Error_report:biobakery_workflows wmgx

Infrastructure and utilities bioBakery workflows
1

root@634f60c5aa0a:/data# biobakery_workflows wmgx --input S10 --output S10_OUTPUT
(Nov 13 06:45:17) [ 0/44 - 0.00%] **Ready ** Task 0: kneaddata____D1-1_combined_R1
(Nov 13 06:45:17) [ 0/44 - 0.00%] **Started ** Task 0: kneaddata____D1-1_combined_R1
(Nov 13 06:45:17) [ 1/44 - 2.27%] **Failed ** Task 0: kneaddata____D1-1_combined_R1
(Nov 13 06:45:17) [ 2/44 - 4.55%] **Failed ** Task 3: kneaddata_read_count_table
(Nov 13 06:45:17) [ 3/44 - 6.82%] **Failed ** Task 4: metaphlan____D1-1_combined_R1
(Nov 13 06:45:17) [ 4/44 - 9.09%] **Failed ** Task 6: metaphlan_join_taxonomic_profiles
(Nov 13 06:45:17) [ 5/44 - 11.36%] **Failed ** Task 7: metaphlan_count_species
(Nov 13 06:45:17) [ 6/44 - 13.64%] **Failed ** Task 25: strainphlan_sample2markers____D1-1_combined_R1
(Nov 13 06:45:17) [ 7/44 - 15.91%] **Failed ** Task 26: strainphlan_print_clades
(Nov 13 06:45:17) [ 8/44 - 18.18%] **Failed ** Task 27: order_clade_list
(Nov 13 06:45:17) [ 9/44 - 20.45%] **Failed ** Task 28: strainphlan_clade_0
(Nov 13 06:45:17) [10/44 - 22.73%] **Failed ** Task 29: strainphlan_clade_1
(Nov 13 06:45:17) [11/44 - 25.00%] **Failed ** Task 30: strainphlan_clade_2
(Nov 13 06:45:17) [12/44 - 27.27%] **Failed ** Task 31: strainphlan_clade_3
(Nov 13 06:45:17) [13/44 - 29.55%] **Failed ** Task 32: strainphlan_clade_4
(Nov 13 06:45:17) [14/44 - 31.82%] **Failed ** Task 33: strainphlan_clade_5
(Nov 13 06:45:17) [15/44 - 34.09%] **Failed ** Task 34: strainphlan_clade_6
(Nov 13 06:45:17) [16/44 - 36.36%] **Failed ** Task 35: strainphlan_clade_7
(Nov 13 06:45:17) [17/44 - 38.64%] **Failed ** Task 36: strainphlan_clade_8
(Nov 13 06:45:17) [18/44 - 40.91%] **Failed ** Task 37: strainphlan_clade_9
(Nov 13 06:45:17) [19/44 - 43.18%] **Failed ** Task 38: strainphlan_clade_10
(Nov 13 06:45:17) [20/44 - 45.45%] **Failed ** Task 39: strainphlan_clade_11
(Nov 13 06:45:17) [21/44 - 47.73%] **Failed ** Task 40: strainphlan_clade_12
(Nov 13 06:45:17) [22/44 - 50.00%] **Failed ** Task 41: strainphlan_clade_13
(Nov 13 06:45:17) [23/44 - 52.27%] **Failed ** Task 42: strainphlan_clade_14
(Nov 13 06:45:17) [24/44 - 54.55%] **Failed ** Task 43: strainphlan_clade_15
(Nov 13 06:45:17) [25/44 - 56.82%] **Failed ** Task 44: strainphlan_clade_16
(Nov 13 06:45:17) [26/44 - 59.09%] **Failed ** Task 45: strainphlan_clade_17
(Nov 13 06:45:17) [27/44 - 61.36%] **Failed ** Task 46: strainphlan_clade_18
(Nov 13 06:45:17) [28/44 - 63.64%] **Failed ** Task 47: strainphlan_clade_19
(Nov 13 06:45:17) [29/44 - 65.91%] **Failed ** Task 8: humann____D1-1_combined_R1
(Nov 13 06:45:17) [30/44 - 68.18%] **Failed ** Task 10: humann_count_alignments_species
(Nov 13 06:45:17) [31/44 - 70.45%] **Failed ** Task 11: humann_regroup_UniRef2EC____D1-1_combined_R1
(Nov 13 06:45:17) [32/44 - 72.73%] **Failed ** Task 13: humann_join_tables_ecs
(Nov 13 06:45:17) [33/44 - 75.00%] **Failed ** Task 16: humann_renorm_ecs_relab____D1-1_combined_R1
(Nov 13 06:45:17) [34/44 - 77.27%] **Failed ** Task 19: humann_join_tables_ecs_relab
(Nov 13 06:45:17) [35/44 - 79.55%] **Failed ** Task 22: humann_count_features_ecs
(Nov 13 06:45:17) [36/44 - 81.82%] **Failed ** Task 12: humann_join_tables_genefamilies
(Nov 13 06:45:17) [37/44 - 84.09%] **Failed ** Task 14: humann_join_tables_pathabundance
(Nov 13 06:45:17) [38/44 - 86.36%] **Failed ** Task 15: humann_renorm_genes_relab____D1-1_combined_R1
(Nov 13 06:45:17) [39/44 - 88.64%] **Failed ** Task 18: humann_join_tables_genes_relab
(Nov 13 06:45:17) [40/44 - 90.91%] **Failed ** Task 21: humann_count_features_genes
(Nov 13 06:45:17) [41/44 - 93.18%] **Failed ** Task 17: humann_renorm_pathways_relab____D1-1_combined_R1
(Nov 13 06:45:17) [42/44 - 95.45%] **Failed ** Task 20: humann_join_tables_pathways_relab
(Nov 13 06:45:17) [43/44 - 97.73%] **Failed ** Task 23: humann_count_features_pathways
(Nov 13 06:45:17) [44/44 - 100.00%] **Failed ** Task 24: humann_merge_feature_counts
Run Finished
Task 0 failed
Name: kneaddata____D1-1_combined_R1
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/usr/local/lib/python3.6/dist-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/usr/local/lib/python3.6/dist-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/usr/local/lib/python3.6/dist-packages/anadama2/util/ init .py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 2] Command `kneaddata --input /data/S10/D1-1_combined_R1.fastq.gz --output /data/S10_OUTPUT/kneaddata/main --threads 1 --output-prefix D1-1_combined_R1 --reference-db /opt/biobakery_workflows_databases/kneaddata_db_human_genome --serial --run-trf && mv /data/S10_OUTPUT/kneaddata/main/D1-1_combined_R1.repeats.removed.fastq /data/S10_OUTPUT/kneaddata/main/D1-1_combined_R1.fastq’ failed.
Out: b’’
Err: b’usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT_DIR\n [-db REFERENCE_DB] [–bypass-trim]\n [–output-prefix OUTPUT_PREFIX] [-t <1>] [-p <1>]\n [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf]\n [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output]\n [–remove-intermediate-output] [–cat-final-output]\n [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG]\n [–trimmomatic TRIMMOMATIC_PATH] [–max-memory MAX_MEMORY]\n [–trimmomatic-options TRIMMOMATIC_OPTIONS]\n [–bypass-trim-repetitive] [–bowtie2 BOWTIE2_PATH]\n [–bowtie2-options BOWTIE2_OPTIONS] [–no-discordant]\n [–reorder] [–serial] [–bmtagger BMTAGGER_PATH]\n [–trf TRF_PATH] [–match MATCH] [–mismatch MISMATCH]\n [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE]\n [–maxperiod MAXPERIOD] [–fastqc FASTQC_PATH]\nkneaddata: error: unrecognized arguments: --run-trf\n’

Task 3 failed
Name: kneaddata_read_count_table
Original error:
Task failed because parent task 0' failed Task 4 failed Name: metaphlan____D1-1_combined_R1 Original error: Task failed because parent task 0’ failed
Task 6 failed
Name: metaphlan_join_taxonomic_profiles
Original error:
Task failed because parent task 4' failed Task 7 failed Name: metaphlan_count_species Original error: Task failed because parent task 6’ failed
Task 25 failed
Name: strainphlan_sample2markers____D1-1_combined_R1
Original error:
Task failed because parent task 4' failed Task 26 failed Name: strainphlan_print_clades Original error: Task failed because parent task 25’ failed
Task 27 failed
Name: Task27
Original error:
Task failed because parent task 26' failed Task 28 failed Name: strainphlan_clade_0 Original error: Task failed because parent task 25’ failed
Task 29 failed
Name: strainphlan_clade_1
Original error:
Task failed because parent task 25' failed Task 30 failed Name: strainphlan_clade_2 Original error: Task failed because parent task 25’ failed
Task 31 failed
Name: strainphlan_clade_3
Original error:
Task failed because parent task 25' failed Task 32 failed Name: strainphlan_clade_4 Original error: Task failed because parent task 25’ failed
Task 33 failed
Name: strainphlan_clade_5
Original error:
Task failed because parent task 25' failed Task 34 failed Name: strainphlan_clade_6 Original error: Task failed because parent task 25’ failed
Task 35 failed
Name: strainphlan_clade_7
Original error:
Task failed because parent task 25' failed Task 36 failed Name: strainphlan_clade_8 Original error: Task failed because parent task 25’ failed
Task 37 failed
Name: strainphlan_clade_9
Original error:
Task failed because parent task 25' failed Task 38 failed Name: strainphlan_clade_10 Original error: Task failed because parent task 25’ failed
Task 39 failed
Name: strainphlan_clade_11
Original error:
Task failed because parent task 25' failed Task 40 failed Name: strainphlan_clade_12 Original error: Task failed because parent task 25’ failed
Task 41 failed
Name: strainphlan_clade_13
Original error:
Task failed because parent task 25' failed Task 42 failed Name: strainphlan_clade_14 Original error: Task failed because parent task 25’ failed
Task 43 failed
Name: strainphlan_clade_15
Original error:
Task failed because parent task 25' failed Task 44 failed Name: strainphlan_clade_16 Original error: Task failed because parent task 25’ failed
Task 45 failed
Name: strainphlan_clade_17
Original error:
Task failed because parent task 25' failed Task 46 failed Name: strainphlan_clade_18 Original error: Task failed because parent task 25’ failed
Task 47 failed
Name: strainphlan_clade_19
Original error:
Task failed because parent task 25' failed Task 8 failed Name: humann____D1-1_combined_R1 Original error: Task failed because parent task 0’ failed
Task 10 failed
Name: humann_count_alignments_species
Original error:
Task failed because parent task 8' failed Task 11 failed Name: humann_regroup_UniRef2EC____D1-1_combined_R1 Original error: Task failed because parent task 8’ failed
Task 13 failed
Name: humann_join_tables_ecs
Original error:
Task failed because parent task 11' failed Task 16 failed Name: humann_renorm_ecs_relab____D1-1_combined_R1 Original error: Task failed because parent task 11’ failed
Task 19 failed
Name: humann_join_tables_ecs_relab
Original error:
Task failed because parent task 16' failed Task 22 failed Name: humann_count_features_ecs Original error: Task failed because parent task 19’ failed
Task 12 failed
Name: humann_join_tables_genefamilies
Original error:
Task failed because parent task 8' failed Task 14 failed Name: humann_join_tables_pathabundance Original error: Task failed because parent task 8’ failed
Task 15 failed
Name: humann_renorm_genes_relab____D1-1_combined_R1
Original error:
Task failed because parent task 8' failed Task 18 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task 15’ failed
Task 21 failed
Name: humann_count_features_genes
Original error:
Task failed because parent task 18' failed Task 17 failed Name: humann_renorm_pathways_relab____D1-1_combined_R1 Original error: Task failed because parent task 8’ failed
Task 20 failed
Name: humann_join_tables_pathways_relab
Original error:
Task failed because parent task 17' failed Task 23 failed Name: humann_count_features_pathways Original error: Task failed because parent task 20’ failed
Task 24 failed
Name: humann_merge_feature_counts
Original error:
Task failed because parent task `21’ failed
Traceback (most recent call last):
File “/usr/local/bin/wmgx.py”, line 183, in
workflow.go()
File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 800, in go
self._handle_finished()
File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 832, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed

1 Like
2

Hello, Thank you for the detailed post! It looks like your kneaddata version is out of sync with the workflows version as it is running with a different option. If you roll back your kneaddata version to < v0.7.8 it should resolve the error you are seeing. We will work on our end to remove the kneaddata option “–run-trf” from the workflow to resolve this error with running with newer versions of kneaddata. Sorry for any confusion!

Thank you,
Lauren

1 Like
3

hello, I also account this error when running biobakery_workflows wmgx:

Traceback (most recent call last):
  File "/share/home/hewei/software_HW/miniconda3/envs/biobakery_workflows/bin/wmgx.py", line 184, in <module>
    workflow.go()
  File "/share/home/hewei/software_HW/miniconda3/envs/biobakery_workflows/lib/python3.7/site-packages/anadama2/workflow.py", line 800, in go
    self._handle_finished()
  File "/share/home/hewei/software_HW/miniconda3/envs/biobakery_workflows/lib/python3.7/site-packages/anadama2/workflow.py", line 832, in _handle_finished
    raise RunFailed()
anadama2.workflow.RunFailed

and my kneaddata version is v0.7.4. , could you please give me some suggestions

5

Use pip install kneaddata==0.7.6
It would be OK.