All task fails - Biobakery workflows wmgx

Infrastructure and utilities bioBakery workflows
1

Hi all,

I have am trying to use Strainphlan via the biobakery/workflows docker image.
I have followed the installation guide for the biobakery/workflow docker image. I manage to install all necessary databases using

biobakery_workflow_databases --install wmgx

When i run

biobakery_workflows wmgx --input folder_with_files  --output output

all task fail.

(Aug 05 23:03:18) [    0/11692 -   0.00%] **Ready    ** Task     3: kneaddata____20e_1e0_1552_R1
(Aug 05 23:03:18) [    0/11692 -   0.00%] **Started  ** Task     3: kneaddata____20e_1e0_1552_R1
(Aug 05 23:03:18) [    1/11692 -   0.01%] **Failed   ** Task     3: kneaddata____20e_1e0_1552_R1
(Aug 05 23:03:18) [    2/11692 -   0.02%] **Failed   ** Task  2918: metaphlan____20e_1e0_1552_R1
(Aug 05 23:03:18) [    3/11692 -   0.03%] **Failed   ** Task 11674: strainphlan_sample2markers____20e_1e0_1552_R1
(Aug 05 23:03:18) [    4/11692 -   0.03%] **Failed   ** Task  4378: humann____20e_1e0_1552_R1
(Aug 05 23:03:18) [    5/11692 -   0.04%] **Failed   ** Task  5836: humann_regroup_UniRef2EC____20e_1e0_1552_R1
(Aug 05 23:03:18) [    6/11692 -   0.05%] **Failed   ** Task  8753: humann_renorm_ecs_relab____20e_1e0_1552_R1
(Aug 05 23:03:18) [    7/11692 -   0.06%] **Failed   ** Task  7296: humann_renorm_genes_relab____20e_1e0_1552_R1
(Aug 05 23:03:18) [    8/11692 -   0.07%] **Failed   ** Task 10210: humann_renorm_pathways_relab____20e_1e0_1552_R1
(Aug 05 23:03:18) [    8/11692 -   0.07%] **Ready    ** Task     5: kneaddata____1fa_8c3_5206_R1
(Aug 05 23:03:18) [    8/11692 -   0.07%] **Started  ** Task     5: kneaddata____1fa_8c3_5206_R1

I do not get an error during the download or installation of the databases, and I am able to run from the same docker image on the same data both methaphlan and strainphlan without issues.

Thanks!
Maurizio

2

@aitor.blancomiguez I have moved the topic to the right session, I guess.Just pinging this up