Comments (1)
Hi @AbeerMM
thanks for your bug report.
The SHAPE integration is done via the API of the ViennaRNA package. Eventually, all parameters are forwarded to its respective functions and used to guide the accessibility computation (done in the fillByRNAplfold()
calls within the verbose output).
It seems, these run fine, but obviously, something went wrong. I would guess, the Vienna lib returns some insane values, which subsequently crash the predict()
call.
@RaumZeit any ideas from the ViennaRNA lib man?
I will have to have a look what in detail goes wrong, but my guess is artificial unpaired probabilities outside of the range [0,1]..
Respective checks are only enabled in debug mode. So if you are curious, you could recompile IntaRNA using --enable-debug
and rerun. It will hopefully fail with some more informative error message.
Will try to find some time soon to look it up myself too.
Best,
Martin
from intarna.
Related Issues (20)
- Multiple output formats per one run HOT 1
- outnolp bug
- configure: check for boost -mt libs
- bug with predefined single-bp seed HOT 2
- Etotal CSV output with SHAPE data
- Reg: Prediction of miRNAs targets using 3' UTRs HOT 1
- intaRNA API in python HOT 2
- IntaRNAhelix parameters HOT 2
- Vienna package not found HOT 4
- scalebar issuses HOT 2
- Source compile error HOT 4
- Make sure program works HOT 3
- Install error: /usr/bin/ld: -f may not be used without -shared HOT 9
- Attaching IntaRNA docker container to VS Code HOT 2
- Exception related to pf_scale HOT 5
- [R|python] CSV input wrapper call script
- --outOverlap=N might be buggy..
- enable sequence subsetting when accessibilities are read from file
- [MS WSL] file output for longer target lists crashes
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from intarna.