Rf -fold does not work with RNA structure

[Frappadoo]

Hi Danny Incarnato,

I have set up RNAframework on my computer and was testing the SHAPE-MaP workflow on here https://rnaframework-docs.readthedocs.io/en/latest/cases/ The ViennaRNA method works amazingly well, however whenere I try to use the RNAstructure method, I get the following error.

rf-fold -m 2 -g -md 500 -w -pk -km 2 -ko 100 -pw 1600 -po 375 -wt 300 -fw 3000 -fo 300 HIV_norm/ -ow

[+] Checking method's requirements... [+] Making output directory tree... [+] Importing XML file(s) [1 imported] [+] Folding RNA structures [Last: none] Thread 1 terminated abnormally: Can't use string (" 2900 ENERGY = -1196.6 HIV_0-2"...) as an ARRAY ref while "strict refs" in use at /Users/francescappadoo/Desktop/RNAFramework/rf-fold line 858.

[+] Folding statistics:

[] Folded transcripts: 0 [] Discarded transcripts: 1 total 0 XML parsing failed 0 constraint file generation failed 0 FASTA file generation failed 0 folding failed 1 I/O error 0 pseudoknotted folding failed

[+] All done.

Do you have any suggestions for this?

Thank you for your help,

Fran

[dincarnato]

Hi Fran,

Thanks for reporting. I will look into this and get back to you. I suspect this might be a bug introduced in the last release.

Danny

[dincarnato]

Did you git pull the very last version?

[Frappadoo]

Hi Danny,

Yes it's version 2.8.3. I ran it with the same conditions that were in the link I previously sent

[dincarnato]

Fixed. Please issue a git pull and try!

[Frappadoo]

Hi,

I have git pulled it and tried it but d I am getting this error still

rf-fold -m 2 -g -md 500 -w -pk -km 2 -ko 100 -pw 1600 -po 375 -wt 300 -fw 3000 -fo 300 HIV_norm/ -ow

[+] Checking method's requirements... [+] Making output directory tree... [+] Importing XML file(s) [1 imported] [+] Folding RNA structures [Last: none]Thread 1 terminated abnormally: Can't use string (" 2900 ENERGY = -1156.4 HIV_0-2"...) as an ARRAY ref while "strict refs" in use at /Users/francescappadoo/Desktop/RNAFramework/rf-fold line 858.

[+] Folding statistics:

[] Folded transcripts: 0 [] Discarded transcripts: 1 total 0 XML parsing failed 0 constraint file generation failed 0 FASTA file generation failed 0 folding failed 1 I/O error 0 pseudoknotted folding failed

[+] All done.

[dincarnato]

Not sure what to say. I could observe the bug before the fix, but it is now gone for me, also just tested in on several RNAs. Can you maybe wipe your RNAFramework install and git clone from scratch? Maybe you have multiple installs on the system and the one in your PATH is not the one you are pulling to? If this doesn't fix, can you share the XML file so I can try replicate the issue on that one?

[Frappadoo]

Hi Danny,

It works now thank you! I had a second copy of RNAframework in my path.

[wangguiqian]

(work) [yqming@sg56 PEDV]$ ~/Software/RNAFramework/rf-fold -m 1 -g -md 500 -w -pk -km 2 -ko 100 -pw 1600 -po 375 -wt 300 -fw 3000 -fo 300 rf-norm/FSE.xml

[+] Checking method's requirements... [+] Making output directory tree... [+] Importing XML file(s) [1 imported]
[+] Folding RNA structures [Last: none] [+] Folding statistics:

[] Folded transcripts: 0 [] Discarded transcripts: 1 total 0 XML parsing failed 0 constraint file generation failed 0 FASTA file generation failed 0 folding failed 0 I/O error 1 pseudoknotted folding failed

[+] All done.

But I using the command to ran ,i get the errors . Could you tell me what happen? @Frappadoo @kenibrewer