Installation error, cd-hit version, cant open file while Combine proteins into a single file

[carolynzy]

Hi, I'm working on WSL system with Roary.

I had the following issue while installation:

$sudo cpanm -f Bio::Roary --> Working on Bio::Roary Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-Roary-3.13.0.tar.gz ... OK Configuring Bio-Roary-3.13.0 ... OK Building and testing Bio-Roary-3.13.0 ... FAIL ! Testing Bio-Roary-3.13.0 failed but installing it anyway. Successfully reinstalled Bio-Roary-3.13.0 1 distribution installed

And when I typed

roary -a

it gave me this message:

2021/10/15 13:38:32 Looking for 'cd-hit' - found /usr/bin/cd-hit Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.30.0/Bio/Roary/External/CheckTools.pm line 131. 2021/10/15 13:38:32 Determined cd-hit version is Use of uninitialized value in numeric lt (<) at /usr/local/share/perl/5.30.0/Bio/Roary/External/CheckTools.pm line 132. 2021/10/15 13:38:32 Roary needs cd-hit 4.6 or higher. Please upgrade and try again.

Then I check my cd-hit version, which is :

cd-hit/focal,now 4.8.1-2build1 amd64 [installed]

I tested the installation with a test sample of 4 samples, the app threw this error message:

Extracting proteins from /mnt/d/420samples/test/9.gff Extracting proteins from fixed_input_files/90.gff Extracting proteins from fixed_input_files/92.gff Extracting proteins from fixed_input_files/96.gff Cant open file: /mnt/d/420samples/roary_1634274207/e3_cQ5H8G5/9.gff.proteome.faaCombine proteins into a single file

My system is Ubuntu20.04. I installed other dependencies with command:

sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank mafft fasttree

Could you help me to identify the cause to this problem? Thank you!

[rpetit3]

Hi @carolynzy

By chance can you try the conda install of Roary? I think it should work with WSL and should hopefully get you the correct version.

Cheers, Robert

[martinmchugh]

I've just installed via bioconda, and I got the same message as @carolynzy

roary -a

2021/12/16 14:08:29 Looking for 'cd-hit' - found /mnt/shared/scratch/mmchugh/apps/conda/envs/roary/bin/cd-hit
Use of uninitialized value in concatenation (.) or string at /mnt/shared/scratch/mmchugh/apps/conda/envs/roary/lib/site_perl/5.26.2/Bio/Roary/External/CheckTools.pm line 131.
2021/12/16 14:08:29 Determined cd-hit version is 
Use of uninitialized value in numeric lt (<) at /mnt/shared/scratch/mmchugh/apps/conda/envs/roary/lib/site_perl/5.26.2/Bio/Roary/External/CheckTools.pm line 132.
2021/12/16 14:08:29 Roary needs cd-hit 4.6 or higher. Please upgrade and try again.

I confirmed cd-hit v4.8.1 is installed in the environment and roary seems to have run to completion on a small test set in any case

[joneson]

I have these same problems, and have installed roary in both ways, in a conda roary environment.