Comments (27)
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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βDear Andrew,Great. Do you want some of the files I am working with as example?Best wishesArnoud From: andrewjpageSent: Monday, 1 June 2015 09:28To: sanger-pathogens/RoaryReply To: sanger-pathogens/RoaryCc: dutchscientistSubject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)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 [email protected]
Thanks a million.
from roary.
Have sent a small dataset (4 genomes) there, made using the don't delete
switch.
On 1 June 2015 at 09:55, andrewjpage [email protected] wrote:
Yea it would be great if you could send them to [email protected]
Thanks a million.
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#132 (comment)
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from roary.
Hi,
I've just updated Roary (version 3.0.0) which should hopefully resolve any
issues you have. Instead of muscle and revtrans it uses PRANK which is
properly packaged. You'll need to install prank first:
apt-get install prank
or
brew install prank
then update Roary
cpanm Bio::Roary
Regards,
Andrew
On 1 June 2015 at 11:50, dutchscientist [email protected] wrote:
Have sent a small dataset (4 genomes) there, made using the don't delete
switch.On 1 June 2015 at 09:55, andrewjpage [email protected] wrote:
Yea it would be great if you could send them to [email protected]
Thanks a million.
β
Reply to this email directly or view it on GitHub
<
#132 (comment).
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#132 (comment)
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from roary.
Great, will give that a go :-)
from roary.
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:
https://drive.google.com/file/d/0BzVZejrtim6RUnVBRUdrTWl2ZGs/view?usp=sharing
(ZIP file with 4 GFF files included)
I do get the following text when installing via "sudo cpanm Bio::Roary" :
--> Working on Bio::Roary
Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz ... OK
Configuring Bio-Roary-3.0.2 ... OK
Building and testing Bio-Roary-3.0.2 ... FAIL
! Testing Bio-Roary-3.0.2 failed but installing it anyway.
Successfully reinstalled Bio-Roary-3.0.2
1 distribution installed
Will try manual install as well.
from roary.
Everything else is working, despite the warning, including the addition of the annotation with the query_pan_genome
from roary.
Thanks for sending me the files.
I'd be interested to know what tests are failing when Roary is
installed,becuase that may well be the root cause (perhaps different
versions of something). Would it be possible for you to reinstall it
with the -v option (verbose) and send me the output? Thanks for helping me
sort out the bugs.
On 13 June 2015 at 02:41, dutchscientist [email protected] wrote:
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:https://drive.google.com/file/d/0BzVZejrtim6RUnVBRUdrTWl2ZGs/view?usp=sharing
(ZIP file with 4 GFF files included)I do get the following text when installing via "sudo cpanm Bio::Roary" :
--> Working on Bio::Roary
Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz
... OK
Configuring Bio-Roary-3.0.2 ... OK
Building and testing Bio-Roary-3.0.2 ... FAIL
! Testing Bio-Roary-3.0.2 failed but installing it anyway.
Successfully reinstalled Bio-Roary-3.0.2
1 distribution installedWill try manual install as well.
β
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#132 (comment)
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from roary.
Hi Andrew,Yes, of course. Will do that tonight. Happy to help, I predict I will use it a lot!Arnoud From: andrewjpageSent: Sunday, 14 June 2015 19:37To: sanger-pathogens/RoaryReply To: sanger-pathogens/RoaryCc: dutchscientistSubject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)Thanks for sending me the files.
I'd be interested to know what tests are failing when Roary is
installed,becuase that may well be the root cause (perhaps different
versions of something). Would it be possible for you to reinstall it
with the -v option (verbose) and send me the output? Thanks for helping me
sort out the bugs.
On 13 June 2015 at 02:41, dutchscientist [email protected] wrote:
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:https://drive.google.com/file/d/0BzVZejrtim6RUnVBRUdrTWl2ZGs/view?usp=sharing
(ZIP file with 4 GFF files included)I do get the following text when installing via "sudo cpanm Bio::Roary" :
--> Working on Bio::Roary
Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.0.2.tar.gz
... OK
Configuring Bio-Roary-3.0.2 ... OK
Building and testing Bio-Roary-3.0.2 ... FAIL
! Testing Bio-Roary-3.0.2 failed but installing it anyway.
Successfully reinstalled Bio-Roary-3.0.2
1 distribution installedWill try manual install as well.
β
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#132 (comment)
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from roary.
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
from roary.
Thanks Arnoud for the output. I 'think' I know which tests is failing, but
I was wondering if you could download the code and run the individual test
which would give specific output? The commands are:
git clone https://github.com/sanger-pathogens/Roary.git
cd Roary
perl t/Bio/Roary/CommandLine/Roary.t
Thanks again for your time, your building up a lot of beer miles here!
On 14 June 2015 at 19:48, dutchscientist [email protected] wrote:
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
... OKBio-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.pmcp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm
blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pmcp lib/Bio/Roary/CommandLine/IterativeCdhit.pm
blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pmcp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm
cp lib/Bio/Roary/CommandLine/QueryRoary.pm
blib/lib/Bio/Roary/CommandLine/QueryRoary.pmcp 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.pmcp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm
blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pmcp 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.pmcp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm
blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pmcp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm
cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm
blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pmcp 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.pmcp 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.pmcp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm
cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm
blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pmcp 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.pmcp lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm
blib/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pmcp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm
blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pmcp lib/Bio/Roary/External/PostAnalysis.pm
blib/lib/Bio/Roary/External/PostAnalysis.pmcp lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm
blib/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pmcp lib/Bio/Roary/External/Makeblastdb.pm
blib/lib/Bio/Roary/External/Makeblastdb.pmcp lib/Bio/Roary/ReformatInputGFFs.pm
blib/lib/Bio/Roary/ReformatInputGFFs.pmcp lib/Bio/Roary/GeneNamesFromGFF.pm blib/lib/Bio/Roary/GeneNamesFromGFF.pm
cp lib/Bio/Roary/ExtractProteomeFromGFF.pm
blib/lib/Bio/Roary/ExtractProteomeFromGFF.pmcp 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.pmcp lib/Bio/Roary/ExtractProteomeFromGFFs.pm
blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pmcp lib/Bio/Roary/ReorderSpreadsheet.pm
blib/lib/Bio/Roary/ReorderSpreadsheet.pmcp 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.pmcp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm
cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm
blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pmcp lib/Bio/Roary/Output/GroupsMultifastas.pm
blib/lib/Bio/Roary/Output/GroupsMultifastas.pmcp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm
cp lib/Bio/Roary/Output/GroupMultifasta.pm
blib/lib/Bio/Roary/Output/GroupMultifasta.pmcp lib/Bio/Roary/ParseGFFAnnotationRole.pm
blib/lib/Bio/Roary/ParseGFFAnnotationRole.pmcp lib/Bio/Roary/Output/QueryGroups.pm
blib/lib/Bio/Roary/Output/QueryGroups.pmcp lib/Bio/Roary/Output/NumberOfGroups.pm
blib/lib/Bio/Roary/Output/NumberOfGroups.pmcp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm
blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pmcp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm
cp lib/Bio/Roary/JobRunner/Parallel.pm
blib/lib/Bio/Roary/JobRunner/Parallel.pmcp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm
blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pmcp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm
cp lib/Bio/Roary/FilterFullClusters.pm
blib/lib/Bio/Roary/FilterFullClusters.pmcp lib/Bio/Roary/MergeMultifastaAlignments.pm
blib/lib/Bio/Roary/MergeMultifastaAlignments.pmcp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm
cp lib/Bio/Roary/PrepareInputFiles.pm
blib/lib/Bio/Roary/PrepareInputFiles.pmcp lib/Bio/Roary/Output/BlastIdentityFrequency.pm
blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pmcp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pmcp 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.pmcp 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_spreadsheetcp bin/iterative_cdhit blib/script/iterative_cdhit
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' --
blib/script/iterative_cdhitcp bin/create_pan_genome blib/script/create_pan_genome
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' --
blib/script/create_pan_genomecp bin/query_pan_genome blib/script/query_pan_genome
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' --
blib/script/query_pan_genomecp 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_groupscp 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.Rcp 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_analysiscp 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_alignmentcp 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_blastpcp 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_nucleotidescp 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_gffManifying 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/*.tt/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.json1 distribution installed
β
Reply to this email directly or view it on GitHub
#132 (comment)
.
from roary.
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.
from roary.
Thanks. It looks like its an issue with the parallel command. Could you
send me the output of these commands?
which parallel
parallel --version
Andrew
On 14 June 2015 at 20:16, dutchscientist [email protected] wrote:
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.gffok 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.gffok 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.gffok 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.gffFailed 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.
From: andrewjpage [mailto:[email protected]]
Sent: 14 June 2015 20:00
To: sanger-pathogens/Roary
Cc: dutchscientist
Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only
(#132)Thanks Arnoud for the output. I 'think' I know which tests is failing, but
I was wondering if you could download the code and run the individual test
which would give specific output? The commands are:git clone https://github.com/sanger-pathogens/Roary.git
cd Roary
perl t/Bio/Roary/CommandLine/Roary.tThanks again for your time, your building up a lot of beer miles here!
On 14 June 2015 at 19:48, dutchscientist [email protected] wrote:
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
... OKBio-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.pmcp lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm
blib/lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pmcp lib/Bio/Roary/CommandLine/IterativeCdhit.pm
blib/lib/Bio/Roary/CommandLine/IterativeCdhit.pmcp lib/Bio/Roary.pm blib/lib/Bio/Roary.pm
cp lib/Bio/Roary/CommandLine/QueryRoary.pm
blib/lib/Bio/Roary/CommandLine/QueryRoary.pmcp lib/Bio/Roary/CombinedProteome.pm
blib/lib/Bio/Roary/CombinedProteome.pmcp lib/Bio/Roary/ChunkFastaFile.pm blib/lib/Bio/Roary/ChunkFastaFile.pm
cp lib/Bio/Roary/CommandLine/Roary.pm
blib/lib/Bio/Roary/CommandLine/Roary.pmcp lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm
blib/lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pmcp 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.pmcp lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm
blib/lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pmcp lib/Bio/Roary/BedFromGFFRole.pm blib/lib/Bio/Roary/BedFromGFFRole.pm
cp lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm
blib/lib/Bio/Roary/ContigsToGeneIDsFromGFF.pmcp 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.pmcp 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.pmcp lib/Bio/Roary/ClustersRole.pm blib/lib/Bio/Roary/ClustersRole.pm
cp lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm
blib/lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pmcp 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.pmcp lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pm
blib/lib/Bio/Roary/CommandLine/ProteinMuscleAlignmentFromNucleotides.pmcp lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm
blib/lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pmcp lib/Bio/Roary/External/PostAnalysis.pm
blib/lib/Bio/Roary/External/PostAnalysis.pmcp lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pm
blib/lib/Bio/Roary/External/ProteinMuscleAlignmentFromNucleotides.pmcp lib/Bio/Roary/External/Makeblastdb.pm
blib/lib/Bio/Roary/External/Makeblastdb.pmcp lib/Bio/Roary/ReformatInputGFFs.pm
blib/lib/Bio/Roary/ReformatInputGFFs.pmcp lib/Bio/Roary/GeneNamesFromGFF.pm
blib/lib/Bio/Roary/GeneNamesFromGFF.pmcp lib/Bio/Roary/ExtractProteomeFromGFF.pm
blib/lib/Bio/Roary/ExtractProteomeFromGFF.pmcp 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.pmcp lib/Bio/Roary/ExtractProteomeFromGFFs.pm
blib/lib/Bio/Roary/ExtractProteomeFromGFFs.pmcp lib/Bio/Roary/ReorderSpreadsheet.pm
blib/lib/Bio/Roary/ReorderSpreadsheet.pmcp 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.pmcp lib/Bio/Roary/GroupStatistics.pm blib/lib/Bio/Roary/GroupStatistics.pm
cp lib/Bio/Roary/Output/DifferenceBetweenSets.pm
blib/lib/Bio/Roary/Output/DifferenceBetweenSets.pmcp lib/Bio/Roary/Output/GroupsMultifastas.pm
blib/lib/Bio/Roary/Output/GroupsMultifastas.pmcp lib/Bio/Roary/LookupGeneFiles.pm blib/lib/Bio/Roary/LookupGeneFiles.pm
cp lib/Bio/Roary/Output/GroupMultifasta.pm
blib/lib/Bio/Roary/Output/GroupMultifasta.pmcp lib/Bio/Roary/ParseGFFAnnotationRole.pm
blib/lib/Bio/Roary/ParseGFFAnnotationRole.pmcp lib/Bio/Roary/Output/QueryGroups.pm
blib/lib/Bio/Roary/Output/QueryGroups.pmcp lib/Bio/Roary/Output/NumberOfGroups.pm
blib/lib/Bio/Roary/Output/NumberOfGroups.pmcp lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm
blib/lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pmcp lib/Bio/Roary/GroupLabels.pm blib/lib/Bio/Roary/GroupLabels.pm
cp lib/Bio/Roary/JobRunner/Parallel.pm
blib/lib/Bio/Roary/JobRunner/Parallel.pmcp lib/Bio/Roary/ParallelAllAgainstAllBlast.pm
blib/lib/Bio/Roary/ParallelAllAgainstAllBlast.pmcp lib/Bio/Roary/IterativeCdhit.pm blib/lib/Bio/Roary/IterativeCdhit.pm
cp lib/Bio/Roary/FilterFullClusters.pm
blib/lib/Bio/Roary/FilterFullClusters.pmcp lib/Bio/Roary/MergeMultifastaAlignments.pm
blib/lib/Bio/Roary/MergeMultifastaAlignments.pmcp lib/Bio/Roary/PostAnalysis.pm blib/lib/Bio/Roary/PostAnalysis.pm
cp lib/Bio/Roary/PrepareInputFiles.pm
blib/lib/Bio/Roary/PrepareInputFiles.pmcp lib/Bio/Roary/Output/BlastIdentityFrequency.pm
blib/lib/Bio/Roary/Output/BlastIdentityFrequency.pmcp lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm
blib/lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pmcp 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.pmcp 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_spreadsheetcp bin/iterative_cdhit blib/script/iterative_cdhit
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' --
blib/script/iterative_cdhitcp bin/create_pan_genome blib/script/create_pan_genome
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' --
blib/script/create_pan_genomecp bin/query_pan_genome blib/script/query_pan_genome
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' --
blib/script/query_pan_genomecp 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_groupscp 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.Rcp 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_analysiscp 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_alignmentcp 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_blastpcp 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_nucleotidescp 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_gffManifying 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/*.tt/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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#132 (comment).
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https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-111864472>
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#132 (comment)
.
from roary.
vanvlia@n85673:/data/listeria$ which parallel/data/listeria$ parallel --version
/usr/local/bin/parallel
vanvlia@n85673:
GNU parallel 20130422
I use this version of parallel as this is required for Prokka.
from roary.
Thanks.
On 14 June 2015 at 20:38, dutchscientist [email protected] wrote:
vanvlia@n85673:
/data/listeria$ which parallel/data/listeria$ parallel --version
/usr/local/bin/parallel
vanvlia@n85673:
GNU parallel 20130422I use this version of parallel as this is required for Prokka.
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#132 (comment)
.
from roary.
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.
from roary.
I've got a test setup on TravisCI with parallel versions 20130922, 20141022
and 20150522 so something else must be up. From looking at your data I
think I know what might be up, but it will be tomorrow before I can confirm
it.
On 14 June 2015 at 21:38, dutchscientist [email protected] wrote:
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.β
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#132 (comment)
.
from roary.
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! ;-)
from roary.
Hi Arnoud,
I've tracked down the problem and fixed it. The latest version is 3.0.3.
The parallel warning messages seem to be a bit of a red herring. Give it a
whirl and let me know how you get along. I've attached the core gene
alignment for your campy data.
Thanks for all the helpful feedback and for your patience. If your ever
over Cambridge direction, I'll buy you a pint or two.
Andrew
On 14 June 2015 at 22:10, dutchscientist [email protected] wrote:
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! ;-)β
Reply to this email directly or view it on GitHub
#132 (comment)
.
from roary.
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:[email protected]]
Sent: 15 June 2015 14:42
To: sanger-pathogens/Roary
Cc: dutchscientist
Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)
Hi Arnoud,
I've tracked down the problem and fixed it. The latest version is 3.0.3.
The parallel warning messages seem to be a bit of a red herring. Give it a
whirl and let me know how you get along. I've attached the core gene
alignment for your campy data.
Thanks for all the helpful feedback and for your patience. If your ever
over Cambridge direction, I'll buy you a pint or two.
Andrew
On 14 June 2015 at 22:10, dutchscientist [email protected] wrote:
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! ;-)β
Reply to this email directly or view it on GitHub
#132 (comment)
.
β
Reply to this email directly or view it on GitHub #132 (comment) . https://github.com/notifications/beacon/AJ8e0MaeDiDd9m9SsMvPOa6H--uSbPm4ks5oTs3BgaJpZM4Exndn.gif
from roary.
There was no attachment by the way, but no worries. My testset is just a few ones I threw together.
from roary.
Hi Arnoud,
3.0.3 is in cpan now, sorry for the delay, I forgot to click a button.
The attachment I sent didnt seem to come through on github.
Andrew
On 15 June 2015 at 21:39, dutchscientist [email protected] wrote:
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:[email protected]]
Sent: 15 June 2015 14:42
To: sanger-pathogens/Roary
Cc: dutchscientist
Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only
(#132)Hi Arnoud,
I've tracked down the problem and fixed it. The latest version is 3.0.3.
The parallel warning messages seem to be a bit of a red herring. Give it a
whirl and let me know how you get along. I've attached the core gene
alignment for your campy data.
Thanks for all the helpful feedback and for your patience. If your ever
over Cambridge direction, I'll buy you a pint or two.
AndrewOn 14 June 2015 at 22:10, dutchscientist [email protected] wrote:
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! ;-)β
Reply to this email directly or view it on GitHub
<
#132 (comment).
β
Reply to this email directly or view it on GitHub <
https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-112074808>
. <
https://github.com/notifications/beacon/AJ8e0MaeDiDd9m9SsMvPOa6H--uSbPm4ks5oTs3BgaJpZM4Exndn.gif>β
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#132 (comment)
.
from roary.
No worries, will try today :-) From: andrewjpageSent: Tuesday, 16 June 2015 08:32To: sanger-pathogens/RoaryReply To: sanger-pathogens/RoaryCc: dutchscientistSubject: Re: [Roary] Use of -e switch gives multifasta file with N's only (#132)Hi Arnoud,
3.0.3 is in cpan now, sorry for the delay, I forgot to click a button.
The attachment I sent didnt seem to come through on github.
Andrew
On 15 June 2015 at 21:39, dutchscientist [email protected] wrote:
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:[email protected]]
Sent: 15 June 2015 14:42
To: sanger-pathogens/Roary
Cc: dutchscientist
Subject: Re: [Roary] Use of -e switch gives multifasta file with N's only
(#132)Hi Arnoud,
I've tracked down the problem and fixed it. The latest version is 3.0.3.
The parallel warning messages seem to be a bit of a red herring. Give it a
whirl and let me know how you get along. I've attached the core gene
alignment for your campy data.
Thanks for all the helpful feedback and for your patience. If your ever
over Cambridge direction, I'll buy you a pint or two.
AndrewOn 14 June 2015 at 22:10, dutchscientist [email protected] wrote:
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! ;-)β
Reply to this email directly or view it on GitHub
<
#132 (comment).
β
Reply to this email directly or view it on GitHub <
https://github.com/sanger-pathogens/Roary/issues/132#issuecomment-112074808>
. <
https://github.com/notifications/beacon/AJ8e0MaeDiDd9m9SsMvPOa6H--uSbPm4ks5oTs3BgaJpZM4Exndn.gif>β
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#132 (comment)
.
βReply to this email directly or view it on GitHub.
from roary.
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.
from roary.
It takes a while to produce the files, but works now, I get the core alignment π
from roary.
Great thanks for letting me know. Yea the final step with aligning all the
sequences takes quite a while, even longer now with prank, but luckily its
paralleliseable.
And thanks for all the feedback.
Andrew
On 16 June 2015 at 13:43, dutchscientist [email protected] wrote:
It takes a while to produce the files, but works now, I get the core
alignment [image: π]β
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#132 (comment)
.
from roary.
Related Issues (20)
- number of conserved/unique genes.Rtab
- Strange Ouput HOT 2
- Number of conserved genes increases through genomoes
- how can i solve this issue
- No newick file
- Missing proteome.faa files
- Cant open file: 14L9VpZJtx/DNA16.gff.proteome.faa Please, help with this issue
- roary_plots.py heatmap coregenome matrix empty
- i cant install Roary by mamba HOT 2
- core_alignment.aln has lower and uppercase in sequences
- cann't install roary 3.13 with mamba/conda
- The singularity image pulled from docker://sangerpathogens/roary does not accept input gff files HOT 2
- Issue with "Error: Cant access the groups file: clustered_proteins" HOT 1
- How can I discover the genetic sequences that are used to group groups in roary?
- Roary grouping genes that don't meet similarity threshold (using `-i 100`, and `-s`) HOT 6
- Order of genes in alignment
- Use of uninitialized value in require at /usr/lib/x86_64-linux-gnu/perl5/5.34/Encode.pm line 70.
- How are genes with frameshift mutations/INDELS handled?
- The number of pan-genes in gene_presence_absence.csv is less than each genome
- Cloud not obtain clear phylogenic tree HOT 1
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from roary.