Metawibele error about mspminer

Microbial community profiling MetaWIBELE
1

Hi, Yancong, thanks for your work on MetaWIBELE, it is a very powerful tool!
I installed MetaWIBELE with conda, and installed its dependencies to use it. Because I failed to download psortb, and interproscan related dependencies were not configured successfully, I ran the MetaWIBELE-characterize workflow with the following codes:

srun -n 1 metawibele characterize --input-sequence "/parastor/home/zhangwj02/MetaWIBELE/Res_First/output_proteins.fasta" \
--input-count "/parastor/home/zhangwj02/MetaWIBELE/Res_First/combined_expression.tsv" \
--input-metadata "/parastor/home/zhangwj02/MetaWIBELE/Res_First/Metadata_information.tsv" \
--output /parastor/home/zhangwj02/MetaWIBELE/Res_First/ \
--bypass-psortb --bypass-interproscan

I received an error (full report attached):

09/18/2024 03:24:48 AM - LoggerReporter - INFO: task 59, abundance_normalization : completed successfully
09/18/2024 03:24:48 AM - LoggerReporter - INFO: task 63, abundance_annotator : ready and waiting for resources
09/18/2024 03:24:48 AM - LoggerReporter - INFO: task 63, abundance_annotator : starting to run
09/18/2024 03:24:49 AM - LoggerReporter - INFO: Executing with shell:  metawibele_abundance_annotator -a /parastor/home/zhangwj02/M                                                                                               etaWIBELE/Res_First/abundance_annotation/metawibele_genecatalogs_nrm.tsv -c /parastor/home/zhangwj02/temp/metawibele_proteinfamilie                                                                                               s.clstr -m /parastor/home/zhangwj02/MetaWIBELE/Res_First/Metadata_information.tsv -f protein -t DNA_abundance -o /parastor/home/zha                                                                                               ngwj02/MetaWIBELE/Res_First/abundance_annotation/metawibele_DNA_proteinfamilies.ORF.abundance.detail.tsv >/parastor/home/zhangwj02/                                                                                               MetaWIBELE/Res_First/abundance_annotation/metawibele_DNA_proteinfamilies.ORF.abundance.detail.log 2>&1
09/18/2024 03:36:21 AM - anadama2.helpers - INFO: Execution complete. Stdout:
Stderr:
09/18/2024 03:36:21 AM - LoggerReporter - INFO: task 63, abundance_annotator : completed successfully
09/18/2024 03:36:21 AM - LoggerReporter - INFO: task 51, sum_to_protein_family_abundance : ready and waiting for resources
09/18/2024 03:36:21 AM - LoggerReporter - INFO: task 51, sum_to_protein_family_abundance : starting to run
09/18/2024 03:36:22 AM - LoggerReporter - INFO: Executing with shell:  metawibele_sum_to_protein_family_abundance -i /parastor/home                                                                                               /zhangwj02/MetaWIBELE/Res_First/abundance_annotation/combined_expression.refined.tsv -c /parastor/home/zhangwj02/temp/metawibele_pr                                                                                               oteinfamilies.clstr -o /parastor/home/zhangwj02/MetaWIBELE/Res_First/abundance_annotation/metawibele_proteinfamilies_counts.all.tsv                                                                                                >/parastor/home/zhangwj02/MetaWIBELE/Res_First/abundance_annotation/metawibele_proteinfamilies_counts.all.log 2>&1
09/18/2024 03:36:46 AM - LoggerReporter - ERROR: task 51, sum_to_protein_family_abundance :  Failed! Error message : Error executin                                                                                               g 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_locall                                                                                               y
    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 `metawibele_sum_to_protein_family_abundance -i /parastor/home/zhangwj02/MetaWIBELE/                                                                                               Res_First/abundance_annotation/combined_expression.refined.tsv -c /parastor/home/zhangwj02/temp/metawibele_proteinfamilies.clstr -o                                                                                                /parastor/home/zhangwj02/MetaWIBELE/Res_First/abundance_annotation/metawibele_proteinfamilies_counts.all.tsv >/parastor/home/zhang                                                                                               wj02/MetaWIBELE/Res_First/abundance_annotation/metawibele_proteinfamilies_counts.all.log 2>&1' failed.
Out:
Err:

09/18/2024 03:36:46 AM - LoggerReporter - ERROR: task 53, abundance_filtering :  Failed! Error message : Task failed because parent                                                                                                task `51' failed

It looks like an error occurred in the sum_to_protein_family_abundance (Task 51) step of the mspminer process. Within a few minutes of this error, MetaWIBELE stopped running and generated an incomplete result file as shown below:

image
image988×291 8.86 KB

The output files in MSPminer_output look fine and are the same as the files generated by running the ./mspminer settings.ini command when I tested mspminer alone. The following figure shows all the result files in the abundance_annotation folder：

image
image1009×487 21.3 KB

The error in metawibele_proteinfamilies_counts.all.log is as follows:

(metaw) [zhangwj02@mu03 MSPminer_1_1_3]$ cat "/parastor/home/zhangwj02/MetaWIBELE/Res_First/abundance_annotation/metawibele_proteinfamilies_counts.all.log"
09/18/2024 03:36:22 AM - metawibele.config - INFO: ### Start sum_to_protein_family_abundance step ####
09/18/2024 03:36:22 AM - metawibele.config - INFO: Get cluster info ......starting
09/18/2024 03:36:46 AM - metawibele.config - INFO: Get cluster info ......done
09/18/2024 03:36:46 AM - metawibele.config - INFO: Assign counts to protein families ......starting
Traceback (most recent call last):
  File "/parastor/home/zhangwj02/miniconda3/envs/mw/bin/metawibele_sum_to_protein_family_abundance", line 10, in <module>
    sys.exit(main())
  File "/parastor/home/zhangwj02/.local/lib/python3.7/site-packages/metawibele/characterize/sum_to_protein_family_abundance.py", line 196, in main
    assign_counts (pep_cluster, values.t, values.i, values.o)
  File "/parastor/home/zhangwj02/.local/lib/python3.7/site-packages/metawibele/characterize/sum_to_protein_family_abundance.py", line 125, in assign_counts
    mys = titles[myindex]
KeyError: 1

I’d very appreciate if you could help me with this problem. Thanks!

2

Hi there,

It seems like that the process was unable to recognize the header line of your input abundance file, combined_expression.tsv. The header should be formatted as "ID ..." (i.e., the first column in the first row must be labeled as “ID”). Could you adjust the header of combined_expression.tsv and try again to see if it resolves the issue?

In general, MetaWIBELE-characterize typically takes MetaWIBELE-preprocess’s outputs as inputs. Users can feed their own inputs to MetaWIBELE-characterize, but they need to format their inputs as required.

Thanks!
Yancong