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Could not run command: cat prokka\/IS\.faa #402
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I will need more information, ideally the whole screen log. What does |
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I think you need to upgrade 3 things, in order of importance:
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Updated the BLAST+ and it worked |
Great news! |
Hello, I seem to have the same kind of problem. I have been trying to look around here for a solution but mainly it seems to be updating packages, but I am up to date I think. (sorry for the spam I already posted on another channel but this one is more recent) I updated the whole Prokka package so I'm guessing everything should be up-to-date) Here is my full log: |
@Evan212 It's just update the blast+. Just that! |
Yes this was fixed in 1.14.0 release. |
I'm on macOS. And I think it should be the latest version no? I downloaded from your link but it does not change the result. Edit: I have blast 2.9 and prokka 1.14 |
Github does not include all the dependences. Well, i do bundle some things, but they are not guaranteed to work. You should use either conda or brew to install. On Mac, homebrew is probably the easiest. Follow instructions at UPDATE: oh i see you are using conda. not sure what is going on. what does You want this order:
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I get this: channels:
I managed to solve my problem by running the exact same thing on my university cluster, so not sure what was wrong with my computer |
That's good. |
I met the same problem.
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Problem persists for Could not run command: cat prokka\/target\.IS\.tmp\.8\.faa | parallel --gnu --plain -j 8 --block 100543 --recstart '>' --pipe blastp -query - -db /opt/conda/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\/target\.IS\.tmp\.8\.blast 2> /dev/null
blastp -version
# 2.10.1
prokka --version
# 1.14.6 Both installed using conda. @tseemann could this be a problem w/ blastp being too recent? |
Hi all - I am having the same issues as above trying to run prokka with the most updated version. I am running this from our university's cluster in a conda environment (all tools are within
shortened output with error included:
Any help would be really appreciated! |
UPDATE: ran |
For those encountering the error even after updating dependencies, Prokka, and resetting the database, you can try re-running the failed command without the 2> /dev/null and you will find out the exact error. In my case, the tmp directory was not found as I had modified the tmp directory path. Resetting the tmp directory path solved the problem.
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I cannot run prokka, whenever I run, it said I need to run setup and the file for the prokka not found. Can anybody help |
Hey, what's happening here?
Help! :)
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