Comments (3)
Also, I guess I'm the (un)lucky one...
I tried the migrate-dbs-quickly
option
--migrate-dbs-quickly
If you chose this, anvi'o will migrate your databases
in place. It will be much faster (and arguably more
fun) than the safe option, but if something goes
wrong, you will lose data. During the first five years
of anvi'o development not a single user lost data
using our migration scripts as far as we know. But
there is always a first, and today might be your lucky
day. (default: False)
anvi-migrate CONTIGS.db --migrate-dbs-quickly -t 20
Config Error: Anvi'o has very bad news for you :( Your migration failed, and anvi'o has no
backups to restore your original database. The current database is likely in a
broken state, and you will unlkely going to be able to use it. So anvi'o renamed
it by adding a prefix '.broken' to its file name. We are very sorry for this
error (and anvi'o will certainly not put salt on the wound by reminding you that
you could have avoided it by using the `--migrate-dbs-safely` flag): "
Config Error: There is an issue but it is easy to resolve and
everything is fine! To continue, please first install the Python module `h5py`
by running `pip install h5py==2.8.0` in your anvi'o environment. The reason
why the standard anvi'o package does not include this module is both
complicated and really unimportant. Re-running the migration after `h5py` is
installed will make things go smootly.
from anvio.
Running things automatically is not the anvi'o way. We believe it is much better if the user explicitly runs each step so they are in full control. It is somewhat inconvenient for new users, and we are sorry for that. It pays off in the long run.
But you don't really need to be a new user of anvi'o. You can move on with your life without having to deal with it at all! :)
Delmont et al MAGs are already available as FASTA files in a standalone data package. What you need is listed in the document referred from the data availability section of the manuscript:
https://merenlab.org/data/tara-oceans-mags/
Here is one of the items at the very top of it:
doi:10.6084/m9.figshare.4902923: FASTA files for 957 non-redundant metagenome-assembled genomes.
from anvio.
Thanks for sending these over! I actually found these fasta files post hoc and should have updated my post. I didn't realize there were multiple figshare links until after.
I agree that it's good to be explicit and not overly automate too many things. I try to practice that philosophy as well and strive for modularity.
I've used anvio quite a bit in the past and I'm a big fan of the pangenome functionality.
from anvio.
Related Issues (20)
- [FEATURE REQUEST] Using a list of gene callers id with anvi-export-functions
- [BUG] anvi-split need `variability_splits` in profile.db HOT 11
- [BUG] Different results when running samples together vs separate HOT 3
- [BUG] pulp v2.8 made API changes that cause errors generating workflow DAG diagrams HOT 1
- [BUG] Can't create phylogenomic tree, as phylogenomic-tree.txt and default collection has different number of items.
- [BUG] Can't create phylogenomic tree, as phylogenomic-tree.txt and default collection has different number of items. HOT 3
- [BUG] Can't visualise the pangenome with average nucleotide identity HOT 1
- [BUG] anvi-setup-scgs-taxonomy STILL writes SCGs database to default location HOT 2
- [FEATURE REQUEST] add parameter --temp for temporary files path HOT 5
- [FEATURE REQUEST] Refactoring Anvio to be more eukaryote friendly/account for different genetic architectures
- [FEATURE REQUEST] Different gene caller option(s) for `anvi-gen-contigs-database` HOT 5
- [FEATURE REQUEST] See external/third-party dependencies on program documentation pages HOT 1
- [FEATURE REQUEST] Adding a program to annotate viral PHROGs via their HMMs
- [FEATURE REQUEST] A shortcut for importing layer orders that doesn't go through `anvi-import-misc-data`
- [FEATURE REQUEST] Environment variables for KEGG, Pfam, and other data directories so sys admins can set a global --xxxx-data-dir value
- [FEATURE REQUEST] Annotate which KOfams were added by our bitscore relaxation heuristic
- [FEATURE REQUEST] A conda package for anvi'o with a minimal installation option
- [BUG] `--prodigal-single-mode` breaks metagenomic workflow HOT 5
- [BUG] anvio-cluster-contigs fails with Generate input data
- [BUG] anvi-meta-pan-genome does not allow me to use gene calls not from prodigal HOT 10
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