-
Notifications
You must be signed in to change notification settings - Fork 7
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Ancillary files not found when trying to remove #1
Comments
Hi Natasha, Thanks for letting me know about this and for providing a detailed issue. Basically, these errors are of no concern. It just has to do with the fact that some of my coding, while it all works as far as I can tell, is a bit ugly. There are a range of ancillary files that could be generated by Cenote-Taker2, and sometimes they are not present at the end. That said, I've update the code to eliminate this message. Also, I've done a couple debugging updates since 3/26/2020, so please 'git pull' the repo. Going through your log file, I did see that the IRF (inverted repeat finder) program isn't found.
IRF was a bit trickier to include in the install as it's not available on Anaconda and is meant for 32 bit systems. A google search supports the idea that this type of error arises from 64 bit/32 bit incompatibility. You might try to resolve this, but this program is not strictly necessary for the rest of the code. You just won't know which contigs are flanked by inverted terminal repeats. I hope this was at least a little bit helpful and please let me know if you run into any other issues. Best, Mike |
Hi @mtisza1 , Thank you so much for your prompt reply and fixes, I highly appreciate it! When we install tools on our HPC cluster, we try to package them in conda packages if that is feasible. Regarding Using the mentioned conda package for I am sorry for the long reply, and I hope what I wrote makes sense. Thank you, |
Hey Natasha, This is really interesting! I'm a bit new to the whole packaging/making images thing, but I will try to keep this conda package updated if possible. However, I tried to install your package
I noticed a few differences from my .yaml file including yours:
Also I didn't see the channels that I listed in my .yaml in yours. I don't know if I'm doing something wrong, but I wanted to make you aware. Let me know if you have ideas. Thanks! |
Hi @mtisza1 , I am sorry, I forgot to mention that our HCC conda packages depend on packages from When we create conda packages for our channel, we try to follow the infrastructure of Regarding the difference in the packages you listed:
As you can see, the idea with the dependencies in the recipe is to not use https://github.com/mtisza1/Cenote-Taker2/blob/master/install_scripts/cenote_install1.sh anymore. With conda recipes, it is preferable to have a conda package for each dependency. So, all the packages you are downloading and installing in the install script and now conda packages that can just be used. I hope this makes sense. Thank you, |
OK I've finally gotten around to trying this. It seems to work! I'll make a note on the repo about this option. I appreciate that you took the time to explain this to me, and I think this is a valuable addition. Best regards, Mike P.S. I'm closing this issue. |
Hi Natasha, It's been a couple years and there have been many updates to You are probably quite busy, but I was wondering if you'd be able to help me update the bioconda package. Overall, the install is much easier than it was 2 years ago. Best, Mike |
Hi,
I am trying to install "cenote-taker2" on our HPC system for a local research group.
I downloaded all databases and dependencies using the commit from 03/26/2020.
I did a test run you have provided in the Wiki page using the command:
Most of the programs finished ok I think, but I am getting the following error at the end:
These files indeed do not exist in the output directory, thus the message.
I was wondering if this type of error message is familiar to you, and whether you have some suggestions on how to fix it.
I am using the "testcontigs_DNA_ct2.fasta" file you have provided, and a dummy "template.sbt" file.
Please find the complete log here, cenote-taker2.log
I am looking forward to hearing from you, and if you need any additional information, please let me know.
Thank you,
Natasha
The text was updated successfully, but these errors were encountered: