Issues rf-fold failed

[jinqiongli]

Hi Danny,

I am very appreciate for using RNAFramework, it helped me a lot ! Unfortunately I've been unable to use the rf-fold to fold RNA. the code is: ~/RNAFramework/rf-fold /home/jql/RNAFramework/201123/norm -t 25 -i -sh -o /home/jql/RNAFramework/201123/vienna Here is my problem: [+] Checking method's requirements... [+] Making output directory tree... [+] Importing XML file(s) [7 imported] [+] Folding RNA structures [Last: none] [+] Folding statistics:

[] Folded transcripts: 0 [] Discarded transcripts: 7 total 2 XML parsing failed 0 constraint file generation failed 0 FASTA file generation failed 5 folding failed 0 I/O error

[+] All done. Because I failed to fold, the output is the empty folder. I don't know how to solve this issue, so I wish I could get help from you. Any suggestion will help me a lot.

Best, Qiongli Jin

[dincarnato]

Dear Qiongli,

to reproduce the error I would need the XML files you are using. Can you please share those (also by email if you prefer)?

Have the XML files been generated by rf-norm?

Best, Danny

[jinqiongli]

Dear Danny，

Thank you for replying. Here is my XML files that I am using for rf-fold.

The XML files have been generated by rf-norm.

Best, Qiongli Jin

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发件人: Danny Incarnato 发送时间: 2020年11月23日 23:58 收件人: dincarnato/RNAFramework 抄送: jinqiongli; Author 主题: Re: [dincarnato/RNAFramework] Issues rf-fold failed (#8)

Dear Qiongli, to reproduce the error I would need the XML files you are using. Can you please share those (also by email if you prefer)? Have the XML files been generated by rf-norm? Best, Danny — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[dincarnato]

Dear Qiongli,

here where? I do not see any file.

Danny

[dincarnato]

Dear Qiongli,

I am sorry but I have tried to use your file with rf-fold and your same parameters "-t 25 -i -sh" and if worked smoothly for me. Can you share the actual XML file? Maybe there is some kind of issue with line-endings or similar?

Danny

PS. The use of the "-i" parameter instruct rf-fold to ignore the reactivities, so to predict the unconstrained structure.

[jinqiongli]

Dear Danny， I want to predict the structure in vitro and ignore the reactivity, so I set -i parameter. I don't know how to show the file on git, so I directly send the xml files to your email, does this OK? Any advise that I can share my xml file to you?

Qiongli

[dincarnato]

Sure, just mail me the files: dincarnato@rnaframework.com

[jinqiongli]

Danny, I guess maybe my rf-fold project have some problem when I installed it. Do you have any test.xml file that I can use to test my rf-fold is OK or not? Qiongli

[dincarnato]

The files you sent me work as well. I do not really understand what kind of problem rf-fold can have. Is there a way I can get remote ssh access to your machine where RNA Framework is installed and try to solve the issue?

[jinqiongli]

Thank you, But I don't know how to remote ssh access to your server, it may take me some time to solve this. your work let me check my RNAFramework and I find that I didn't install RNAStructure (Because I don't intend to use it). I will install RNAStructure first and test whether I can use rf-fold or not. If this isn't worked, I will contact you again.

[dincarnato]

Dear Qiongli,

No need to install it, that's not the reason. The program is complaining on XML parsing, and on folding. Can you please try to execute "RNAfold -h" and show me the output?

[jinqiongli]

RNAfold 2.3.3

Calculate minimum free energy secondary structures and partition function of RNAs

Usage: RNAfold [OPTIONS]...

The program reads RNA sequences, calculates their minimum free energy (mfe) structure and prints the mfe structure in bracket notation and its free energy. If not specified differently using commandline arguments, input is accepted from stdin, and output printed to stdout. If the -p option was given it also computes the partition function (pf) and base pairing probability matrix, and prints the free energy of the thermodynamic ensemble, the frequency of the mfe structure in the ensemble, and the ensemble diversity to stdout.

It also produces PostScript files with plots of the resulting secondary structure graph and a "dot plot" of the base pairing matrix. The dot plot shows a matrix of squares with area proportional to the pairing probability in the upper right half, and one square for each pair in the minimum free energy structure in the lower left half. For each pair i-j with probability p>10E-6 there is a line of the form

i j sqrt(p) ubox

in the PostScript file, so that the pair probabilities can be easily extracted.

Sequences may be provided in a simple text format where each sequence occupies a single line. Output files are named "rna.ps" and "dot.ps". Existing files of the same name will be overwritten. It is also possible to provide sequence data in FASTA format. In this case, the first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively. Once FASTA input was provided all following sequences must be in FASTA format too. The program will continue to read new sequences until a line consisting of the single character @ or an end of file condition is encountered.

-h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit --full-help Print help, including hidden options, and exit -V, --version Print version and exit

General Options: Command line options which alter the general behavior of this program

-v, --verbose Be verbose.

                                (default=off)

-i, --infile= Read a file instead of reading from stdin

-o, --outfile= Print output to file instead of stdout

  --noPS                    Do not produce postscript drawing of the mfe
                              structure.

                                (default=off)
  --noconv                  Do not automatically substitute nucleotide
                              "T" with "U"

                                (default=off)
  --auto-id                 Automatically generate an ID for each sequence.
                                (default=off)
  --id-prefix=prefix        Prefix for automatically generated IDs (as used
                              in output file names)

                                (default=`sequence')

Structure Constraints: Command line options to interact with the structure constraints feature of this program

  --maxBPspan=INT           Set the maximum base pair span

                                (default=`-1')

-C, --constraint[=] Calculate structures subject to constraints. (default=`') --batch Use constraints for multiple sequences. (default=off) --canonicalBPonly Remove non-canonical base pairs from the structure constraint

                                (default=off)
  --enforceConstraint       Enforce base pairs given by round brackets ( )
                              in structure constraint

                                (default=off)
  --shape=<filename>        Use SHAPE reactivity data to guide structure
                              predictions

  --shapeMethod=[D/Z/W] + [optional parameters]
                            Select method to incorporate SHAPE reactivity
                              data.
                                (default=`D')
  --shapeConversion=M/C/S/L/O  + [optional parameters]
                            Select method to convert SHAPE reactivities to
                              pairing probabilities.
                                (default=`O')

Algorithms: Select additional algorithms which should be included in the calculations. The Minimum free energy (MFE) and a structure representative are calculated in any case.

-p, --partfunc[=INT] Calculate the partition function and base pairing probability matrix. (default=1') --MEA[=gamma] Calculate an MEA (maximum expected accuracy) structure, where the expected accuracy is computed from the pair probabilities: each base pair (i,j) gets a score 2*gamma*p_ij and the score of an unpaired base is given by the probability of not forming a pair. (default=1.') -c, --circ Assume a circular (instead of linear) RNA molecule.

                                (default=off)

-g, --gquad Incoorporate G-Quadruplex formation into the structure prediction algorithm.

                                (default=off)

Model Details: -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C.

-4, --noTetra Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. (default=off) -d, --dangles=INT How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops (default=`2') --noLP Produce structures without lonely pairs (helices of length 1). (default=off) --noGU Do not allow GU pairs

                                (default=off)
  --noClosingGU             Do not allow GU pairs at the end of helices

                                (default=off)

-P, --paramFile=paramfile Read energy parameters from paramfile, instead of using the default parameter set.

If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.

[dincarnato]

Ok, let's try to find out the problem. The program says that 2 files failed XML parsing, and 5 files failed folding. Can you please send all of the 7 files?

[dincarnato]

There is an undocumented parameter in rf-fold, the “-KT” parameter. Can you please re-execute rf-fold with that parameter added? This will make rf-fold leave the “tmp/“ folder in your output folder. I will need to look to the content of the tmp folder. Please compress it and send it to me.

Danny

[jinqiongli]

wait me for a little second

[dincarnato]

I think the issue might be caused by your ViennaRNA version. Can you please try installing the latest version?

[jinqiongli]

conda list viennarna packages in environment at /home/jql/.conda/envs/RNAFramework: Name Version Build Channel viennarna 2.3.3 hfc679d8_2 bioconda conda update viennarna Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed. conda list viennarna packages in environment at /home/jql/.conda/envs/RNAFramework:

Name Version Build Channel viennarna 2.3.3 hfc679d8_2 bioconda

[dincarnato]

This is not the latest version. You should install it manually from the package. You need ViennaRNA v2.4.11 or greater.

[jinqiongli]

I install it from packages ViennaRNA v2.4.16, but I don't know how to let RNAFramework use the latest version not the conda viennarna, could you teach me?

[dincarnato]

What's the full path to the ViennaRNA 2.4.16?

[jinqiongli]

/home/jql/ViennaRNA-2.4.16

[dincarnato]

Are the executables in that folder? Does /home/jql/ViennaRNA-2.4.16/RNAfold exist?

[dincarnato]

did you compile it? or did you just downloaded the package? check the manual, you should issue the "./configure", then "make" and "make install".

[jinqiongli]

Dear Danny, Really appreciate you, thank you for spending so much time for solving my problem. I am desperate for 3 days , because I am a green hand in data analysis, no one could help me and I am stucking in my problems, this is the first time I asking for help on Internet. I think we could close the issue, Thank you again! Best wishes, Qiongli Jin

[dincarnato]

Great to hear it worked! Best,

Danny