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SourceTracker2
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sourcetracker always got error even in sample data run #108

Open chloelulu opened 5 years ago

chloelulu commented 5 years ago

Hi, community,

I have been test run on code "nohup sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example7/ --jobs 5 --per_sink_feature_assignments". But it always gives me error in the attachment.

I installed st2 based on the manual, and upgrade it to the latest version "sourcetracker2, version 2.0.1-dev".

Looking forward to the suggestions.

Thanks.

error1.txt

wdwvt1 commented 5 years ago

Hi Chloe, Not sure what is happening, possibly an incompatible version of numpy. Also plausibly an error in the development version.

Can you activate the environment in which you use SourceTracker2, then give me the following things:

  1. Open bash/terminal and give me the output of "which python"

  2. Open a python terminal, and post the output of the following commands:

import numpy as np print(np.version, np.file)

Best, Will

On Mon, Jul 30, 2018, 3:16 PM Chloe notifications@github.com wrote:

Hi, community,

I have been test run on code "nohup sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example7/ --jobs 5 --per_sink_feature_assignments". But it always gives me error in the attachment.

I installed st2 based on the manual, and upgrade it to the latest version "sourcetracker2, version 2.0.1-dev".

Looking forward to the suggestions.

Thanks.

error1.txt https://github.com/biota/sourcetracker2/files/2243068/error1.txt

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chloelulu commented 5 years ago

Hi, @wdwvt1 ,

Thanks so much for the reply.

  1. which python /home/anaconda3/envs/st2/bin/python python --version Python 3.5.5 :: Anaconda, Inc.

  2. 1.14.5 /home/anaconda3/envs/st2/lib/python3.5/site-packages/numpy/init.py Appreaciate it!

Best. Chloe

wdwvt1 commented 5 years ago

hmm, i am running numpy 1.11.1 but I can't imagine there was a significant change with 1.14.5 that was backwards incompatible. seems like it is likely a bug that I have to track down.

I am currently not working on ST2 much, so I will try to hunt the bug this weekend.

In the meantime, does the stable release version work for you?

chloelulu commented 5 years ago

Hi, @wdwvt1, Thanks for tracking. Yes. The anaconda stable release version works for me. But it does not have the full outputs. Can I downgrade numpy to 1.11.1, and will this problem disappear?

Thanks so much. Sincerely. Chloe

wdwvt1 commented 5 years ago

I am not sure if it will - it might be worth a shot since you can do it easily with conda.

You can get the full output if you use the gibbs python API call (in _sourcetracker.py) rather than using the command line. There is a usage example that could guide you do what you want. The variable fas in that usage example is the full feature table output.

Obviously this is a sub-optimal solution, but if you need it to work now, you can do it this way.

chloelulu commented 5 years ago

I see. Thanks so much for the suggestions! I will try soon. Best.

Chloe