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elizabethmcd / metabolisHMM

Tool for constructing phylogenies and summarizing metabolic characteristics based on curated and custom profile HMMs
GNU General Public License v3.0
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no hmmersearch for summarize-metabolism #40

Closed Thexiyang closed 4 years ago

Thexiyang commented 4 years ago

Hi! Thanks for the tool. I installed the software using the conda way. For summarize-metabolism workflow, it did not perform hmmsearch (empty files for out folder); while search-custom-markers workflow did that. Could you check if there is any issue with the summarize-metabolism script? Here is my cmd line: summarize-metabolism --input faa --output summaries --metadata ../genomeinfo.csv --aggregate ON. Thanks!

elizabethmcd commented 4 years ago

Thanks for trying the tool out! I will double check that workflow. Did you get any errors associated with not getting any output?

elizabethmcd commented 4 years ago

I'm going to guess this might be due to how the workflow checks for the curated markers as brought up in issue #41. I'll be making a fix to that workflow and a couple other things and try and get a new version pushed out within a couple of days.

Thexiyang commented 4 years ago

Thanks for the reply. There is no error message shown but empty files and it went to the end with production of a heatmap (all markers read as zero). The issue 41 did happen to me. But when I downloaded the curated markers and run the workflow in this file as the working file, the software could find the makers itself without reporting any error.

elizabethmcd commented 4 years ago

Oh you ran the workflow from within the curated_markers folder so it knew where to find metabolic_markers. Interesting that hmmsearch worked for the custom workflow but not this one. Will check on this tomorrow. Unless it's how you're defining your input folder... can you try adding a slash to the end of the faa folder like faa/? I doubt this is the issue but worth trying.

Thexiyang commented 4 years ago

It should not be due to this, as it indeed performed reformatting procedure. Anyway, I just tried as you suggested, same results.

elizabethmcd commented 4 years ago

I just pushed version 2.1 to PyPi, so if you could update with python3 -m pip install metabolisHMM --upgrade you should get the newest version and see if that fixes things.

Thexiyang commented 4 years ago

Thanks! It indeed solved the issue. but there is still one like issue #41. If I used the flag--aggregate ON, then it came across the same error message: ValueError: zero-size array to reduction operation minimum which has no identity. I guess it may have something related how to prepare the csv files. Could you make a template file in the github files?

elizabethmcd commented 4 years ago

There is a template in the aquifer demo tutorial. What does your CSV file look like? Does this error only happen if you have the aggregate option ON? What happens if you turn it OFF?

Thexiyang commented 4 years ago

My CSV file exactly looks like your template. When it was turned off, it is good; but when it was on , it showed the error message.

elizabethmcd commented 4 years ago

I have been unable to reproduce this error on my system. See the latest comment of issue #41 for further information. I'm going to close this issue as now it is redundant with the other issue and I will continue troubleshooting there.