rf-fold - 1 folding failed

[laure-g]

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]

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]

Dear Danny,

Thank you for the reply. Please find attached the tmp.zip file.

Best wishes,

Laure

---

De : Danny Incarnato @.***> Envoyé : lundi 15 juillet 2024 14:55:25 À : dincarnato/RNAFramework Cc : Laure Gauthé; Author Objet : Re: [dincarnato/RNAFramework] rf-fold - 1 folding failed (Issue #65)

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

— Reply to this email directly, view it on GitHubhttps://github.com/dincarnato/RNAFramework/issues/65#issuecomment-2228440220, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BJS34KJOWTHI4LOOTKVG4D3ZMPBD3AVCNFSM6AAAAABK4NZ7AWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRYGQ2DAMRSGA. You are receiving this because you authored the thread.Message ID: @.***>

[dincarnato]

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

[laure-g]

Dear Danny,

Please find attached the tmp.zip file. (2nd attempt)

Best wishes,

Laure

De : Laure Gauthé @.> Date : lundi 15 juillet 2024 à 3:20 PM À : dincarnato/RNAFramework @.>, dincarnato/RNAFramework @.> Cc : Author @.> Objet : RE: [dincarnato/RNAFramework] rf-fold - 1 folding failed (Issue #65)

Dear Danny,

Thank you for the reply. Please find attached the tmp.zip file.

Best wishes,

Laure

---

De : Danny Incarnato @.***> Envoyé : lundi 15 juillet 2024 14:55:25 À : dincarnato/RNAFramework Cc : Laure Gauthé; Author Objet : Re: [dincarnato/RNAFramework] rf-fold - 1 folding failed (Issue #65)

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

— Reply to this email directly, view it on GitHubhttps://github.com/dincarnato/RNAFramework/issues/65#issuecomment-2228440220, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BJS34KJOWTHI4LOOTKVG4D3ZMPBD3AVCNFSM6AAAAABK4NZ7AWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRYGQ2DAMRSGA. You are receiving this because you authored the thread.Message ID: @.***>

[dincarnato]

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

[laure-g]

Dear Danny,

I sent it again to @.**@.>.

Best wishes, Laure

De : Danny Incarnato @.> Répondre à : dincarnato/RNAFramework @.> Date : lundi 15 juillet 2024 à 4:29 PM À : dincarnato/RNAFramework @.> Cc : Laure Gauthé @.>, Mention @.***> Objet : Re: [dincarnato/RNAFramework] rf-fold - 1 folding failed (Issue #65)

@laure-ghttps://github.com/laure-g no attachment that I can see. Please mail it to me.

— Reply to this email directly, view it on GitHubhttps://github.com/dincarnato/RNAFramework/issues/65#issuecomment-2228643189, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BJS34KOXQFGZ4RX54643L2TZMPMFDAVCNFSM6AAAAABK4NZ7AWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRYGY2DGMJYHE. You are receiving this because you were mentioned.Message ID: @.***>

[dincarnato]

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

[dincarnato]

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

[laure-g]

Dear Danny,

I transmitted all the info to our IT and wait for his feedback! I’ll come back to you asap.

Best wishes Laure

De : Danny Incarnato @.> Répondre à : dincarnato/RNAFramework @.> Date : mardi 16 juillet 2024 à 1:26 PM À : dincarnato/RNAFramework @.> Cc : Laure Gauthé @.>, Mention @.***> Objet : Re: [dincarnato/RNAFramework] rf-fold - 1 folding failed (Issue #65)

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

— Reply to this email directly, view it on GitHubhttps://github.com/dincarnato/RNAFramework/issues/65#issuecomment-2230656538, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BJS34KI7HD34DUP2NSPQWNDZMT7QBAVCNFSM6AAAAABK4NZ7AWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMZQGY2TMNJTHA. You are receiving this because you were mentioned.Message ID: @.***>

[dincarnato]

Closing the issue cause it's solved