00b_split_by_type.sh - grepping issue

[bensutherland]

00b_split_by_type.sh - grepping issue

[bensutherland]

Hello @midwesternmouse ,
Are you able to please provide an example file that causes the error (is it test_072022/identified_E-AFR090512_S75_L001_R1 ?), the version of any relevant software being applied (obitools, other?) and the operating system being used?
Currently this pipeline hasn't been maintained/ updated for a little while, and so it is possible that your question may be best directed towards the obitools developers, but I will help if I can!

Ben

[midwesternmouse]

Hi @bensutherland !

I'm currently using The OBITools 3 - Version 3.0.1b17 on MacOS 10.15.7.

I think the file that's used in the command line causing the error (test_072022/identified_E-Agr090512_S75_L001_R1) is a view within the obitools3 environment. I'm not fully sure what file type it is. Although checking now, I see it, too, has 0 entries -- could explain why 0 entries were grepped: identified_E-BOY210712_S47_L001_R1: Date created: Thu Jun 30 18:42:36 2022 ; Line count: 0.

This brings up a whole new issue of after running the code
for sample in $(cat samples_R1)
do
echo "On sample: $sample"
obi ngsfilter -t ngsfile -u test_072022/unidentified_${sample} test_072022/${sample} test_072022/identified_${sample}
done
I am left with files w/ Line count: 0. Is this something you have encountered before with ngsfilter?

I apologize, there is now a completely different problem at hand!

[midwesternmouse]

Hi, just following up with this issue of Line count: 0 after assigning ngsfilter tags. I've modified my code so my imported files are kept as .fastq's, but I still have all my assigned ngsfilter files coming up as Line count:0.

[bensutherland]

Hi @midwesternmouse ,
Unfortunately, I am not able to help with this issue. This pipeline was built around an earlier version of OBITools (I believe it was OBITools 1, but I am confirming this now). It is not currently being actively maintained or developed with new versions of OBITools.

I did try to follow instructions here:
https://git.metabarcoding.org/obitools/obitools3/-/wikis/Installing-the-OBITools3
...to see if I could recover the error observed in your code with the demo data, but I was not successful even at installing the new OBITools.

Therefore, in this case, this issue would be best directed towards the developers of OBITools 3, who I believe will be much better suited to help you in this error or potential bug. My apologies that I cannot be of help.

I am going to add a flag to the pipeline README to indicate that it is only designed to work with OBITools 1, as well as ensure there is clear indication that it is not being actively maintained currently.

I'll leave the thread open for a bit just to be sure I'm not missing anything. I wish you good luck with your project!

Ben

[bensutherland]

Hi @midwesternmouse , I can confirm now that this pipeline was fully designed using OBITools v.1.2.11, and I suspect it would require some significant edits to make it functional with new OBITools.
Ben

[midwesternmouse]

Hi @bensutherland, that makes a lot of sense, thank you for checking which pipeline this used. I have been trying to contact the developers of Obitools 3 & will continue my efforts there! Thank you for being so responsive, especially i/r/t old code!
I do have a quick last question -- if this is old code, and you no longer use Obitools, what program / coding do you use now (if you still do metabarcoding)? Are there other programs you would suggest aside from Obitools?

[bensutherland]

Hi @midwesternmouse , That is a good plan, hopefully the developers are able to solve the issue. I am not actively doing metabarcoding at the moment, but if I were to start a new project, I would probably adapt the pipeline to OBITools3, try it with OBITools v.1, or there is a pipeline here developed by a very talented colleague of mine that I would give a try as well:
https://github.com/enormandeau/barque
I'll close this issue now, but please feel free to contact me by email if there is anything else I can help with. My email can be found here: http://benjgsutherland.com

Ben