Hi,
Dont worry about the error. By default roary checks the dependancies and
continues (rather than exiting), so it expects to have some input files.
Regards,
Andrew

On 10 June 2016 at 10:51, jinlizhang200706 notifications@github.com wrote:

I tested roary using "roary -a" , seemed all the dependencies were
successfully installed, I'm confused about this error especially when all
the dependencies was detected.
this is the result of "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
Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A.
Keane, Julian Parkhill,
"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics,
2015 Nov 15;31(22):3691-3693
doi: http://doi.org/10.1093/bioinformatics/btv421
Pubmed: 26198102

2016/06/10 18:02:18 Looking for 'Rscript' - found
/home/jinli/soft/R-3.0.1/bin/Rscript
2016/06/10 18:02:18 Determined Rscript version is 3.0
2016/06/10 18:02:18 Looking for 'awk' - found /usr/bin/awk
2016/06/10 18:02:18 Looking for 'bedtools' - found
/opt/third_party/bedtools-2.17.0/bedtools
2016/06/10 18:02:18 Determined bedtools version is 2.17
2016/06/10 18:02:18 Looking for 'blastp' - found
/home/jinli/soft/third/ncbi-blast-2.3.0+/bin/blastp
2016/06/10 18:02:18 Determined blastp version is 2.3.0
2016/06/10 18:02:18 Looking for 'grep' - found /bin/grep
2016/06/10 18:02:18 Looking for 'kraken' - found
/home/jinli/soft/third/kraken-master/kraken
2016/06/10 18:02:18 Determined kraken version is 0.10.6-unreleased
2016/06/10 18:02:18 Looking for 'kraken-report' - found
/home/jinli/soft/third/kraken-master/kraken-report
2016/06/10 18:02:18 Determined kraken-report version is 0.10.6-unreleased
2016/06/10 18:02:18 Looking for 'mafft' - found /home/jinli/bin/mafft
2016/06/10 18:02:18 Determined mafft version is 7.221
2016/06/10 18:02:18 Looking for 'makeblastdb' - found
/home/jinli/soft/third/ncbi-blast-2.3.0+/bin/makeblastdb
2016/06/10 18:02:18 Determined makeblastdb version is 2.3.0
2016/06/10 18:02:18 Looking for 'mcl' - found /home/jinli/bin/mcl
2016/06/10 18:02:18 Determined mcl version is 14-137
2016/06/10 18:02:18 Looking for 'parallel' - found
/home/jinli/soft/third/linuxbrew-master/bin/parallel
2016/06/10 18:02:18 Determined parallel version is 20160422
2016/06/10 18:02:18 Looking for 'prank' - found /home/jinli/bin/prank
2016/06/10 18:02:18 Looking for 'sed' - found /bin/sed
2016/06/10 18:02:18 Looking for 'cd-hit' - found /home/jinli/bin/cd-hit
2016/06/10 18:02:18 Determined cd-hit version is 4.6
2016/06/10 18:02:18 Looking for 'FastTree' - found
/home/jinli/soft/third/linuxbrew-master/bin/FastTree
2016/06/10 18:02:18 Determined FastTree version is 2.1
2016/06/10 18:02:18 Roary version 1.006924
2016/06/10 18:02:18 Error: You need to provide at least 2 files to build a
pan genome
Usage: roary [options] *.gff
##########

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thank you so much. I supplied two gff files in this process and it worked. thank you.