-
Notifications
You must be signed in to change notification settings - Fork 37
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Test_backend folder missing for test_suite.py #13
Comments
I see this is similar to #11 . I'll close and wait to see if the test_suite.py gets fixed in the future. |
Hi Jeff, Sorry about this inconvenience. All that's needed is a blank folder in the tests folder called test_backend. You can either make it yourself, or download the new version (1.1.2) which will include it. Best, |
Thanks, that worked to get it started. I did get an error, however:
It isn't clear to me at which calculation this failed, but it was Let me know if I should open this up in a new issue. Jeff |
Hmm. What does the following command show? It could be that one of the dependencies is not working
$ dRep bonus test --check_dependencies
… On Aug 25, 2017, at 3:44 PM, Jeff Kimbrel ***@***.***> wrote:
Thanks, that worked to get it started. I did get an error, however:
Traceback (most recent call last):
File "test_suite.py", line 633, in <module>
test_short()
File "test_suite.py", line 617, in test_short
cluster_test()
File "test_suite.py", line 581, in cluster_test
verifyCluster.run()
File "test_suite.py", line 328, in run
self.skipsecondary_test()
File "test_suite.py", line 367, in skipsecondary_test
assert compare_dfs(db1, db2), "{0} is not the same!".format('Mdb')
AssertionError: Mdb is not the same!
It isn't clear to me at which calculation this failed, but it was step4 after functional test 1 passed.
Let me know if I should open this up in a new issue.
Jeff
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub <#13 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AMzWTT7Ic3h2vxOH9YO2mcOJnfatGQuZks5sb05ggaJpZM4PB_wb>.
|
Yep, it looks like there are dependencies missing, but the missing ones are listed as optional. I suppose that the test python script uses these dependencies?
|
Hmm- yes some of those dependencies are used by the test suite, but with the ones you have working I wouldn't really expect it to crash there. Is the program working when you use it on your own data? |
It seems like I keep running into problems with checkM not installed. I am trying to run all of this on my laptop, and therefore don't have checkM because it requires >16gb of memory. I actually do have it installed, but don't have all of the data files downloaded. Running on my own files...
When I use the Also, I manage python environments using Anaconda rather than Thanks for your help. |
So a problem is that the choose module does require checkm. This is because
that's how it decides which bin is the "best" from each cluster.
What is your goal with dRep? If your goal is to figure out which genomes
are similar, I would suggest using the "compare_wf" option. If your goal is
to generate a representative genome list, I would be happy to work with you
to try and figure out a way to get checkM running.
…-Matt
On Sep 7, 2017, at 1:41 PM, Jeff Kimbrel <notifications@github.com> wrote:
It seems like I keep running into problems with checkM not installed. I am
trying to run all of this on my laptop, and therefore don't have checkM
because it requires >16gb of memory. I actually do have it installed, but
don't have all of the data files downloaded.
$ dRep dereplicate_wf dRep_test -g bins/*.fasta --skipCheckM
When I use the --skipCheckM flag I can get through the Filtering and
Clustering steps, but it fails on the Choose step after it also attempts to
run checkM (disregarding the flag).
Also, I manage python environments using Anaconda rather than pyenv. My
default python is 3.4.5. I wonder if that is also messing something up... I
think checkM is the only thing requiring python 2.X, correct?
Thanks for your help.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
<#13 (comment)>, or mute
the thread
<https://github.com/notifications/unsubscribe-auth/AMzWTf4ezjcxQeHHcFoLrFle3Xvjusgjks5sgFT3gaJpZM4PB_wb>
.
|
I have figured out how to run checkM on NERSC... is it possible to use an "external" checkM results dataset with dRep? My goals are pretty much what the advertised purpose is. I have tons of metagenomes that would be too computationally expensive to combine and co-assemble. So I want to take bins from either single metagenomes, or co-assembled replicates, and "merge" the bins. |
Yes- there is a way to use "external" checkM results. When using the dereplicate_wf (probably what you want), there's an option They need to be in the --table_table format, though. The checkM command to generate this is:
An example of how it should look is attached. Finally, make sure that for the "Bid Id" column, you have the name of the genome WITH the file extension, and WITHOUT the path to the genome (as is the case in the example sheet provided). Best, |
I'm checking to see if dRep installed correctly, so I am running the
test_suite.py
script from thetests
folder. I get an error:Indeed, this isn't in the
tests
folder. Is there a work around to get the test scripts to work?Thanks.
The text was updated successfully, but these errors were encountered: