DIAMOND on Galaxy

Question: DIAMOND on Galaxy

2.6 years ago by

cryomics • 0 wrote:

I'm getting an error "Insufficient arguments. Use diamond -h for help." whenever I try to run the DIAMOND module from usegalaxy.org or test.galaxyproject.org.

I suspect that in the background diamond has been upgraded from 0.6.13 (the claimed version) to 0.7.10 but that the modules have not been updated to account for the differences in command line flags between the versions. Can anyone verify this or make any other suggestions on getting it to work?

software error galaxy • 1.2k views

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modified 21 months ago by Bjoern Gruening ♦ 5.1k • written 2.6 years ago by cryomics • 0

2.6 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

I answered on github: https://github.com/galaxyproject/tools-iuc/pull/465#issuecomment-208751740

But to fix this problem we need to have a more detailed error message.

Thanks, Bjoern

ADD COMMENT • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k

2.6 years ago by

cryomics • 0

cryomics • 0 wrote:

That's the extent of the error message. In the history it shows up green as if it completed, but the output is empty and the error is shown in the preview box.

galaxy diamond error

ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by cryomics • 0

Is this now fixed for you?

ADD REPLY • link written 2.6 years ago by Bjoern Gruening ♦ 5.1k

Hello,

I am also having the exact same problem. What could I do to look for a solution? Thanks

ADD REPLY • link written 21 months ago by souzatm • 0

22 months ago by

chryzoumas • 0

chryzoumas • 0 wrote:

Greetings,

I seem to be having exactly the same problem (empty output, "Insufficient arguments. Use diamond -h for help." message)

ADD COMMENT • link written 22 months ago by chryzoumas • 0

21 months ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

We have updated the Diamond wrapper last week and fixed hopefully all issues. Let me know if it does not work for you.

ADD COMMENT • link written 21 months ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern! I am running Diamond as above but still facing the same error ("insufficient arguments. Use diamond -h for help"). In order to be clear this is what I did:

Created a diamond_database (customized by uploading my own protein sequences, format = .fasta) using --> Diamond makedb
Uploaded my nucleotide sequences (format = .fasta)
Set up Diamond (I changed: blast parameter, from Blastp --> Blastx according to my data, reference database --> as point 1).

The rest of the parameters was as the same as default.

However I still get the same "error".

Can you help me?

Thank you in advance

Luca

ADD REPLY • link written 19 months ago by luca.marisaldi • 30

I have just tried running diamond in the same way as Luca, and get the same error: viz. Insufficient arguments. Use diamond -h for help. David

ADD REPLY • link written 19 months ago by david.hughes • 0

Can you tell me the version of the tool you are using please?

ADD REPLY • link written 19 months ago by Bjoern Gruening ♦ 5.1k

Hello! I am having the same problem, here is what I found regarding the version of the tool:

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.1.6.0 Galaxy Tool Version: 0.1.6.0 This tool requires diamond (Version 0.6.13)

I am using the main Galaxy instance.

Thanks,

Silvia

ADD REPLY • link written 18 months ago by silvia.raineri • 0

Sorry, I forgot to mention:

Job dependencies diamond tool_shed_package 0.6.13

ADD REPLY • link written 18 months ago by silvia.raineri • 0

I am using the main galaxy instance usegalaxy.org). It says: Diamond alignment tool for short sequences against a protein database (Galaxy Version 0.1.6.0)

ADD REPLY • link written 18 months ago by david.hughes • 0

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