Open Jlee795 opened 4 months ago
Hi @KrisKieft is there any ideas with this issue. I saw a closed issue with a solution to this by @BikramDroid. I tried their solution but this hasn't worked for me and I am still not really sure how to sort this.
Any help greatly appreciated,
Kind Regards,
Jlee795
I'm not sure what may have gone wrong but it looks like the database did not fully finish setting up. Can you please try removing KEGG_profiles_prokaryotes.HMM.h3i
and then run hmmpress KEGG_profiles_prokaryotes.HMM
in the directory where these files are stored.
Hi @KrisKieft. This issue has been resolved and Vibrant now runs things. However getting another problem. I was running your mixed example test dataset and had a look at the log file on the github page, your log file says four phages found but when I run the mixed test example dataset my log file says no phages found. Pretty sure that I should get the same output in the log as you get. Do you have any suggestions as to the cause? Any help is greatly appreciated. Thank you,
Kind Regards,
Jlee795
This is the output from my log file:
Command: ../VIBRANT_run.py -i mixed_example_1.fasta -t 2 -folder example_test_mixed_3 Date: 2024-04-01 Start: 21:45:12 End: 21:46:18 Runtime: 1.1 minutes Program: VIBRANT v1.2.1
10 scaffolds were read in. 7 scaffolds met minimum requirements: at least 1000bp and 4 ORFs. 0 putative phages were identified.
CAUTION: running a version of Numpy lower than v1.17.0 will likely cause issues. With pip you can update by running "pip install --upgrade numpy==1.17.0".
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the version of Numpy in my environment is the very version it is mentioning under the caution. So I am not sure as to whether that is the cause. I downloaded VIBRANT as a git clone so it is version 1.2.1
@KrisKieft getting this error from the annotation log, which I think the problem of why no phages are found may be related to:
Traceback (most recent call last):
File "/home/crk_w19039039/VIBRANT/databases/VIBRANT/scripts/VIBRANT_annotation.py", line 1422, in
Not really sure how to solve this. any help would be greatly appreciated,
Kind Regards Jlee795
Hi,
I have been trying to use VIBRANT on linux. I installed it through Gitclone as I had trouble trying to install the usual way. I had the message saying vibrant was good to go but when I tried to run it on my data it didn't work. I checked the log and saw this message
"VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py"
I did what it said and ran vibrant set up script and can see the pressed files in the databases folder e.g. KEGG_profiles_prokaryotes.HMM KEGG_profiles_prokaryotes.HMM.h3i Pfam-A_v32.HMM Pfam-A_v32.HMM.h3f Pfam-A_v32.HMM.h3i Pfam-A_v32.HMM.h3m Pfam-A_v32.HMM.h3p
VOGDB94_phage.HMM VOGDB94_phage.HMM.h3f VOGDB94_phage.HMM.h3i VOGDB94_phage.HMM.h3m VOGDB94_phage.HMM.h3p
tried running the command on my own data again and still got the same error message, can anyone advise what to do to fix this please?
Kind Regards,
Jen