Open d4straub opened 1 year ago
I agree! Re-running Trycycler reconcile over and over can be time consuming, especially for the cluster of chromosomal contigs (larger sequences take longer to run).
I hope to re-engineer Trycycler's high-friction parts (like this) at some point. So I'll keep this issue open as an enhancement request until then.
Ryan
I've just pushed (52b8c1f) a small improvement to this issue: trycycler reconcile
now attempts to circularise all the contigs before it quits with an error message. So if 3 contigs can't be circularised, it will tell you about all three at once.
I'll leave this issue open because trycycler reconcile
is still not as efficient as it could be.
Ryan
Hi there,
first of all, trycycler seems a great tool, thanks for this! Disclaimer: I am using it the first time.
What I really found extremely annoying is that
trycycler reconsile
stops after the first contig doesnt meet requirements.For example, I use
trycycler reconsile
and it stops complainingThat is alright, I remove it and try again, however, same problem with the second contig. I get skeptic, but try a third round after removing the second contig. Third contig also cannot be circularized, again an error. I realize that this genome part might be linear (a qucik literature confirms that this might be true), re-add all contigs, add the appropriate command (--linear), run it a forth time and it passes. However:
Alright, so I remove those bad contigs, and restart it 5th time, but
Again, I remove those contigs and restart 6th time.
Essentially, I am just wondering whether it wouldn't be more effective to have
trycycler reconsile
continue after it encounters the first "error" but stops with all those error reports in one run. I could have seen immediately that none of the contigs are circular and used --linear instead of running it 3 times. I could have immediately removed contigs with bad pairwise identities and pairwise indels.Maybe circularisation is required to calculate indentities & indels and it has to stop when circularisation is failing, but at least it could report all contigs that fail to circularize? And maybe pairwise identities and pairwise indels could be another block that fails in one go? That would have left me with 3 instead of 6 runs, much better imho.
Best, Daniel