Elaboration of motif analysis

[frankligy]

Hi,

Firstly thanks so much for developing this wonderful tool!

I am trying to figure out how to get the step3: motif analysis running. I've already managed to get step1 and step2 running using the example data, so I've already had model.pkl file generated.

I downloaded WebLogo and untar it, put the folder under /iDeepE, where model.pkl files are stored. Then I downloaded MEME suite, I followed the configuration step including ./configure, make, make test, make install. The MEME folder is also under /iDeepE

After finishing all aforementioned step, I started to run step3, the command that shown in README, but I am not able to generate any files in /motifs folder, but only a filters_meme.txt file, content is as below:

MEME version 4

ALPHABET= ACGU

Background letter frequencies: A 0.2502 C 0.2243 G 0.2430 U 0.2824

Would you mind providing me some instructions on how to get motif analysis running? Please let me know if you need any other error info from me. Much appreiciated!

Frank

[xypan1232]

Do you have any log file and report any bug?

you first need have trained model.pkl in local directory. python ideepe.py --posi=GraphProt_CLIP_sequences/ALKBH5_Baltz2012.train.positives.fa --nega=GraphProt_CLIP_sequences/ALKBH5_Baltz2012.train.negatives.fa --model_type=CNN --model_file=model.pkl --motif=True --motif_dir=motifs

[frankligy]

Hi,

Thank you for your reply, I had model.pkl.global and model.pkl.local file avaiable before I ran step3. I attached my stderr and stdout file for your reference. log.txt

[xypan1232]

no display name and no $DISPLAY environment variable， you cannot plot using matplotlib in your server, you need add below: import matplotlib matplotlib.use('Agg')

https://stackoverflow.com/questions/37604289/tkinter-tclerror-no-display-name-and-no-display-environment-variable

[frankligy]

Thanks a lot, the issue solved!