dincarnato/RNAFramework

rf-fold - 1 folding failed

Closed this issue · 10 comments

laure-g commented

Dear Danny,

I am running the SHAPE-Map Application Case. All steps work until rf-fold, I get

[myfolder]$ 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]
[+] Folding statistics:

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

[+] All done.

Our IT told me even though the RNA.pm file is present (path = /usr/local/share/perl5/5.32/), it seems the script cannot find it. Is there a way to fix this issue please?

I checked closed issues as well but it did not help us to fix the issue.

Best wishes,

Laure

dincarnato commented

Dear Laure,

i don't think that's the issue. If the program wouldn't be able to find RNA.pm, it would say so, and it is not (judging from the output you pasted above).

There must be some other issue. Can you please re-run the program by appending the -KT parameter? This will cause the temporary tmp/ dir inside your output folder to be kept.

Can you please zip that folder and share it with me?

Best,
Danny

laure-g commented
dincarnato commented

I do not see any attachment. Can you mail it to me?

laure-g commented
dincarnato commented

@laure-g no attachment that I can see. Please mail it to me.

laure-g commented
dincarnato commented

Ok, maybe we can jump on a call and look into this together if you want

dincarnato commented

Let me know if you want to try and get this fixed.

laure-g commented
dincarnato commented

Closing the issue cause it's solved