roary-3.0.2/t/data/query_5.gff Bio-Roary-3.0.2/t/data/query_6.gff Bio-Roary-3.0.2/t/data/query_groups Bio-Roary-3.0.2/t/data/query_groups_all_merged Bio-Roary-3.0.2/t/data/query_groups_missing_genes Bio-Roary-3.0.2/t/data/raxml.tre Bio-Roary-3.0.2/t/data/real_data_1.gff Bio-Roary-3.0.2/t/data/real_data_2.gff Bio-Roary-3.0.2/t/data/real_data_core_gene_alignment.aln Bio-Roary-3.0.2/t/data/reformat_input_gffs/ Bio-Roary-3.0.2/t/data/reorder_isolates.tre Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_alpha.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_creation.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_height.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_breadth_revalpha.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_alpha.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_creation.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_height.csv Bio-Roary-3.0.2/t/data/reorder_isolates_expected_output_depth_revalpha.csv Bio-Roary-3.0.2/t/data/reorder_isolates_input.csv Bio-Roary-3.0.2/t/data/sequences_with_unknowns.faa Bio-Roary-3.0.2/t/data/shred1.gff Bio-Roary-3.0.2/t/data/shred1.shred.fa Bio-Roary-3.0.2/t/data/shred2.gff Bio-Roary-3.0.2/t/data/shred2.shred.fa Bio-Roary-3.0.2/t/data/sopB.fa.aln Bio-Roary-3.0.2/t/data/speH.fa.aln Bio-Roary-3.0.2/t/data/split_groups/ Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/ Bio-Roary-3.0.2/t/data/uneven_sequences.fa Bio-Roary-3.0.2/t/data/uneven_sequences.fa.sorted.fa Bio-Roary-3.0.2/t/data/variable_core/ Bio-Roary-3.0.2/t/data/variable_core/gene_1.fa.aln Bio-Roary-3.0.2/t/data/variable_core/gene_2.fa.aln Bio-Roary-3.0.2/t/data/variable_core/gene_3.fa.aln Bio-Roary-3.0.2/t/data/variable_core/gene_4.fa.aln Bio-Roary-3.0.2/t/data/variable_core/gene_5.fa.aln Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/argF.fa Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/different.fa Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/hly.fa Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/reannotated_groups_file Bio-Roary-3.0.2/t/data/split_pan_genome_sequences/speH.fa Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters1 Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters2 Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters3 Bio-Roary-3.0.2/t/data/split_groups/paralog_clusters4 Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters1 Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters2 Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters3 Bio-Roary-3.0.2/t/data/split_groups/paralog_exp_clusters4 Bio-Roary-3.0.2/t/data/split_groups/paralogs1.fa Bio-Roary-3.0.2/t/data/split_groups/paralogs2.fa Bio-Roary-3.0.2/t/data/split_groups/paralogs3.fa Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_2.gff Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_fixed_query_3.gff Bio-Roary-3.0.2/t/data/reformat_input_gffs/expected_real_1.gff Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_1.gff Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_2.gff Bio-Roary-3.0.2/t/data/reformat_input_gffs/query_3.gff Bio-Roary-3.0.2/t/data/reformat_input_gffs/real_1.gff Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.header.embl Bio-Roary-3.0.2/t/data/post_analysis_expected/accessory.tab Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.header.embl Bio-Roary-3.0.2/t/data/post_analysis_expected/core_accessory.tab Bio-Roary-3.0.2/t/data/post_analysis_expected/gene_presence_absence.csv Bio-Roary-3.0.2/t/data/post_analysis/_clustered Bio-Roary-3.0.2/t/data/post_analysis/_clustered.bak.clstr Bio-Roary-3.0.2/t/data/post_analysis/_clustered.clstr Bio-Roary-3.0.2/t/data/post_analysis/_combined_files Bio-Roary-3.0.2/t/data/post_analysis/_combined_files.groups Bio-Roary-3.0.2/t/data/post_analysis/_fasta_files Bio-Roary-3.0.2/t/data/post_analysis/_gff_files Bio-Roary-3.0.2/t/data/post_analysis/_uninflated_mcl_groups Bio-Roary-3.0.2/t/data/post_analysis/query_1.gff.proteome.faa Bio-Roary-3.0.2/t/data/post_analysis/query_2.gff.proteome.faa Bio-Roary-3.0.2/t/data/post_analysis/query_6.gff.proteome.faa Bio-Roary-3.0.2/t/data/pan_genome_sequences/argF.fa Bio-Roary-3.0.2/t/data/pan_genome_sequences/hly.fa Bio-Roary-3.0.2/t/data/pan_genome_sequences/speH.fa Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff Bio-Roary-3.0.2/t/data/locus_tag_gffs/query_5.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/kraken_test/database.idx Bio-Roary-3.0.2/t/data/kraken_test/database.jdb Bio-Roary-3.0.2/t/data/kraken_test/database.kdb Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/ Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/names.dmp Bio-Roary-3.0.2/t/data/kraken_test/taxonomy/nodes.dmp Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff Bio-Roary-3.0.2/t/data/genbank_gbff/genbank1.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff Bio-Roary-3.0.2/t/data/genbank_gbff/genbank2.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff Bio-Roary-3.0.2/t/data/genbank_gbff/genbank3.gff.proteome.faa.expected Bio-Roary-3.0.2/t/data/genbank_gbff/genbank_gene_presence_absence.csv Bio-Roary-3.0.2/t/data/core_alignment/argF.fa.aln Bio-Roary-3.0.2/t/data/core_alignment/hly.fa.aln Bio-Roary-3.0.2/t/data/core_alignment/speH.fa.aln Bio-Roary-3.0.2/t/data/accessory_graphs/core_deletion Bio-Roary-3.0.2/t/data/accessory_graphs/core_island Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.fa Bio-Roary-3.0.2/t/data/accessory_graphs/file_1.gff Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.fa Bio-Roary-3.0.2/t/data/accessory_graphs/file_2.gff Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.fa Bio-Roary-3.0.2/t/data/accessory_graphs/file_3.gff Bio-Roary-3.0.2/t/data/accessory_graphs/no_accessory Bio-Roary-3.0.2/t/data/accessory_graphs/one_branch Bio-Roary-3.0.2/t/data/accessory_graphs/one_bubble Bio-Roary-3.0.2/t/data/accessory_graphs/single_gene_contig Bio-Roary-3.0.2/t/data/accessory_graphs/two_graphs Bio-Roary-3.0.2/t/Bio/Roary/ Bio-Roary-3.0.2/t/Bio/Roary/AnalyseGroups.t Bio-Roary-3.0.2/t/Bio/Roary/AnnotateGroups.t Bio-Roary-3.0.2/t/Bio/Roary/ChunkFastaFile.t Bio-Roary-3.0.2/t/Bio/Roary/CombinedProteome.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ Bio-Roary-3.0.2/t/Bio/Roary/ContigsToGeneIDsFromGFF.t Bio-Roary-3.0.2/t/Bio/Roary/External/ Bio-Roary-3.0.2/t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t Bio-Roary-3.0.2/t/Bio/Roary/ExtractProteomeFromGFFs.t Bio-Roary-3.0.2/t/Bio/Roary/FilterFullClusters.t Bio-Roary-3.0.2/t/Bio/Roary/GeneNamesFromGFF.t Bio-Roary-3.0.2/t/Bio/Roary/GroupLabels.t Bio-Roary-3.0.2/t/Bio/Roary/GroupStatistics.t Bio-Roary-3.0.2/t/Bio/Roary/InflateClusters.t Bio-Roary-3.0.2/t/Bio/Roary/OrderGenes.t Bio-Roary-3.0.2/t/Bio/Roary/Output/ Bio-Roary-3.0.2/t/Bio/Roary/ParallelAllAgainstAllBlast.t Bio-Roary-3.0.2/t/Bio/Roary/PrepareInputFiles.t Bio-Roary-3.0.2/t/Bio/Roary/QC/ Bio-Roary-3.0.2/t/Bio/Roary/ReformatInputGFFs.t Bio-Roary-3.0.2/t/Bio/Roary/ReorderSpreadsheet.t Bio-Roary-3.0.2/t/Bio/Roary/SampleOrder.t Bio-Roary-3.0.2/t/Bio/Roary/SequenceLengths.t Bio-Roary-3.0.2/t/Bio/Roary/SortFasta.t Bio-Roary-3.0.2/t/Bio/Roary/SplitGroups.t Bio-Roary-3.0.2/t/Bio/Roary/QC/Report.t Bio-Roary-3.0.2/t/Bio/Roary/Output/DifferenceBetweenSets.t Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastaProtein.t Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastas.t Bio-Roary-3.0.2/t/Bio/Roary/Output/GroupsMultifastasNucleotide.t Bio-Roary-3.0.2/t/Bio/Roary/Output/NumberOfGroups.t Bio-Roary-3.0.2/t/Bio/Roary/Output/QueryGroups.t Bio-Roary-3.0.2/t/Bio/Roary/External/Blastp.t Bio-Roary-3.0.2/t/Bio/Roary/External/Cdhit.t Bio-Roary-3.0.2/t/Bio/Roary/External/Makeblastdb.t Bio-Roary-3.0.2/t/Bio/Roary/External/Mcl.t Bio-Roary-3.0.2/t/Bio/Roary/External/Prank.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/QueryRoary.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/Roary.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryCoreAlignment.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryPostAnalysis.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t Bio-Roary-3.0.2/t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t Bio-Roary-3.0.2/t/bin/dummy_blastp Bio-Roary-3.0.2/t/bin/dummy_cd-hit Bio-Roary-3.0.2/t/bin/dummy_makeblastdb Bio-Roary-3.0.2/t/bin/dummy_mcl Bio-Roary-3.0.2/t/bin/dummy_mcxdeblast Bio-Roary-3.0.2/t/bin/dummy_segmasker Bio-Roary-3.0.2/lib/Bio/ Bio-Roary-3.0.2/lib/Bio/Roary/ Bio-Roary-3.0.2/lib/Bio/Roary.pm Bio-Roary-3.0.2/lib/Bio/Roary/AnalyseGroups.pm Bio-Roary-3.0.2/lib/Bio/Roary/AnnotateGroups.pm Bio-Roary-3.0.2/lib/Bio/Roary/BedFromGFFRole.pm Bio-Roary-3.0.2/lib/Bio/Roary/ChunkFastaFile.pm Bio-Roary-3.0.2/lib/Bio/Roary/ClustersRole.pm Bio-Roary-3.0.2/lib/Bio/Roary/CombinedProteome.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ Bio-Roary-3.0.2/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm Bio-Roary-3.0.2/lib/Bio/Roary/Exceptions.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/ Bio-Roary-3.0.2/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFF.pm Bio-Roary-3.0.2/lib/Bio/Roary/ExtractProteomeFromGFFs.pm Bio-Roary-3.0.2/lib/Bio/Roary/FilterFullClusters.pm Bio-Roary-3.0.2/lib/Bio/Roary/FilterUnknownsFromFasta.pm Bio-Roary-3.0.2/lib/Bio/Roary/GeneNamesFromGFF.pm Bio-Roary-3.0.2/lib/Bio/Roary/GroupLabels.pm Bio-Roary-3.0.2/lib/Bio/Roary/GroupStatistics.pm Bio-Roary-3.0.2/lib/Bio/Roary/InflateClusters.pm Bio-Roary-3.0.2/lib/Bio/Roary/IterativeCdhit.pm Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/ Bio-Roary-3.0.2/lib/Bio/Roary/LookupGeneFiles.pm Bio-Roary-3.0.2/lib/Bio/Roary/MergeMultifastaAlignments.pm Bio-Roary-3.0.2/lib/Bio/Roary/OrderGenes.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/ Bio-Roary-3.0.2/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm Bio-Roary-3.0.2/lib/Bio/Roary/ParseGFFAnnotationRole.pm Bio-Roary-3.0.2/lib/Bio/Roary/PostAnalysis.pm Bio-Roary-3.0.2/lib/Bio/Roary/PrepareInputFiles.pm Bio-Roary-3.0.2/lib/Bio/Roary/QC/ Bio-Roary-3.0.2/lib/Bio/Roary/ReformatInputGFFs.pm Bio-Roary-3.0.2/lib/Bio/Roary/ReorderSpreadsheet.pm Bio-Roary-3.0.2/lib/Bio/Roary/SampleOrder.pm Bio-Roary-3.0.2/lib/Bio/Roary/SequenceLengths.pm Bio-Roary-3.0.2/lib/Bio/Roary/SortFasta.pm Bio-Roary-3.0.2/lib/Bio/Roary/SplitGroups.pm Bio-Roary-3.0.2/lib/Bio/Roary/QC/Report.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/BlastIdentityFrequency.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/DifferenceBetweenSets.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/EmblGroups.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupMultifasta.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastas.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/NumberOfGroups.pm Bio-Roary-3.0.2/lib/Bio/Roary/Output/QueryGroups.pm Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Local.pm Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Parallel.pm Bio-Roary-3.0.2/lib/Bio/Roary/JobRunner/Role.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/Blastp.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/Cdhit.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/IterativeCdhit.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/Makeblastdb.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/Mcl.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/PostAnalysis.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/Prank.pm Bio-Roary-3.0.2/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Common.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/CreatePanGenome.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/IterativeCdhit.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/QueryRoary.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/Roary.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm Bio-Roary-3.0.2/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm Bio-Roary-3.0.2/contrib/roary_plots/ Bio-Roary-3.0.2/contrib/roary_plots/README.md Bio-Roary-3.0.2/contrib/roary_plots/roary.html Bio-Roary-3.0.2/contrib/roary_plots/roary_files/ Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.ipynb Bio-Roary-3.0.2/contrib/roary_plots/roary_plots.py Bio-Roary-3.0.2/contrib/roary_plots/roary_files/jquery.min.js Bio-Roary-3.0.2/contrib/roary_plots/roary_files/MathJax.js Bio-Roary-3.0.2/contrib/roary_plots/roary_files/require.min.js Bio-Roary-3.0.2/binaries/darwin/ Bio-Roary-3.0.2/binaries/linux/ Bio-Roary-3.0.2/binaries/linux/bedtools Bio-Roary-3.0.2/binaries/linux/blastp Bio-Roary-3.0.2/binaries/linux/cd-hit Bio-Roary-3.0.2/binaries/linux/makeblastdb Bio-Roary-3.0.2/binaries/linux/mcl Bio-Roary-3.0.2/binaries/linux/mcxdeblast Bio-Roary-3.0.2/binaries/linux/parallel Bio-Roary-3.0.2/binaries/linux/prank Bio-Roary-3.0.2/binaries/darwin/bedtools Bio-Roary-3.0.2/binaries/darwin/blastp Bio-Roary-3.0.2/binaries/darwin/cd-hit Bio-Roary-3.0.2/binaries/darwin/makeblastdb Bio-Roary-3.0.2/binaries/darwin/mcl Bio-Roary-3.0.2/binaries/darwin/mcxdeblast Bio-Roary-3.0.2/binaries/darwin/parallel Bio-Roary-3.0.2/binaries/darwin/prank Bio-Roary-3.0.2/bin/create_pan_genome Bio-Roary-3.0.2/bin/create_pan_genome_plots.R Bio-Roary-3.0.2/bin/extract_proteome_from_gff Bio-Roary-3.0.2/bin/iterative_cdhit Bio-Roary-3.0.2/bin/pan_genome_core_alignment Bio-Roary-3.0.2/bin/pan_genome_post_analysis Bio-Roary-3.0.2/bin/pan_genome_reorder_spreadsheet Bio-Roary-3.0.2/bin/parallel_all_against_all_blastp Bio-Roary-3.0.2/bin/protein_muscle_alignment_from_nucleotides Bio-Roary-3.0.2/bin/query_pan_genome Bio-Roary-3.0.2/bin/roary Bio-Roary-3.0.2/bin/transfer_annotation_to_groups Configuring Bio-Roary-3.0.2 ... Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Roary Writing MYMETA.yml and MYMETA.json OK Building and testing Bio-Roary-3.0.2 ... cp lib/Bio/Roary/External/IterativeCdhit.pm blib/lib/Bio/Roary/External/IterativeCdhit.pm cp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm cp lib/Bio/Roary/CommandLine/IterativeCdhit.pm blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pm cp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm cp lib/Bio/Roary/CommandLine/QueryRoary.pm blib/lib/Bio/Roary/CommandLine/QueryRoary.pm cp lib/Bio/Roary/CombinedProteome.pm blib/lib/Bio/Roary/CombinedProteome.pm cp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm cp lib/Bio/Roary/CommandLine/Roary.pm blib/lib/Bio/Roary/CommandLine/Roary.pm cp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm cp lib/Bio/Roary/AnalyseGroups.pm blib/lib/Bio/Roary/AnalyseGroups.pm cp lib/Bio/Roary/Exceptions.pm blib/lib/Bio/Roary/Exceptions.pm cp lib/Bio/Roary/External/Cdhit.pm blib/lib/Bio/Roary/External/Cdhit.pm cp lib/Bio/Roary/CommandLine/Common.pm blib/lib/Bio/Roary/CommandLine/Common.pm cp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm cp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm cp lib/Bio/Roary/External/Blastp.pm blib/lib/Bio/Roary/External/Blastp.pm cp lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm blib/lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm cp lib/Bio/Roary/External/Prank.pm blib/lib/Bio/Roary/External/Prank.pm cp lib/Bio/Roary/CommandLine/CreatePanGenome.pm blib/lib/Bio/Roary/CommandLine/CreatePanGenome.pm cp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm cp lib/Bio/Roary/AnnotateGroups.pm blib/lib/Bio/Roary/AnnotateGroups.pm cp lib/Bio/Roary/External/Mcl.pm blib/lib/Bio/Roary/External/Mcl.pm cp lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm blib/lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm cp lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm cp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm cp lib/Bio/Roary/External/PostAnalysis.pm blib/lib/Bio/Roary/External/PostAnalysis.pm cp lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm blib/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm cp lib/Bio/Roary/External/Makeblastdb.pm blib/lib/Bio/Roary/External/Makeblastdb.pm cp lib/Bio/Roary/ReformatInputGFFs.pm blib/lib/Bio/Roary/ReformatInputGFFs.pm cp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm cp lib/Bio/Roary/ExtractProteomeFromGFF.pm blib/lib/Bio/Roary/ExtractProteomeFromGFF.pm cp lib/Bio/Roary/JobRunner/Local.pm blib/lib/Bio/Roary/JobRunner/Local.pm cp lib/Bio/Roary/Output/GroupsMultifastaProtein.pm blib/lib/Bio/Roary/Output/GroupsMultifastaProtein.pm cp lib/Bio/Roary/ExtractProteomeFromGFFs.pm blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pm cp lib/Bio/Roary/ReorderSpreadsheet.pm blib/lib/Bio/Roary/ReorderSpreadsheet.pm cp lib/Bio/Roary/QC/Report.pm blib/lib/Bio/Roary/QC/Report.pm cp lib/Bio/Roary/Output/EmblGroups.pm blib/lib/Bio/Roary/Output/EmblGroups.pm cp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pm cp lib/Bio/Roary/Output/GroupsMultifastas.pm blib/lib/Bio/Roary/Output/GroupsMultifastas.pm cp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm cp lib/Bio/Roary/Output/GroupMultifasta.pm blib/lib/Bio/Roary/Output/GroupMultifasta.pm cp lib/Bio/Roary/ParseGFFAnnotationRole.pm blib/lib/Bio/Roary/ParseGFFAnnotationRole.pm cp lib/Bio/Roary/Output/QueryGroups.pm blib/lib/Bio/Roary/Output/QueryGroups.pm cp lib/Bio/Roary/Output/NumberOfGroups.pm blib/lib/Bio/Roary/Output/NumberOfGroups.pm cp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm cp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm cp lib/Bio/Roary/JobRunner/Parallel.pm blib/lib/Bio/Roary/JobRunner/Parallel.pm cp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm cp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm cp lib/Bio/Roary/FilterFullClusters.pm blib/lib/Bio/Roary/FilterFullClusters.pm cp lib/Bio/Roary/MergeMultifastaAlignments.pm blib/lib/Bio/Roary/MergeMultifastaAlignments.pm cp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm cp lib/Bio/Roary/PrepareInputFiles.pm blib/lib/Bio/Roary/PrepareInputFiles.pm cp lib/Bio/Roary/Output/BlastIdentityFrequency.pm blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pm cp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm cp lib/Bio/Roary/JobRunner/Role.pm blib/lib/Bio/Roary/JobRunner/Role.pm cp lib/Bio/Roary/InflateClusters.pm blib/lib/Bio/Roary/InflateClusters.pm cp lib/Bio/Roary/OrderGenes.pm blib/lib/Bio/Roary/OrderGenes.pm cp lib/Bio/Roary/FilterUnknownsFromFasta.pm blib/lib/Bio/Roary/FilterUnknownsFromFasta.pm cp lib/Bio/Roary/SplitGroups.pm blib/lib/Bio/Roary/SplitGroups.pm cp lib/Bio/Roary/SortFasta.pm blib/lib/Bio/Roary/SortFasta.pm cp lib/Bio/Roary/SampleOrder.pm blib/lib/Bio/Roary/SampleOrder.pm cp lib/Bio/Roary/SequenceLengths.pm blib/lib/Bio/Roary/SequenceLengths.pm cp bin/pan_genome_reorder_spreadsheet blib/script/pan_genome_reorder_spreadsheet "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_reorder_spreadsheet cp bin/iterative_cdhit blib/script/iterative_cdhit "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/iterative_cdhit cp bin/create_pan_genome blib/script/create_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome cp bin/query_pan_genome blib/script/query_pan_genome "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/query_pan_genome cp bin/roary blib/script/roary "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/roary cp bin/transfer_annotation_to_groups blib/script/transfer_annotation_to_groups "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/transfer_annotation_to_groups cp bin/create_pan_genome_plots.R blib/script/create_pan_genome_plots.R "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/create_pan_genome_plots.R cp bin/pan_genome_post_analysis blib/script/pan_genome_post_analysis "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_post_analysis cp bin/pan_genome_core_alignment blib/script/pan_genome_core_alignment "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/pan_genome_core_alignment cp bin/parallel_all_against_all_blastp blib/script/parallel_all_against_all_blastp "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parallel_all_against_all_blastp cp bin/protein_muscle_alignment_from_nucleotides blib/script/protein_muscle_alignment_from_nucleotides "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/protein_muscle_alignment_from_nucleotides cp bin/extract_proteome_from_gff blib/script/extract_proteome_from_gff "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/extract_proteome_from_gff Manifying 12 pod documents Manifying 26 pod documents Manifying 26 pod documents Manifying 14 pod documents PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/.t t/Bio/Roary/.t t/Bio/Roary/CommandLine/.t t/Bio/Roary/External/.t t/Bio/Roary/Output/.t t/Bio/Roary/QC/*.t t/Bio/Roary/AnalyseGroups.t ...................................... ok t/Bio/Roary/AnnotateGroups.t ..................................... ok t/Bio/Roary/ChunkFastaFile.t ..................................... ok t/Bio/Roary/CombinedProteome.t ................................... ok t/Bio/Roary/CommandLine/ExtractProteomeFromGff.t ................. ok t/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.t ............ ok t/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.t .. ok t/Bio/Roary/CommandLine/QueryRoary.t ............................. ok t/Bio/Roary/CommandLine/Roary.t .................................. Dubious, test returned 2 (wstat 512, 0x200) Failed 1/9 subtests t/Bio/Roary/CommandLine/RoaryCoreAlignment.t ..................... ok t/Bio/Roary/CommandLine/RoaryPostAnalysis.t ...................... ok t/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.t ................ ok t/Bio/Roary/CommandLine/TransferAnnotationToGroups.t ............. ok t/Bio/Roary/ContigsToGeneIDsFromGFF.t ............................ ok t/Bio/Roary/External/Blastp.t .................................... ok t/Bio/Roary/External/Cdhit.t ..................................... ok t/Bio/Roary/External/Makeblastdb.t ............................... ok t/Bio/Roary/External/Mcl.t ....................................... ok t/Bio/Roary/External/Prank.t ..................................... ok t/Bio/Roary/ExtractCoreGenesFromSpreadsheet.t .................... ok t/Bio/Roary/ExtractProteomeFromGFFs.t ............................ ok t/Bio/Roary/FilterFullClusters.t ................................. ok t/Bio/Roary/GeneNamesFromGFF.t ................................... ok t/Bio/Roary/GroupLabels.t ........................................ ok t/Bio/Roary/GroupStatistics.t .................................... ok t/Bio/Roary/InflateClusters.t .................................... ok t/Bio/Roary/OrderGenes.t ......................................... ok t/Bio/Roary/Output/DifferenceBetweenSets.t ....................... ok t/Bio/Roary/Output/GroupsMultifastaProtein.t ..................... ok t/Bio/Roary/Output/GroupsMultifastas.t ........................... ok t/Bio/Roary/Output/GroupsMultifastasNucleotide.t ................. ok t/Bio/Roary/Output/NumberOfGroups.t .............................. ok t/Bio/Roary/Output/QueryGroups.t ................................. ok t/Bio/Roary/ParallelAllAgainstAllBlast.t ......................... ok t/Bio/Roary/PrepareInputFiles.t .................................. ok t/Bio/Roary/QC/Report.t .......................................... ok t/Bio/Roary/ReformatInputGFFs.t .................................. ok t/Bio/Roary/ReorderSpreadsheet.t ................................. ok t/Bio/Roary/SampleOrder.t ........................................ ok t/Bio/Roary/SequenceLengths.t .................................... ok t/Bio/Roary/SortFasta.t .......................................... ok t/Bio/Roary/SplitGroups.t ........................................ ok t/requires_external.t ............................................ ok Test Summary Report t/Bio/Roary/CommandLine/Roary.t (Wstat: 512 Tests: 9 Failed: 1) Failed test: 9 Non-zero exit status: 2 Parse errors: No plan found in TAP output Files=43, Tests=572, 70 wallclock secs ( 0.30 usr 0.08 sys + 62.44 cusr 7.66 csys = 70.48 CPU) Result: FAIL FAIL Manifying 12 pod documents Manifying 26 pod documents Manifying 26 pod documents Manifying 14 pod documents Appending installation info to /usr/lib/perl/5.18/perllocal.pod Successfully reinstalled Bio-Roary-3.0.2 Installing /usr/local/share/perl/5.18.2/x86_64-linux-gnu-thread-multi/.meta/Bio-Roary-3.0.2/install.json 1 distribution installed |
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Thanks Arnoud for the output. I 'think' I know which tests is failing, but git clone https://github.com/sanger-pathogens/Roary.git Thanks again for your time, your building up a lot of beer miles here! On 14 June 2015 at 19:48, dutchscientist notifications@github.com wrote:
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Hi Andrew, see below: vanvlia@n85673:~/Roary$ perl t/Bio/Roary/CommandLine/Roary.t ok 1 - use Bio::Roary::CommandLine::Roary; ok 2 - use Bio::Roary::CommandLine::CreatePanGenome; ok 3 - Actual output file exists gene_presence_absence.csv --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ok 4 - Actual and expected match output excluding variable columns ok 5 - Actual output file exists gene_presence_absence.csv -j Local --dont_split_groups t/data/genbank_gbff/genbank1.gff t/data/genbank_gbff/genbank2.gff t/data/genbank_gbff/genbank3.gff ok 6 - Actual and expected match output excluding variable columns ok 7 - Actual output file exists gene_presence_absence.csv -j Local -t 1 --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff ok 8 - Actual and expected match output excluding variable columns parallel: Error: Command (--no-notice) starts with '-'. Is this a wrong option? not ok 9 - Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff Failed test 'Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff 'at t/lib/TestHelper.pm line 176.Tests were run but no plan was declared and done_testing() was not seen.Looks like your test exited with 2 just after 9. |
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Thanks. It looks like its an issue with the parallel command. Could you which parallel Andrew On 14 June 2015 at 20:16, dutchscientist notifications@github.com wrote:
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vanvlia@n85673: I use this version of parallel as this is required for Prokka. |
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Thanks. On 14 June 2015 at 20:38, dutchscientist notifications@github.com wrote:
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I will check with Torsten Seemann how much flexibility there is with the Parallel version. I assume it won't be possible to run multiple versions. |
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I've got a test setup on TravisCI with parallel versions 20130922, 20141022 On 14 June 2015 at 21:38, dutchscientist notifications@github.com wrote:
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OK, very happy to do more tests, just remember, I am not a Linux expert. The instructions given were very helpful, that level I can do! ;-) |
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Hi Arnoud, On 14 June 2015 at 22:10, dutchscientist notifications@github.com wrote:
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Hi Andrew, CPAN still has 3.0.2 on it, while the website has 3.0.3? The "sudo cpanm -f Bio::Roary" command gives 3.0.2 (I have done sudo apt-get update). Beers are always a good idea! From: andrewjpage [mailto:notifications@github.com] Hi Arnoud, On 14 June 2015 at 22:10, dutchscientist notifications@github.com wrote:
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There was no attachment by the way, but no worries. My testset is just a few ones I threw together. |
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Hi Arnoud, On 15 June 2015 at 21:39, dutchscientist notifications@github.com wrote:
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3.0.3 is in cpan now, sorry for the delay, I forgot to click a button. On 15 June 2015 at 21:39, dutchscientist notifications@github.com wrote:
—Reply to this email directly or view it on GitHub. |
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OK, installs fine but still the error message (from verbose output): Failed test 'Actual output file exists gene_presence_absence.csv -j Parallel --dont_split_groups t/data/query_1.gff t/data/query_2.gff t/data/query_5.gff 'at t/lib/TestHelper.pm line 176.Wil give it a shot. |
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It takes a while to produce the files, but works now, I get the core alignment 👍 |
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Great thanks for letting me know. Yea the final step with aligning all the On 16 June 2015 at 13:43, dutchscientist notifications@github.com wrote:
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I have Muscle and revtrans.py (v1.4) installed and in the PATH, but the .aln file produced contains only N's. The GFF's are from Prokka and work fine for creating the gene lists, but somewhere it goes wrong in the reverse translation.
Any thoughts?
The commandline is: roary -v -i 90 -e *.gff.
Edit: the temporary files are created fine, so the revtrans.py works fine, it is just in the conversion of all the temporary files to the final alignment which goes wrong
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