Hi, again, Yancong, thanks for your work on MetaWIBELE. I run the MetaWIBELE-characterize workflow with my own processed non-redundant protein sequences, gene counts and metadata files. I have encountered other errors before and solved them with your help. This time I encountered a new error in mspminer process:
(Oct 09 00:19:31) [27/45 - 60.00%] **Failed ** Task 31: mspminer
(Oct 09 00:19:31) [27/45 - 60.00%] **Ready ** Task 30: ln__counts_file
(Oct 09 00:19:31) [27/45 - 60.00%] **Started ** Task 30: ln__counts_file
(Oct 09 00:19:31) [28/45 - 62.22%] **Completed** Task 30: ln__counts_file
(Oct 09 00:19:31) [28/45 - 62.22%] **Ready ** Task 24: store__uniref_taxa
(Oct 09 00:19:31) [28/45 - 62.22%] **Started ** Task 24: store__uniref_taxa
(Oct 09 00:19:37) [29/45 - 64.44%] **Completed** Task 24: store__uniref_taxa
(Oct 09 00:19:37) [30/45 - 66.67%] **Failed ** Task 34: mspminer_msp
(Oct 09 00:19:37) [31/45 - 68.89%] **Failed ** Task 36: mspminer_msp_uniref_annotation
(Oct 09 00:19:37) [32/45 - 71.11%] **Failed ** Task 38: mspminer_msp_taxonomy_annotation
(Oct 09 00:19:37) [33/45 - 73.33%] **Failed ** Task 40: mspminer_protein
(Oct 09 00:19:37) [34/45 - 75.56%] **Failed ** Task 46: mspminer_protein_family_taxonomy
(Oct 09 00:19:37) [35/45 - 77.78%] **Failed ** Task 50: store__mymsp_detail_taxa
(Oct 09 00:19:37) [36/45 - 80.00%] **Failed ** Task 49: store__mymsp_detail_taxa_all_family
(Oct 09 00:19:37) [37/45 - 82.22%] **Failed ** Task 48: store__mymsp_detail_taxa_family
(Oct 09 00:19:37) [38/45 - 84.44%] **Failed ** Task 44: msp_protein_family
(Oct 09 00:19:37) [39/45 - 86.67%] **Failed ** Task 42: mspminer_protein_family
(Oct 09 00:19:37) [40/45 - 88.89%] **Failed ** Task 69: summary_function_annotation
(Oct 09 00:19:37) [41/45 - 91.11%] **Failed ** Task 76: finalize_annotation
(Oct 09 00:19:37) [42/45 - 93.33%] **Failed ** Task 73: summary_all_annotation
(Oct 09 00:19:37) [43/45 - 95.56%] **Failed ** Task 66: summary_function_annotation
(Oct 09 00:19:37) [44/45 - 97.78%] **Failed ** Task 74: finalize_annotation
(Oct 09 00:19:37) [45/45 - 100.00%] **Failed ** Task 71: summary_all_annotation
Run Finished
Task 31 failed
Name: mspminer
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/runners.py", line 200, in _run_task_locally
action_func(task)
File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/helpers.py", line 107, in actually_sh
ret = _sh(s, **kwargs)
File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/util/__init__.py", line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8')))
anadama2.util.ShellException: [Errno 255] Command `mspminer /parastor/home/zhangwj02/MetaWIBELE/Res_First1/abundance_annotation/MSPminer_setting.cfg >/parastor/home/zhangwj02/MetaWIBELE/Res_First1/abundance_annotation/metawibele_MSPminer_msp.run_mspminer.log 2>&1' failed.
Could you please tell me how to deal with this?
Because of the error, I tried again to run the preprocessing workflow with the raw fastq data, and Everything went smoothly at first, until usearch reported an error:
10/16/2024 01:17:07 PM - LoggerReporter - INFO: task 886, format_protein_sequences : completed successfully
10/16/2024 01:17:07 PM - LoggerReporter - INFO: task 888, usearch__sorting : ready and waiting for resources
10/16/2024 01:17:07 PM - LoggerReporter - INFO: task 888, usearch__sorting : starting to run
10/16/2024 01:17:07 PM - LoggerReporter - INFO: Executing with shell: usearch -sortbylength /parastor/home/zhangwj02/MetaWIBELE/Res_First_Rawdata/finalized/First_raw_combined_protein.faa -fastaout /parastor/home/zhangwj02/MetaWIBELE/Res_First_Rawdata/finalized/First_raw_combined_protein.sorted.faa -minseqlength 0 >/parastor/home/zhangwj02/MetaWIBELE/Res_First_Rawdata/finalized/First_raw_combined_protein.sorted.log 2>&1
10/16/2024 01:17:07 PM - LoggerReporter - ERROR: task 888, usearch__sorting : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/runners.py", line 200, in _run_task_locally
action_func(task)
File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/helpers.py", line 107, in actually_sh
ret = _sh(s, **kwargs)
File "/parastor/home/zhangwj02/miniconda3/envs/mw/lib/python3.7/site-packages/anadama2/util/__init__.py", line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode('utf-8'), ret[1].decode('utf-8')))
anadama2.util.ShellException: [Errno 1] Command `usearch -sortbylength /parastor/home/zhangwj02/MetaWIBELE/Res_First_Rawdata/finalized/First_raw_combined_protein.faa -fastaout /parastor/home/zhangwj02/MetaWIBELE/Res_First_Rawdata/finalized/First_raw_combined_protein.sorted.faa -minseqlength 0 >/parastor/home/zhangwj02/MetaWIBELE/Res_First_Rawdata/finalized/First_raw_combined_protein.sorted.log 2>&1 ' failed.
Could you please help me with these two problems? Thank you very much!