error running camitax about camitax

[abremges]

Sorry for not responding earlier, @stefcamp, I was on parental leave and didn't see your issue earlier.

CAMITAX cannot find or access the CheckM reference data. Did you run nextflow run CAMI-challenge/CAMITAX/init.nf --db /path/to/db/folder prior to executing CAMITAX to download the reference data? Else please let me know whether you run CAMITAX with -profile docker to make use of BioContainers or installed all dependencies manually, and we'll take it from there.

[nixon444]

Hi I keep having this same issue. I thought it was an installation issue (even though it worked fine previously), so I installed on a new virtual machine. I am still getting the same error though with a new installation.

I ran:

nextflow run CAMI-challenge/CAMITAX -profile docker --db ../../camitax_data/ --i ./ --x fasta

And got this error:

Error executing process > 'checkm (K_1000.001)'

Caused by:
Process checkm (K_1000.001) terminated with an error exit status (126)

Command executed:

Set CheckM root data location

echo camitax_data/checkm/ | checkm data setRoot camitax_data/checkm/

Extract 16S rRNA gene sequences with Nhmmer

checkm ssu_finder -t 8 -x fasta K_1000.001.fasta . ssu_finder 2>&1
ln -s ssu_finder/ssu.fna K_1000.001.ssu.fna

Phylogenetic placement onto reduced reference tree

checkm lineage_wf -t 8 --reduced_tree -x fasta . checkm
checkm qa -o 2 --tab_table checkm/lineage.ms checkm > K_1000.001.checkm.tsv

Command exit status:
126

Command output:
(empty)

Command error:
docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.39/containers/create?name=nxf-IA0bM3ooRxKasszrIFcvWZWq: dial unix /var/run/docker.sock: connect: permission denied.
See 'docker run --help'.

Work dir:
/home/ubuntu/camitax_analyses/sharon/work/2d/f08fdbc10808d640d5e3e4ca7368d4

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

Please help!

[nixon444]

I think I have soved this issue - an problem with the docker configuration and permissions on my server. Camitax is now running, so hopefully no more errors!

[AlphaSquad]

I'm glad you solved the problem, unfortunately docker sometimes has problems with permissions.
If anything comes up, feel free to reopen