Biobakery workflow fails all tasks

Microbial community profiling StrainPhlAn
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 /home/morri/Desktop/Desktop/EVVY/raw_fasta/test/ --output output

all task are started and they fail immediately, without error neither during the installation of the databases or the command itself. Any help would be great!

(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
2

An update : if I run first metaphlan and then strainphlan separated, the commands seems to work and I do get both tsv profiles and pkl files. It seems that the whole workflow does not manage to run from the beginning, so I am wondering if the problem is not with kneaddata

3

Hi @Mmorri86
Thanks for reporting this problem. Could you post it in the biobakery workflows subforum bioBakery workflows - The bioBakery help forum ?

4

done, I have created a new topic All task fails - Biobakery workflows wmgx

thank you!