The bioBakery help forum

Metawibele preprocess fail

We installed your metawibele by pulling image from Docker, and found the step of “annotation” step (software: prokka) frequently failed.
I think that it might be something wrong with the prokka version, but we cannot change the stuff in your docker image. Also we found that the prokka command, the parameter –metagenome, will cause some errors. We don’t know how to deal with that kind of issues, please let us know how to do without those fatal errors.

BTW, we also tried to install your software from conda, but fail(conda install -c biobakery metawibele python=2.7.1). Consequently, there might be something wrong with the environment conflicts??

thank you!!

1 Like

Hi there,

Re1.: It looks like an issue arising from the license requirement by tbl2asn used by prokka. tbl2asn expires every 6-12 methods and needs to be re-downloaded from NCBI (https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/) and reinstalled in Docker image.
For example, you can replace the older version by:

$ wget -O tbl2asn.gz ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
$ gunzip tbl2asn.gz
$ chmod +x tbl2asn
$ cp tbl2asn /usr/local/bin/

Re2.: MetaWIBELE is built on Python3 and has been tested with Python 3.6 and 3.7. Please try Python 3.6+ to install the conda packages.

We recommend using the latest version of MetaWIBELE (v0.4.2). It includes a couple of updates (documented in the manual and tutorial in GitHub - biobakery/metawibele: MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome) and has been released to pip and conda already. The new Docker image will come out soon as well. Thanks for your interest in MetaWIBELE.

Best,
Yancong

1 Like

Hello :wave:,
Thanks for your detailed reply :smiley:, and I will try to reinstall your tools in these days.

Looking forward to your new version docker image too!

Sorry to bother you again.
I recently tried on the preprocess part of your tool metawibele. Prokka could work smoothly, but I faced the different failure in task 41/43 ?
Do you have any idea about these messages?
PS. I have checked that the required files are present in the according path, so it might be memory issue or something else ?
Thank you in advance.

(Nov 17 13:35:21) [30/48 - 62.50%] **Failed ** Task 41: combine_gene_sequences
Task 41 failed
Name: combine_gene_sequences
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 1] Command `metawibele_combine_gene_sequences -p /home/batch_9/metawibele-out/gene_annotation/ -e ffn -o /home/batch_9/metawibele-out/b9_combined_gene.fna > /home/batch_9/metawibele-out/b9_combined_gene.log 2>&1 ’ failed.
Out: b’’
Err: b’’

(Nov 17 13:35:21) [32/48 - 66.67%] **Ready ** Task 43: format_protein_sequences
Task 43 failed
Name: format_protein_sequences
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 1] Command `metawibele_format_protein_sequences -p /home/batch_9/metawibele-out/gene_annotation/ -q /home/batch_9/metawibele-out/gene_calls/ -e faa -o /home/batch_9/metawibele-out/b9_combined_protein.faa -m /home/batch_9/metawibele-out/b9_gene_info.tsv >/home/batch_9/metawibele-out/b9_combined_protein.log 2>&1 ’ failed.
Out: b’’
Err: b’’

In addition to the main log file for recording the running status of all tasks, MetaWIBELE also reports the detailed processing of each task into an individual log file which could help us do further debugging when needed. So for task 41, you could check its specific log file ( /home/batch_9/metawibele-out/b9_combined_gene.log) and see whether there are more messages there. Similarly, for task 43, check /home/batch_9/metawibele-out/b9_combined_protein.log.

To check whether these failures were caused by limited memory, one quick easy way is to test MetaWIBELE using a small dataset (e.g. the demo data in the tutorial: metawibele · biobakery/biobakery Wiki · GitHub) and see whether this small set can be run successfully on your system. Feel free to let me know if you have any further questions and I am happy to help.

Best,
Yancong

Dear YancongZhang,
I have chenck the file b9_combined_protein.log, and error messages are as follows:

Start format_protein_sequences.py -p /home/batch_9/metawibele-out/gene_annotation/

Get sequence info …starting
Traceback (most recent call last):
File “/usr/local/bin/metawibele_format_protein_sequences”, line 11, in
sys.exit(main())
File “/usr/local/lib/python3.6/dist-packages/metawibele/tools/format_protein_sequences.py”, line 296, in main
gff, types, partial = collect_sequence (values.p, values.e, values.q, values.o)
File “/usr/local/lib/python3.6/dist-packages/metawibele/tools/format_protein_sequences.py”, line 100, in collect_sequence
myid = myid.group(1)
AttributeError: ‘NoneType’ object has no attribute ‘group

Thank you in advance!

Thanks for sharing the detailed log info! It looks like that you are using a bit old version of MetaWIBELE (I am guessing v0.3.7?). We have fixed several issues since then. I think the error you pointed out here should be fixed in newer versions. Could you try our latest released v0.4.2 instead? It is available via pip and conda now.

Best,
Yancong

Dear YancongZhang,

I installed the required environment in your docker image, and I will tried to update the version via pip and conda.

Thank you :blush:

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