Test_backend folder missing for test_suite.py about drep HOT 10 CLOSED

I see this is similar to #11 . I'll close and wait to see if the test_suite.py gets fixed in the future.

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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,
-Matt

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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

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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?

$ dRep bonus test --check_dependencies
Loading work directory
Checking dependencies
mash.................................... all good        (location = /usr/local/bin/mash)
nucmer.................................. all good        (location = .../scripts/MUMmer3.23/nucmer)
checkm.................................. !!! ERROR !!!   (location = None)
ANIcalculator........................... !!! ERROR !!!   (location = None)
prodigal................................ all good        (location = .../scripts/prodigal)
centrifuge.............................. !!! ERROR !!!

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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?

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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...

$ 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.

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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.

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Yes- there is a way to use "external" checkM results.

When using the dereplicate_wf (probably what you want), there's an option --Chdb which can be used to provide external checkM results.

They need to be in the --table_table format, though. The checkM command to generate this is:

checkm qa --tab_table -o 2

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,
-Matt

Chdb.csv.zip

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