problem with scanpy: The tool "Normalization with scanpy" seems not work!

#1

hallo, galaxy users,

thanks for fixing the problem I showed here last time. Now I am continuing to follow the training "Clustering 3K PBMCs " by Bérénice Batut et al. I was stopped this time at the step “normalize with Scanpy”. Every time I got the message “An error occurred with this dataset:
This job was resubmitted to the queue because it encountered a tool detected error condition on its compute resource. File “/data/dnb03/galaxy_db/job_working_directory/015/987/15987443/configs/tmp943xjhku”, line 18
layers[str(x.strip()) for x in str(A.” I tried different versions available in the galaxy, and it came out similar error texts.

I checked the files produced before this step and all of my operations again and again, and have no idea what was wrong with the tool.

#2

Hello, which server are you using?

use galaxy.eu, or usegalaxy.org?

#3

Dear Mr. Neiman,

Thanks so much for your quick feedback. I am using Galaxy europe for carrying out this job. But I have also an account at Galaxy usa.

Best

Hongyu Liu

#4

Hello,

Can you share your history with me – I am unable to reproduce this problem.
My email for sharing is: mtekman89@gmail.com

#5

hallo, dear Dr. mtekmann, thank you very much for your help. you can try the linke here under to get acess to my history. I tried at first to follow the tutorial to do the data processing with Star solo and RaceldD. Since the down streaming analysis with RacelD did not work, I uploaded the datasets from the tutorial “Clustering 3K PBMC data with scanpy” and learn scanpy step by step.

Galaxy | Europe (usegalaxy.eu)

thanks again.
Best

Hongyu Liu

#6

here the link to my history: https://usegalaxy.eu/u/hliu96501/h/sc-rna-10x-data-tutorial-star-and-scanpy
Best

Hongyu LIu

#7

Hello again,

Can you repeat the step, but this time remove the keyword All from the “List of layers to normalize”. It should still work without it

#8

thanks so much! It works after I deleted “All”.
Best
Hongyu

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