Question: problem with diamond
0
gravatar for rahul.sg98
14 months ago by
rahul.sg980
rahul.sg980 wrote:

Hello. I am trying to use diamond but fail to do so, due there was no reference genome for me and I did not find any inbuilt NCBI database.Any comments will be appreciated. Regards Rahul

assembly rna seq blast diamond • 310 views
ADD COMMENTlink modified 5 days ago by eltonsarmanho0 • written 14 months ago by rahul.sg980
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello Rahul,

To create reference data for this tool, use this tool first: Diamond makedb Build database from a FASTA file

Hopefully this helps! Jen, Galaxy team

ADD COMMENTlink modified 13 months ago • written 13 months ago by Jennifer Hillman Jackson22k
0
gravatar for eltonsarmanho
5 days ago by
eltonsarmanho0 wrote:

There is an error while running enter image description here How to solve this?

ADD COMMENTlink modified 5 days ago • written 5 days ago by eltonsarmanho0
1

Your reference genome has description content. Remove that with the tool NormalizeFasta wrapping the sequence to 80 bases and truncating the title line at the first whitespace.

The job itself probably failed because the genome was not first added using a "fetch genome" DM. The format issue will come up later (with DMs or when the indexed genome is used with tools). Fix the format first before running any DMs.

So - start with these DMs, in this order, before running the Diamond DM:

  • 1 data_manager_fetch_genome_dbkeys_all_fasta
  • 2 data_manager_sam_fasta_index_builder
  • 3 data_manager_picard_index_builder
  • 4 (optinal but recommended) data_manager_twobit_builder
  • 5 data_manager_diamond_database_builder
  • 6 any other indexes you need

This is a pretty small genome, so I wouldn't expect the job to fail for a memory error if your Galaxy instance has at least 16 GB of memory available (the minimum recommended size). When executing tools later, be aware that some may require more memory. It depends on the tools and inputs. A general guideline is that same resources needed to run a tool line-command are needed when running the same tool within Galaxy.

Other issues could be present depending on your config (especially if a cluster is used to run jobs), but that is a different situation. If the "data_manager_fetch_genome_dbkeys_all_fasta" DM fails, then looking into memory and potential cluster issues would be needed (with an admin's help, unless you are doing the config yourself).

ADD REPLYlink modified 5 days ago • written 5 days ago by Jennifer Hillman Jackson22k

Thanks a lot...

Now I have another mistake. My galaxy runs this command: diamond makedb --threads "${GALAXY_SLOTS:-12}" --in '/home/eltonss/Downloads/galaxy-dev/database/files/000/dataset_18.dat' --db ./database

Error generated is Usage: diamond [options] diamond: error: no such option: --threads

I performed this command on the terminal differently: diamond makedb -p 8 --in '/home/eltonss/Downloads/galaxy-dev/database/files/000/dataset_18.dat' --db ./database , where -p equals --Threads. But showed another error : Usage: diamond [options] diamond: error: no such option: --in

How to solve this?

ADD REPLYlink written 5 days ago by eltonsarmanho0
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