I’ve been trying to use the --existing-alignment subcommand in augur align. With smaller previous alignments the command works and the build run smoothly (less than 100 total genomes), but when I use larger previous alignments I get the following error:
shell exited 1 when running: mafft --add results/aligned.fasta.to_align.fasta --keeplength --reorder --anysymbol --nomemsave --adjustdirection --thread 1 config/aligned.fasta.ref.fasta 1> results/aligned.fasta 2> results/aligned.fasta.log
Error during alignment
[Wed Jul 22 17:36:11 2020]
Error in rule align:
augur align --existing-alignment config/aligned.fasta --sequences results/filtered.fasta --reference-sequence config/reference.gb --output results/aligned.fasta --remove-reference --fill-gaps (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Removing output files of failed job align since they might be corrupted:
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message.
It’s worth noting that the build will run without error if I remove the ‘–existing-alignment’ line in the snakefile. Has anyone run into this issue before?