Q2-fragment-insertion runtime

@Stefan I used q2-fragment-insertion as an alternative for MAFFT to acquire the Phylogeny[Rooted]. I used the following commands:
qiime fragment-insertion sepp --i-representative-sequences …/rep-seqs-dn-99.qza --o-tree insertion-tree.qza --o-placements insertion-placements.qza
This job has been running for a week and still running. I am wondering how long does it take to finish this step? I am running this command in jetstream where I have sufficient resources. Can I run this job in multiple threads? Any suggestions to sort out this issue will be appreciated.
Thank you
Best Regards
Bishnu Adhikari

Just a note, I think @Stefan is in the middle of moving so he might not see this for a while. We’ll keep your topic [queued] so that no-one forgets about it.

Based on this table it does seem like your job is taking a bit longer than expected. How many features do you have?

Hi Bishnu,
glad to see you using my plugin. Have you seen the section about “Expected Runtimes” on my github page: https://github.com/biocore/q2-fragment-insertion?
Try the command qiime fragment-insertion sepp --help and you will find the parameter --p-threads to specify the number of cores to be used.
Can you give me some ballpark numbers for the fragment length and number of sequences in your input rep-seqs-dn-99.qza or even better send me your input to give me the chance to look at it? sjanssen@ucsd.edu


Hi Stefan,

Thank you very much for your quick response and suggestions. I am giving a try with an increase in threads to 24. I will see what happens and get back to you with more details.

Thank you

Bishnu Adhikari

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