Empty accessory_binary_genes.fa

[andrewjpage]

From Rosemarie.Sadsad [...] health.nsw.gov.au on CPAN.

Hi,

I am running Bio-Roary v3.7.0 as part of the Nullarbor pipeline, however the accessory_binary_genes.fa produced is empty.

0 Dec 8 22:56 accessory_binary_genes.fa 0 Dec 8 22:56 accessory_binary_genes.fa.newick.svg 3241 Dec 8 22:56 accessory_graph.dot 18876 Dec 8 22:56 accessory.header.embl 12959 Dec 8 22:56 accessory.tab 35 Dec 8 22:56 blast_identity_frequency.Rtab 92530 Dec 8 22:56 clustered_proteins 171501 Dec 8 22:56 core_accessory_graph.dot 377768 Dec 8 22:56 core_accessory.header.embl 354393 Dec 8 22:56 core_accessory.tab

Linux login1 2.6.32-642.3.1.el6.x86_64 #1 SMP Tue Jul 12 18:30:56 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Perl 5.24.0

Thanks, Rosie

[andrewjpage]

Could you run 'roary -a' and send me the results?

[r0sies]

Hi Andrew,

roary -a

Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reute r, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julia n Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatic s, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Pubmed: 26198102

2016/12/15 12:00:47 Optional tool 'Rscript' not found in your $PATH 2016/12/15 12:00:47 Looking for 'awk' - found /bin/awk 2016/12/15 12:00:47 Looking for 'bedtools' - found /usr/local/bedtools/2.26.0/bi n/bedtools 2016/12/15 12:00:47 Determined bedtools version is 2.26 2016/12/15 12:00:47 Looking for 'blastp' - found /usr/local/prokka/1.11/bin/blas tp 2016/12/15 12:00:47 Determined blastp version is 2.2.29 2016/12/15 12:00:47 Looking for 'grep' - found /bin/grep 2016/12/15 12:00:47 Looking for 'kraken' - found /usr/local/kraken/0.10.5-beta/k raken Use of uninitialized value in concatenation (.) or string at /usr/local/perl/5.2 4.0/lib/site_perl/5.24.0/Bio/Roary/External/CheckTools.pm line 129. 2016/12/15 12:00:47 Determined kraken version is 2016/12/15 12:00:47 Looking for 'kraken-report' - found /usr/local/kraken/0.10.5 -beta/kraken-report Use of uninitialized value in concatenation (.) or string at /usr/local/perl/5.2 4.0/lib/site_perl/5.24.0/Bio/Roary/External/CheckTools.pm line 129. 2016/12/15 12:00:47 Determined kraken-report version is 2016/12/15 12:00:47 Looking for 'mafft' - found /usr/local/mafft/7.300/bin/mafft Use of uninitialized value in concatenation (.) or string at /usr/local/perl/5.2 4.0/lib/site_perl/5.24.0/Bio/Roary/External/CheckTools.pm line 129. 2016/12/15 12:00:47 Determined mafft version is 2016/12/15 12:00:47 Looking for 'makeblastdb' - found /usr/local/prokka/1.11/bin /makeblastdb 2016/12/15 12:00:47 Determined makeblastdb version is 2.2.29 2016/12/15 12:00:47 Looking for 'mcl' - found /usr/local/mcl/14-137/bin/mcl 2016/12/15 12:00:47 Determined mcl version is 14-137 2016/12/15 12:00:47 Looking for 'parallel' - found /usr/local/parallel/20160222/ bin/parallel 2016/12/15 12:00:47 Determined parallel version is 20160222 2016/12/15 12:00:47 Looking for 'prank' - found /usr/local/prank/150803/bin/pran k 2016/12/15 12:00:47 Looking for 'sed' - found /bin/sed 2016/12/15 12:00:47 Looking for 'cd-hit' - found /usr/local/cd-hit/4.6.5/bin/cd- hit 2016/12/15 12:00:47 Determined cd-hit version is 4.6 2016/12/15 12:00:47 Looking for 'FastTree' - found /usr/local/fasttree/2.1.9/bin /FastTree 2016/12/15 12:00:47 Determined FastTree version is 2.1 2016/12/15 12:00:47 Roary version 3.7.0 2016/12/15 12:00:47 Error: You need to provide at least 2 files to build a pan g enome Usage: roary [options] *.gff

Options: -p INT number of threads [1] -o STR clusters output filename [clustered_proteins] -f STR output directory [.] -e create a multiFASTA alignment of core genes using PRANK -n fast core gene alignment with MAFFT, use with -e -i minimum percentage identity for blastp [95] -cd FLOAT percentage of isolates a gene must be in to be core [99] -qc generate QC report with Kraken -k STR path to Kraken database for QC, use with -qc -a check dependancies and print versions -b STR blastp executable [blastp] -c STR mcl executable [mcl] -d STR mcxdeblast executable [mcxdeblast] -g INT maximum number of clusters [50000] -m STR makeblastdb executable [makeblastdb] -r create R plots, requires R and ggplot2 -s dont split paralogs -t INT translation table [11] -z dont delete intermediate files -v verbose output to STDOUT -w print version and exit -y add gene inference information to spreadsheet, doesnt work wi th -e -h this help message

Example: Quickly generate a core gene alignment using 8 threads roary -e --mafft -p 8 *.gff

For further info see: http://sanger-pathogens.github.io/Roary/

[s4251484]

hi there, i encounter the same problem. some info about my input: two bacterial subspecies, known to be highly identical

less summary_statistics.txt Core genes (99% <= strains <= 100%) 1642 Soft core genes (95% <= strains < 99%) 0 Shell genes (15% <= strains < 95%) 328 Cloud genes (0% <= strains < 15%) 0 Total genes (0% <= strains <= 100%) 1970