Hello. I have been working on setting up a functional nextstrain pipeline for the last few weeks at case western reserve university in Cleveland. I was able to get the example covid build to work just fine, but when I try to run the same build with the GISAID metadata and sequences, I continue to get the same error. The build will make it all the way up until the “augur tree” command and then stagnate there until it returns this error message:
I have been troubleshooting this error for quite awhile now through the nextstrain tools, but can’t seem to get it to bypass this error. I’m thinking it might have something to do with IQ tree or maybe just the massive amount of data. I’d love to see if anyone has any input on what might be causing this problem. Thanks!