Conda command line and web based do not show the same output result

[paolabc]

Hi Everyone!

I am performing the analysis using the command line version. I double-checked the result on the web, and I noticed that the output is quite different using the same input. I also adjust parameters to make both sources comparable. May I ask for your help to understand it?

As output, the command line returned 5 results , but the web only returned 2 results. Also, the results do not match. Am I doing something wrong in parameters adjustments?

Command line IntaRNA -t $file_path -m $other_file_path -s 5 -p 7 -w 150 -L 100 -o

Web

[martin-raden]

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Eventually, given your command line arguments, I guess you are using the outdated original IntaRNA version 1 !!!!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If this is not working, you are definitely using the outdated old version...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

[paolabc]

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!