When running the pipeline my run failed after about two minutes at rule align. The error message in logs/align_local-data.txt is “Error: when running the pipeline: Fasta stream: stream reached an invalid state which should not be reached”. I am using the fasta file downloaded from GISAID under the Genomic Epi download section.
Is this an indication that the fasta file is corrupted?
what version of augur and the workflow are you using. The error you are getting is from nextalign, but the problem might be caused by an upstream script (sanitize_sequences.py) that might fail when you are not using the latest augur version. this problem showed up in one of our workflows.
I am using augur version 11.1.2, and I pulled latest version of the ncov repo yesterday.
yep. you need augur 12.*
Thanks! Will update. Appreciate your help.
hi @rneher I’m using augur v 12.0 and I’m getting the error. Any leads on what you might have done when you saw the error other than upgrade augur?
Thank you
I sorted the issue by upgrading my local install to v7 that was released on May 28. Something in there fixed the issue.