Problems running Roary

Question

[SushiRoll]

Hi everyone!

I'm having problems running roary, I have a set of gff3 files and run:

roary -e -mafft *.gff3

as suggested in the manual but I get:

Cant open file: /home/service/data/14L9VpZJtx/DNA16.gff.proteome.faa(base)

I also tried running the same but with sudo even though in theory there should be no need and get the same message.

I've tried: roary -g -mafft -z *.gff3 to keep the temporary files but even if that works, and the temporary files are indeed retained, I still get the "Can't open .... " message.

At this point I checked the dependencies by using roary -a and get the following:

2024/01/04 15:39:35 Looking for 'Rscript' - found /usr/bin/Rscript
2024/01/04 15:39:35 Determined Rscript version is 3.6
2024/01/04 15:39:35 Looking for 'awk' - found 
2024/01/04 15:39:35 Looking for 'bedtools' - found 
2024/01/04 15:39:35 Determined bedtools version is 2.30 
2024/01/04 15:39:35 Looking for 'blastp' - found
2024/01/04 15:39:35 Determined blastp version is 2.13.0 
2024/01/04 15:39:35 Looking for 'grep' - found
2024/01/04 15:39:35 Optional tool 'kraken' not found in your $PATH 
2024/01/04 15:39:35 Optional tool 'kraken-report' not found in your $PATH 
2024/01/04 15:39:35 Looking for 'mafft' - found
2024/01/04 15:39:35 Determined mafft version is 7.453
2024/01/04 15:39:35 Looking for 'makeblastdb' - found
2024/01/04 15:39:35 Determined makeblastdb version is 2.13.0 
2024/01/04 15:39:35 Looking for 'mcl' - found
2024/01/04 15:39:35 Determined mcl version is 14-137
2024/01/04 15:39:35 Looking for 'parallel' - found
2024/01/04 15:39:35 Determined parallel version is 20220722
2024/01/04 15:39:35 Looking for 'prank' - found 
2024/01/04 15:39:35 Determined prank version is 170427
2024/01/04 15:39:35 Looking for 'sed' - found 
2024/01/04 15:39:35 Looking for 'cd-hit' - found 
Use of uninitialized value in concatenation (.) or string at /usr/perl5/Bio/Roary/External/CheckTools.pm line 131. 
2024/01/04 15:39:35 Determined cd-hit version is Use of uninitialized value in numeric lt (<) at /usr/perl5/Bio/Roary/External/CheckTools.pm line 132. 
2024/01/04 15:39:35 Roary needs cd-hit 4.6 or higher. Please upgrade and try again. 
2024/01/04 15:39:35 Looking for 'FastTree' - found 
2024/01/04 15:39:35 Determined FastTree version is 2.1
2024/01/04 15:39:35 Roary version 3.13.0

I feel that maybe it has something to do with the cd-hit version not being recognised as newer than 4.6 even if I have cd-hit 4.8.1.

Has anyone experienced something like this? Any suggestions would be greatly appreciated.

[Ram]

What does file /home/service/data/14L9VpZJtx/DNA16.gff.proteome.faa say?

[SushiRoll]

Hey Ram

Thanks for the reply. Actually the file per se is not created in the temporary folder 14L9VpZJtx, I have DNA16.gff.proteome.faa.tmp.filtered instead and it is a protein multifasta:

> HFFBGCFM_00001
MIFFLYMYVCFASAVYIPELWPTHLRLRGSGFVNAVGRIVAVFTPYGVAALLTHYGSITV
FMVLGVMLLLCALVLSIFGIETRKVSLEEISEVN*
> HFFBGCFM_00002
MPPRALLLVDLQNDFCAGGALAVPEGDSTVDVANRLIDWCQSRGEAVIASQDWHPANHGS
FASQHGVEPYTPGQLDGLPQTFWPDHCVQNSEGAQLHPLLHQKAIAAVFHKGENPLVDSY
SAFFDNGRRQKTSLDDWLRDHEIDELIVMGLATDYCVKFTVLDALQLGYKVNVITDGCRG
VNIQPQDSAHAFMEMSAAGATLYTLADWEETQG*

These are the first two lines as an example. The names of each protein do contain the > before HFFBGCFM_*, I just can't type it here without it being detected as a Blockquote starter.

[Ram]

You need a code fence (or the 101010 code button on the toolbar) to code-format the text that you need represented without markdown interpretation. I've done it for you this time.