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roblanf / minion_qc

Quality control for MinION sequencing data
MIT License
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All graphs aren't generating #42

Closed peflanag closed 5 years ago

peflanag commented 5 years ago

Hi, I'm running MinIONQC but have noticed that not all graphs generate. I've attached a screen shot of my terminal window. Any help would be great. I'm not terminal or R savvy so maybe its something simple!

Cheers.

screen shot 2018-11-26 at 15 22 05
roblanf commented 5 years ago

It looks like you might be missing some dependencies. My first suggestion would be to make sure you've got the latest version of all the dependencies, and try again.

I'm not totally sure of the best way to manage R dependencies with anaconda, but if you have a basic R install, the simplest way to get the dependencies is to fire up R with

R

and then just run this code to install/update the dependencies you need:

install.packages(c("data.table", 
                   "futile.logger",
                   "ggplot2",
                   "optparse",
                   "plyr",
                   "readr",
                   "reshape2",
                   "scales",
                   "viridis",
                   "yaml"))

After that, try again and let me know.

Rob

peflanag commented 5 years ago

Sorry for the delay in replying! I had checked that they were all up to date and ran your suggestion too. Unfortunately same error came back. Iv'e also tried running the command in R and it doesnt work

roblanf commented 5 years ago

As far as I can tell from googling the error message you are getting, this is an issue with your R installation not being able to find certain files. The easiest solution is probably to remove and reinstall R, making sure to get rid of the anaconda installation as well.

On Tue, 4 Dec 2018 at 00:45, peflanag notifications@github.com wrote:

Sorry for the delay in replying! I had checked that they were all up to date and ran your suggestion too. Unfortunately same error came back. Iv'e also tried running the command in R and it doesnt work

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/roblanf/minion_qc/issues/42#issuecomment-443714674, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pEyf8vW81a9u7UbSslE6gJRcffJskks5u1SrtgaJpZM4Y1D65 .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra

www.robertlanfear.com

peflanag commented 5 years ago

Ok perfect I’ll try that so! Cheers for the advice! This stuff isn’t really my background!

roblanf commented 5 years ago

thanks for persevering. It's all very easy until you hit something tricky like this, and then it can be a huge pain.

On Tue, 4 Dec 2018 at 08:37, peflanag notifications@github.com wrote:

Ok perfect I’ll try that so! Cheers for the advice! This stuff isn’t really my background!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/roblanf/minion_qc/issues/42#issuecomment-443879738, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pEyvE6eNK5Ux_M2gxXdUsQ4FoWoZNks5u1ZmmgaJpZM4Y1D65 .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra

www.robertlanfear.com

peflanag commented 5 years ago

Oh yea! I’ve hit many stumbles along the way with some of the bioinformatics for my Nanopore stuff. This is he new thing now! Lol

peflanag commented 5 years ago

I've tried uninstalling and reinstalling all again and it still just wont run for me! do i need to launch R in the terminal window first? I have tried that but the the Rscript command doesn't work

roblanf commented 5 years ago

You don't run it from within R. The error message you were getting is likely because you have changed something about your R installation since you set it up, and my guess from looking at it was that there may be some conflict between your base R installation and an anaconda installation. Did you remove both?

Beyond that, I'm afraid I'm not going to be able to be much help!

On Thu, 6 Dec 2018 at 02:47, peflanag notifications@github.com wrote:

I've tried uninstalling and reinstalling all again and it still just wont run for me! do i need to launch R in the terminal window first? I have tried that but the the Rscript command doesn't work

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/roblanf/minion_qc/issues/42#issuecomment-444532875, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pE6lUSnZ1E64XG0JBrhyH6nnJiCZYks5u1-qAgaJpZM4Y1D65 .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra

www.robertlanfear.com

peflanag commented 5 years ago

Cheers for the reply. As far as I know I removed it from both but will have a look again. TBH, the first few graphs it chucked out is probably enough for what I need anyway!

Cheers for all the help! I might try get one of the IT guys in one of the other departments to look at it!

roblanf commented 5 years ago

If you're able to send me your sequencing summary file, I'd be happy to double check that it's not a bug in the code itself. This is of course possible!

R

On Thu, 6 Dec 2018 at 06:51, peflanag notifications@github.com wrote:

Cheers for the reply. As far as I know I removed it from both but will have a look again. TBH, the first few graphs it chucked out is probably enough for what I need anyway!

Cheers for all the help! I might try get one of the IT guys in one of the other departments to look at it!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/roblanf/minion_qc/issues/42#issuecomment-444621765, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pExyIl2Qw0Uw7v3_4GIhDtjeWBtbLks5u2CPYgaJpZM4Y1D65 .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra

www.robertlanfear.com

peflanag commented 5 years ago

Sure! If you have an email address you can DM I’ll forward it on!

roblanf commented 5 years ago

http://robertlanfear.com/contact

On Thu, 6 Dec 2018 at 06:58, peflanag notifications@github.com wrote:

Sure! If you have an email address you can DM I’ll forward it on!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/roblanf/minion_qc/issues/42#issuecomment-444624459, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2pE3ShXxkf-D8Pc30gIKVYmtoewGJ6ks5u2CV8gaJpZM4Y1D65 .

-- Rob Lanfear Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra

www.robertlanfear.com

peflanag commented 5 years ago

Cheers! I’ve just sent it there! I reallly appreciate it!

roblanf commented 5 years ago

A note that this is now resolved - the solution was to update all of the relevant R packages using anaconda.