Comments (2)
Hi @paolabc,
thanks for your question and detailed check.
Eventually, given your command line arguments, I guess you are using the outdated original IntaRNA version 1 !!!!
You get the recent version either via conda or via manual installation from Github, see here
You can check what version you are using on the command line via
IntaRNA --version
If this is not working, you are definitely using the outdated old version...
The webserver is not running the most recent version but something close, i.e.
IntaRNA version 3.3.1 linking Vienna RNA package 2.5.0
Here the command excuted by the webserver:
IntaRNA --query=input_query.fa --seedBP=7 --out=pMinE:pairMinE.csv --out=qMinE:QueryMinE.csv --target=input_target.fa --seedMaxE=0 --outOverlap=Q --tAccW=150 --outMaxE=0 --outDeltaE=100 --seedNoGUend --mode=H --qAccW=150 --outNumber=5 --outBestSeedOnly --outMode=C --temperature=37.0 --outNoGUend --outCsvSort=E --energyVRNA=Turner04 --qAccL=100 --outCsvCols=id1,start1,end1,seedStart1,seedEnd1,ED1,id2,start2,end2,seedStart2,seedEnd2,ED2,E,E_hybrid,E_norm,subseqDP,hybridDP,seq1,seq2 --outNoLP --tIdxPos0=1 --out=tMinE:TargetMinE.csv --seedMaxUP=0 --qIdxPos0=1 --seedMinPu=0 --tAccL=100 --out=predictions.sorted.csv
Hope that helps! Let me know if you still face issues!
Best,
Martin
from intarna.
Hi
Thank you for your answer. Indeed, I installed the first from conda the first time. And yes, I got the same result with this parameters.
Thank you!
from intarna.
Related Issues (20)
- 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
- Segmentation fault (core dumped) HOT 1
- 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
- IntaRNA --version does not reflect the installed conda package version? HOT 4
- IntaRNAsTar Exception raised HOT 2
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from intarna.