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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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Error running summarize-metabolism #57

Closed bbaker567 closed 2 years ago

bbaker567 commented 2 years ago

Hello, I am running the workflow summarize-metabolism and I keep running into an error but without much detail.

FileNotFoundError: [Errno 2] No such file or directory: '/home/brittany/Dropbox/PhD_2020/other_mags/metabolisHMM/dallol_subset_Jan25/out/DAL/DAL-WCL_45_84C1R-fdhA_TIGR01591.out'

I am not quite sure how to fix this. Or what the work around is. Any suggestions are appreciated!

Thank you!

More details of the std output : ############################################# metabolisHMM v2.21 Reformatting fasta files... Screening curated metabolic markers... Parsing all results... /home/brittany/.local/bin/summarize-metabolism:162: DeprecationWarning: 'U' mode is deprecated with open(result, "rU") as input: Traceback (most recent call last): File "/home/brittany/.local/bin/summarize-metabolism", line 162, in with open(result, "rU") as input: FileNotFoundError: [Errno 2] No such file or directory: '/home/brittany/Dropbox/PhD_2020/other_mags/metabolisHMM/dallol_subset_Jan25/out/DAL/DAL-WCL_45_84C1R-fdhA_TIGR01591.out'

elizabethmcd commented 2 years ago

In the out subdirectory in your results folder, is there anything there? If not it suggests something is wrong with running the HMM-search step for each marker. Alternatively, I think because you have dashes/hyphens in your genome names that needs to be changed, which you can do with: rename 's/-/_/g' * because these files need to be formatted where it spilts on - to compare each genome-marker pair. This is explained in the wiki but I should add a function to check if filenames have dashes in them and warn the user.

Hope that helps!

bbaker567 commented 2 years ago

rename 's/-/_/g' * fixed it! Thank you, I should have read the wiki more carefully :)