NOTE: Instead of opening issues in github, please consider creating a new topic in https://forum.biobakery.org/. Please read for more details.

[sagun98]

The bioBakery support forum provides software support and tutorials for methods for microbial community profiling developed by the Huttenhower lab. Please consider creating a new topic in the bioBakery support forum before opening issues in Github.

[cjfields]

Hi @sagun98 , a number of issues have been reported in the forums but have not been addressed or replied to. For example, all three of the following have similar issues. We are also seeing this problem. Should we add a ticket here or hold out hope that someone will reply there?

https://forum.biobakery.org/t/paired-end-data-results-in-unpaired-output/928/12
https://forum.biobakery.org/t/paired-end-data-showing-error-on-bypass-trim-option/2759/7
https://forum.biobakery.org/t/kneaddata-a-non-very-explicit-error-message/3334/2

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

[cjfields]

@sagun98 it also looks like the GH actions shut this stub ticket down even though I just commented on it, apologies!

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

[ljmciver]

Hi @sagun98 , a number of issues have been reported in the forums but have not been addressed or replied to. For example, all three of the following have similar issues. We are also seeing this problem. Should we add a ticket here or hold out hope that someone will reply there?

https://forum.biobakery.org/t/paired-end-data-results-in-unpaired-output/928/12 https://forum.biobakery.org/t/paired-end-data-showing-error-on-bypass-trim-option/2759/7 https://forum.biobakery.org/t/kneaddata-a-non-very-explicit-error-message/3334/2

Hi @cjfields Thank you for the heads up. I think I got a response to all of them. Please let me know if we are missing any in the future. Feel free to DM me in discourse.

Sorry kneaddata is not more clear. It actually does not matter what the file names are but the formatting of the read identifiers for older versions. The newer version lets the user specify the R1 and R2 which I think should make it clearer. Feel free to reach out with any additional questions/issues.

Thanks!
Lauren

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.