No gene annotation in gene_presence_absence.csv output

[dinesh1st]

Can you please advise me why I am not getting gene annotation in gene_presence_absence.csv output file? My previous experience was I got the name of all the genes and annotations in this output. However, this time Roary gave me only group numbers. The difference between these two attempts was earlier one I have used draft genomes and this time I am using complete genomes. Does it make difference?

[tseemann]

@dinesh1st can you paste the first 3 lines of the gene_presence_absence.csv here?
eg. run head -n 3 gene_presence_absence.csv

Also, paste these 3 lines from one of your .gff input files
eg. run grep CDS YOURFILE.gff | head -n 3

[dinesh1st]

My csv output looks like

Gene	Non-unique Gene name	Annotation	No. isolates	No. sequences	Avg sequences per isolate	Genome Fragment	Order within Fragment	Accessory Fragment	Accessory Order with Fragment	QC	Min group size nuc	Max group size nuc	Avg group size nuc	1	2	3	4
group_1			4	4	1									PAO1_01930(+)	PA14_03260(-)	PA34_03444(-)	VRFPA01_02925(+)
group_1000		4	4	1									PAO1_03900(+)	PA14_01208(-)	PA34_01191(-)	VRFPA01_04900(+)
group_1001		4	4	1									PAO1_03912(-)	PA14_01196(+)	PA34_01179(+)	VRFPA01_04912(-)

One of my gff file looks like
##gff-version 3
##sequence-region gnl|Prokka|PAO1_1 1 6264404
gnl|Prokka|PAO1_1 Prodigal:2.6 CDS 483 2027 . + 0 ID=PAO1_00001;Parent=PAO1_00001_gene;Name=dnaA;gene=dnaA;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:UniProtKB:P03004;locus_tag=PAO1_00001;product=Chromosomal replication initiator protein DnaA;protein_id=gnl|Prokka|PAO1_00001
gnl|Prokka|PAO1_1 prokka gene 483 2027 . + . ID=PAO1_00001_gene;Name=dnaA;gene=dnaA;locus_tag=PAO1_00001

[andrewjpage]

Could you paste the output of roary -a ?

[dinesh1st]

2018/10/23 22:13:17 Optional tool 'Rscript' not found in your $PATH
2018/10/23 22:13:17 Looking for 'awk' - found /usr/bin/awk
2018/10/23 22:13:17 Looking for 'bedtools' - found /Users/dinesh/anaconda2/bin/bedtools
2018/10/23 22:13:17 Determined bedtools version is 2.27
2018/10/23 22:13:17 Looking for 'blastp' - found /Users/dinesh/anaconda2/bin/blastp
2018/10/23 22:13:20 Determined blastp version is 2.7.1
2018/10/23 22:13:20 Looking for 'grep' - found /usr/bin/grep
2018/10/23 22:13:20 Optional tool 'kraken' not found in your $PATH
2018/10/23 22:13:20 Optional tool 'kraken-report' not found in your $PATH
2018/10/23 22:13:20 Looking for 'mafft' - found /Users/dinesh/anaconda2/bin/mafft
2018/10/23 22:13:20 Determined mafft version is 7.407
2018/10/23 22:13:20 Looking for 'makeblastdb' - found /Users/dinesh/anaconda2/bin/makeblastdb
2018/10/23 22:13:20 Determined makeblastdb version is 2.7.1
2018/10/23 22:13:20 Looking for 'mcl' - found /Users/dinesh/anaconda2/bin/mcl
2018/10/23 22:13:20 Determined mcl version is 14-137
2018/10/23 22:13:20 Looking for 'parallel' - found /Users/dinesh/anaconda2/bin/parallel
2018/10/23 22:13:21 Determined parallel version is 20160622
2018/10/23 22:13:21 Looking for 'prank' - found /Users/dinesh/anaconda2/bin/prank
2018/10/23 22:13:21 Looking for 'sed' - found /usr/bin/sed
2018/10/23 22:13:21 Looking for 'cd-hit' - found /Users/dinesh/anaconda2/bin/cd-hit
2018/10/23 22:13:21 Determined cd-hit version is 4.7
2018/10/23 22:13:21 Looking for 'FastTree' - found /Users/dinesh/anaconda2/bin/FastTree
2018/10/23 22:13:21 Determined FastTree version is 2.1
2018/10/23 22:13:21 Roary version 3.7.0
2018/10/23 22:13:21 Error: You need to provide at least 2 files to build a pan genome
Usage: roary [options] *.gff

[andrewjpage]

It looks like you are running an older version of Roary (released 2 years ago). Please upgrade to the latest version and try again.