I’m trying to use tool “Combine MetaPhlAn and HUMAnN outputs”
to combine the outputs of metaphaln and Humann. But, the run ended up with error as follows;
Traceback (most recent call last):
File “/mnt/nfs/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/01ac9954c27f/combine_metaphlan2_humann2/combine_metaphlan_humann.py”, line 118, in
combine_metaphlan_humann(args)
File “/mnt/nfs/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/01ac9954c27f/combine_metaphlan2_humann2/combine_metaphlan_humann.py”, line 67, in combine_metaphlan_humann
clade_abund = extract_clade_abundance(args.metaphlan_fp)
File “/mnt/nfs/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/01ac9954c27f/combine_metaphlan2_humann2/combine_metaphlan_humann.py”, line 23, in extract_clade_abundance
abundance = split_line[2]
IndexError: list index out of range
This error is usually due to a data format problem inside the input files. Meaning, the tool was looking for a particular piece of data that it couldn’t find or something else similar.
Do you want to share the work? We could review and offer advice. Or, you could review our tutorials that include the tool and compare your input format/content to the examples to troubleshoot. Find tutorial links at the bottom of tool forms.
How to share is in the banner at the top of this forum, or please see these:
I’m following the tutorial “Metatranscriptomics analysis using microbiome RNA-seq data” . each tool I used ran smooth, except for this step
the tutorial’s authors mentioned that during updating the tutorial script they found “Comment: Disagreemnet between MetaPhlAn and HUMAnN database”
I’m convinced that the error may be attributed to a similar thing with my data.
How could I send the history link to you to have a look?
Both of the links I posted explain how to generate a shared history link, and you can post that back here.
But – if you think this is due to scientific reasons, or problems with the data formats output from these tools that others have also noticed, then we might not be able to help much more. The underlying tools wrapped in Galaxy are the same as used anywhere else, and we wouldn’t be able to modify that here unless it is some minor format change you want to explore the how-to for.
All that said, I’m still willing to take a look though, and we can bring in the tutorial authors as needed for more feedback. If this is with your own data, be sure to try running this with the tutorial data first, and compare your methods to those. You might notice what needs to be changed.
as the authors mentioned the differences were in the scientific names for some taxa which were updated in one database (e.g for Metaphlan) but not in another one (e.g for Humann)
for the history, I prefer to share it privately not in public if that possible.
Ok, thanks for explaining more. I see the portion of the tutorial that references this type of discrepancy. Exact link for reference.
It seems that you’ll need to identify the variables that need to be modified, then the files will be compatible. This would probably involve a “replace” operation as shown in the tutorial.
Are you at that step? Did you have problems with the replace? If you want to copy/paste out the to/from values, then screenshot the tool form used to do the replace we can help to troubleshoot that.
Tools will want “exact” values to do the manipulations, so being careful about whitespace and remember that capitalization will matter. You don’t even need to use that exact tool in the tutorial … there are many replace functions. Some are shown in the last tutorial here https://training.galaxyproject.org/training-material/search2?query=olympics. That last one is a cheatsheet translating common command-line utilities into their versions as wrapped in Galaxy, the others are about more direct methods in different interactive environments that incorporate the utilities directly.
Even if I saw the history, this is probably where the advice would end up. So you don’t need to share publicly. Sorry for misunderstanding originally!
this is the point, I don’t know which taxa are different between the two tools. For the replace I can do it with " Replace parts of text"
I apologize if my previous reply about sharing the history wasn’t clear, I meant I could let you only have the link to the history not publish it here.
thanking your help
Thanks for clarifying, that is the part I was wondering about.
I don’t know if someone has created a mapping between databases or not, or even which databases, if any!
So … I’ve cross-posted this over to the GTN chat for feedback. They might reply here or there, and feel free to join the chat, too You're invited to talk on Matrix
