Yes, I installed Nextstain Conda environment. I ran the tutorial from nextstrain in my system with the example data of SARs-CoV-2 and I was able to make the .JSON file. Then I created my own data from GISAID following the nextstarin data preparation guidelines. I believe once I prepare TSV and FASTA file, I just need to change the build.yaml and config.yaml file. Then I run the following command after activating the nextstain in my system.
nextstrain build . --cores 4 --use-conda
Please find the error below:
If you notice, the error said “MissingOutputException in line 99 of /home/sksunny/ncov/workflow/snakemake_rules/main_workflow.smk:”
I do not know how to increase the latency time as it suggested to increase the latency time:
“This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait.”