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michelleapaz / T3E

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The third step seems not performed #2

Closed ch8316f5eyu closed 1 year ago

ch8316f5eyu commented 1 year ago

Hi, thanks the tool!

It seems the third step is not performed.

This is the end of of the log: `# Counting for TE families/subfamilies... Alu 1251.0222224411 AluJb 186720.523919374 AluJo 99942.0269172959 Completed in 2 minute(s) and 3 second(s) Analysis Dox5_Input... 17322803 reads

Intersecting BED file and REPEATS...

chr1 11505 11675 L1MC5a|| chr1 11678 11780 MER5B|chr1 11685 11824 A00783:990:H5JFMDSX3:2:2169:5321:9455;chr1 11685 11824 A00783:990:H5JFMDSX3:2:2169:5321:9455;chr1 11716 11855 A00783:990:H5JFMDSX3:2:1534:27995:29183;chr1 11739 11878 A00783:990:H5JFMDSX3:2:1534:27995:29183|95;95;64;41 chr1 15265 15355 MIR3|chr1 15260 15399 A00783:990:H5JFMDSX3:2:2342:26205:20729;chr1 15299 15438 A00783:990:H5JFMDSX3:2:2538:14660:25128;chr1 15328 15467 A00783:990:H5JFMDSX3:2:2342:26205:20729|90;56;27

Counting for TE families/subfamilies...

Alu 1379.42784693047 AluJb 162581.087485273 AluJo 90989.7022871328 Completed in 3 minute(s) and 27 second(s) `

Nothing else. What's wrong?

Thanks!

michelleapaz commented 1 year ago

Hello, Weiyu.

Thanks for your message!

After this reported preprocessing step, another log (specific for the sample you are running) should be created. Now two other python scripts should be running (probabilities.py followed by t3e.py).

Please, check if the actual log file is created and if the python scripts are running. Also, check if you have provided enough memory.

Best,

Michelle

ch8316f5eyu commented 1 year ago

Hi, Michelle,

It's very weird, I acknowledged it.

But I encountered it very time, then I have to delete the code ahead to run it again.

And my memory is 2T, I think it's enough.

Thanks.

michelleapaz commented 1 year ago

Hello,

Definitely, 2TB RAM is enough!

At this stage you should have:

The immediate next step is the calculation of the input-based background probabilities. The "probability" files should be created in the input control subfolder of the results folder.

Let me know if you could find these output files.

I'd suggest you running the test set provided or only one iteration of your own dataset to test it. So I can better help you!

Thank you.

Michelle