New User-Failure to run dgenome, any help appreciated!

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Daniel Fucich

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Feb 19, 2020, 10:32:07 PM2/19/20

to DuctApe

Hello and thank you in advance DuctApe Users!

I am a graduate student attempting to use dgenome to compare multiple genomes (I do not need the phenomic features). I am not sure if this is the correct place for troubleshooting, but please see my struggle below:

I have an issue upon trying to use dgenome in the DuctApe software.

When attempting to use dgenome to add my KEGG files myorgx.tab etc...

I receive an error message that amounts to:

Traceback (most recent call last):
File "../dgenome", line 477, in <module>
ret = options.func(options, wdir, project)
File "../dgenome", line 178, in daddKo
from ductape.genome.map2KO import OnlineSearch
File "/data1/dfucich/DuctApe-latest/ductape/genome/map2KO.py", line 10, in <module>
from ductape.common.commonmultiprocess import CommonMultiProcess
File "/data1/dfucich/DuctApe-latest/ductape/common/commonmultiprocess.py", line 9, in <module>
from ductape.common.commonthread import CommonThread
File "/data1/dfucich/DuctApe-latest/ductape/common/commonthread.py", line 9, in <module>
import Queue
ModuleNotFoundError: No module named 'Queue'

From what I can tell these are python errors and I am not sure how to fix them.

When running the

bash test.sh

I receive the same message followed by of course:

############
dape init
Test failed!
############

Any help or insight is appreciated! Thank you for your patience, and apologies about the lengthy email.

Very Respectfully,

Dan

Marco Galardini

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Feb 20, 2020, 4:14:53 PM2/20/20

to Daniel Fucich, DuctApe

Hi Daniel,

DuctApe only works with python2, and I suspect you are using python3. If you use pip you can use the following command to install ductape under python2:

python2 -m pip install ductape

Hope this helps,

Marco

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