The bioBakery help forum

Tasks failed during Maaslin2

Dear Developer,

I am trying to run metawibble example when an error occurred (Seems that maaslin2 failed) I checked the masslin2 and run the demo test for masslin2. The software seems okay. Do you have any suggestions for this issue? below is the log file:

(Nov 11 14:19:53) [54/70 - 77.14%] Completed Task 87: ln__proteinfamilies_relab_feature
(Nov 11 14:19:53) [54/70 - 77.14%] **Ready ** Task 88: transpose
(Nov 11 14:19:53) [54/70 - 77.14%] **Started ** Task 88: transpose
(Nov 11 14:19:53) [55/70 - 78.57%] Completed Task 88: transpose
(Nov 11 14:19:53) [55/70 - 78.57%] **Ready ** Task 92: maaslin2
(Nov 11 14:19:53) [55/70 - 78.57%] **Started ** Task 92: maaslin2
(Nov 11 14:20:10) [56/70 - 80.00%] **Failed ** Task 92: maaslin2
(Nov 11 14:20:10) [57/70 - 81.43%] **Failed ** Task 94: maaslin2_collection
(Nov 11 14:20:10) [58/70 - 82.86%] **Failed ** Task 96: maaslin2_summary
(Nov 11 14:20:10) [59/70 - 84.29%] **Failed ** Task 99: maaslin2_annotator
(Nov 11 14:20:10) [60/70 - 85.71%] **Failed ** Task 101: maaslin2_annotator
(Nov 11 14:20:10) [61/70 - 87.14%] **Failed ** Task 98: maaslin2_summary
(Nov 11 14:20:10) [62/70 - 88.57%] **Failed ** Task 102: maaslin2_annotator
(Nov 11 14:20:10) [63/70 - 90.00%] **Failed ** Task 103: maaslin2_annotator
(Nov 11 14:20:10) [64/70 - 91.43%] **Failed ** Task 104: summary_function_annotation
(Nov 11 14:20:10) [65/70 - 92.86%] **Failed ** Task 109: summary_all_annotation
(Nov 11 14:20:10) [66/70 - 94.29%] **Failed ** Task 112: finalize_annotation
(Nov 11 14:20:10) [66/70 - 94.29%] **Ready ** Task 82: abundance_annotator
(Nov 11 14:20:10) [66/70 - 94.29%] **Started ** Task 82: abundance_annotator
(Nov 11 14:20:10) [67/70 - 95.71%] Completed Task 82: abundance_annotator
(Nov 11 14:20:10) [67/70 - 95.71%] **Ready ** Task 107: summary_function_annotation
(Nov 11 14:20:10) [67/70 - 95.71%] **Started ** Task 107: summary_function_annotation
(Nov 11 14:20:10) [68/70 - 97.14%] Completed Task 107: summary_function_annotation
(Nov 11 14:20:10) [68/70 - 97.14%] **Ready ** Task 111: summary_all_annotation
(Nov 11 14:20:10) [68/70 - 97.14%] **Started ** Task 111: summary_all_annotation
(Nov 11 14:20:10) [69/70 - 98.57%] Completed Task 111: summary_all_annotation
(Nov 11 14:20:10) [69/70 - 98.57%] **Ready ** Task 114: finalize_annotation
(Nov 11 14:20:10) [69/70 - 98.57%] **Started ** Task 114: finalize_annotation
(Nov 11 14:20:10) [70/70 - 100.00%] Completed Task 114: finalize_annotation

Thank you for your help!
Best wishes,
Shen

Hi Shen,

Thanks for your interest in MetaWIBELE! Based on the above log, it looks like maaslin2 failed for some reason. To debug this, you could check the detailed log file of maaslin2: characterization/abundance_annotation/DA/maaslin2_metadata.results.log. This file would report more details on how maaslin2 was running. Please make sure that 1) Maaslin2 can be run by command line in your computing system (easy to check it by Maaslin2.R --help); 2) the parameter configuration is correct in the global config file metawibele.cfg.

Best,
Yancong