Comments (10)
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.
from drep.
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
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Related Issues (20)
- Inquiry on Optimal Workflow for Metagenomic Binning and Dereplication HOT 2
- Drep error with fastANI HOT 1
- Drep error with fastANI HOT 2
- Steps to implement checkm2 quality report to dRep HOT 8
- Halt: the pair-wise MASH clustering step HOT 5
- extra_weight_table flag HOT 3
- Issue with ANImf: 0% ANI despite similar nucleotide sequences HOT 11
- Is there any plan to add skani as ANI calculation method? HOT 2
- drep stoped during clustering HOT 9
- drep conda installation dependencies HOT 4
- dRep: Argument list too long HOT 3
- stuck on checkm HOT 1
- Question abunt the output of dRep HOT 1
- file exists but get os.path.isfile(genome), "{0} is not a file".format(genome) error HOT 10
- ValueError: mash isn't working- make sure its installed HOT 2
- checkM overwriting itself? HOT 4
- checkM failed, properly related HMM file HOT 1
- Contrast of text in dendograms HOT 1
- assert os.path.isfile(genome), "{0} is not a file".format(genome) AssertionError: ......./b1.fasta is not a file HOT 2
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