Stefan

It was a memory issue at first, but I think I got around that issue (I probably shouldn't have mentioned it, sorry for the confusion) To clarify, `funannotate predict` is...

Just tried all of your suggestions with no luck. A couple of questions to try to get around this issue: 1. what are the expected outputs when tbl2asn is done?...

Ah, then it sounds like tbl2asn is working fine because those files were generated...

Annoyingly works like a charm: ``` (funannotate) [thatguy0@n6459 fun_predict]$ tbl2asn -t /u/project/kruglyak/thatguy0/conda/envs/funannotate/lib/python3.7/site-packages/funannotate/config/test.sbt \ > -M n -V b -c f -a r10u -p predict_misc/tbl2asn [tbl2asn] Flatfile genome [tbl2asn] Validating genome...

I don't load any modules from the cluster apart from glibc for this particular step. Agreed, would be awesome if it worked in my hands ;_; I am looking at...

Awesome, I will def test it out. The test run you suggested failed in my hands at the tbl2asn, though with some additional messages: ``` [May 25 02:21 PM]: ERROR:...

Hello @sangtaekim, From what I can tell, I just used the standard calling approach for the first pass calling. What does "--callContinuousVf III" do? Here is the workflow Call variants...

Great, that's what I figured. From my simple simulations (take a reference genome, insert random sequences of defined ength and position, align reference fastq, call insertions) Manta did the best...

I just ran into this issue and am trying to re-run on a single thread. I'm hopeful given the above thread!

Just following up - changing `smoove genotype -p 1` solved the discrepancy in number of sites per sample. Not sure that I'd be able to reproduce the problem, but can...