Error "Cant open file: _uninflated_mcl_groups"

[thorellk]

Hi!

I have downloaded roary 3.2.7 using homebrew on my Mac OSX Yosemite. It seemed to have installed properly but when I run there seems to be some problem with an intermediate file not being created/found. I ran it in verbose mode to see if I could get more clues but cannot see what is the root of the problem. Do you know what could be the problem? I append the command line output below.

Best wishes

Kaisa

roary -e -v *.gff

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 (2015), "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics,
doi: http://doi.org/10.1093/bioinformatics/btv421

2015/09/23 11:26:57 Fixing input GFF files
2015/09/23 11:27:03 Extracting proteins from GFF files
Extracting proteins from 513A.gff
Extracting proteins from PC2022III.gff
Extracting proteins from PC2777IV.gff
Extracting proteins from PC3053II.gff
Extracting proteins from PC3517II.gff
Extracting proteins from PC3714II.gff
Extracting proteins from PC390II.gff
Extracting proteins from PC3939II.gff
Extracting proteins from PC3997IV.gff
Extracting proteins from PC4226IV.gff
Extracting proteins from PC4580III.gff
Extracting proteins from PC4597II.gff
Extracting proteins from PC5099IV.gff
Extracting proteins from PC5538III.gff
Extracting proteins from PC5587platt.gff
Extracting proteins from PC5587u.gff
Extracting proteins from W1090330.gff
Combine proteins into a single file
Iteratively run cd-hit
Parallel all against all blast
Cluster with MCL
2015/09/23 11:51:37 Running command: pan_genome_post_analysis -o clustered_proteins -p pan_genome.fa -s gene_presence_absence.csv -c _clustered.clstr --output_multifasta_files -i _gff_files -f _fasta_files -t 11 --dont_create_rplots -v -j Local --processors 1 --group_limit 50000 -cd 99
2015/09/23 11:51:37 Reinflate clusters
Cant open file: _uninflated_mcl_groups
KaisaTiMac:kaisa$ ls
513A.gff PC3714II.gff.proteome.faa PC4597II.gff W1090330.gff.proteome.faa
513A.gff.proteome.faa PC390II.gff PC4597II.gff.proteome.faa _clustered
PC2022III.gff PC390II.gff.proteome.faa PC5099IV.gff _clustered.clstr
PC2022III.gff.proteome.faa PC3939II.gff PC5099IV.gff.proteome.faa _combined_files
PC2777IV.gff PC3939II.gff.proteome.faa PC5538III.gff _combined_files.groups
PC2777IV.gff.proteome.faa PC3997IV.gff PC5538III.gff.proteome.faa _fasta_files
PC3053II.gff PC3997IV.gff.proteome.faa PC5587platt.gff _gff_files
PC3053II.gff.proteome.faa PC4226IV.gff PC5587platt.gff.proteome.faa blast_identity_frequency.Rtab
PC3517II.gff PC4226IV.gff.proteome.faa PC5587u.gff
PC3517II.gff.proteome.faa PC4580III.gff PC5587u.gff.proteome.faa
PC3714II.gff PC4580III.gff.proteome.faa W1090330.gff

[andrewjpage]

Hi Kaisa,
It looks like an issue with MCL. Could you send me the output of these commands:

which mcl
mcl --version

which mcxdeblast

copy the full path into the next command and run with perl

perl /full/path/to/mcxdeblast -h

[thorellk]

Hi!

Turned out mcl was installed by homebrew but not linked. When I linked it, it worked.

Thank you for the fast reply!

//Kaisa