Comments (4)
EduEyras
commented on July 22, 2024
Hi Kirito,
Did you check whether you run out of disc space or RAM during your run?
I cc Favour, AJ, and Stefan, in case they have seen this before in a CHEUI
or similar analysis.
Best
E.
…On Mon, 19 Feb 2024 at 18:29, kir1to455 ***@***.***> wrote:
Hi,
When I use CHEUI model 1 to predict modifications in individual reads, I
saw "pickle data was truncated" in the log file.
image.png (view on web)
<https://github.com/comprna/CHEUI/assets/87375686/851df307-546e-4d43-a602-efc148c4e51c>
Has there been an error here or has its prediction been successful?
Best wishes,
Kirito
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pre-mRNA
commented on July 22, 2024
Hi,
Most likely, there was an issue with your prepreocssing which causes this issue when trying to run model 1.
What was the exit code for your preprocess command?
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kir1to455
commented on July 22, 2024
Hi,
When I running preprocessing step, if I use the C++version, the subsequent process will not make any errors, but when I use the Python version, the error "pickle data was truncated" will occur.
This may be the reason I changed the Python script, as I changed the "with open" to "with gzip.open".
Because my eventalign signal file is particularly large, I don't want to decompress it.
Anyway, when I decompressed the eventalign signal file and preprocessed it using C++version, everything ran normally.
Best wishes,
Kirito
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pre-mRNA
commented on July 22, 2024
Okay, thanks! In future, you can split your input fast5, and preprocess and run model 1 in smaller chunks.
The data would need to be merged prior to running model 2.
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Related Issues (20)
- multi-threading in running model 1 HOT 2
- Regarding output of the m6A probability and stoichiometry command HOT 3
- CHEUI model 2: prediction of stoichiometry and modification probability at transcriptomic sites : Executed with Error HOT 5
- Column header _position_ in site_level_prediction HOT 7
- Regarding CHEUI tool HOT 6
- Issue with the signal rejoining script and model 2 with the 4 dimensional issues HOT 3
- CHEUI preprocess C++ compiling issue
- Low m5C modification site number overlapped with m5c-atlas database HOT 1
- SQK-RNA004 HOT 2
- Regarding prediction of stoichiometry HOT 1
- Do CHEUI models work on Bacterial RNA modification detection? HOT 1
- Understanding of the read-level prediction file output HOT 1
- Do CHEUI models work on SARS-CoV-2 RNA modification detection? HOT 1
- 2 Questions about model 2 and python/c++ preprocess HOT 1
- Compatibility with the new direct RNA seq kit HOT 2
- CHEUI_preprocess_m5C.py give error HOT 17
- Problem with preprocessm6A HOT 2
- stoichiometry and probability columns in the solo output HOT 2
- Question about preprocessing HOT 3
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