Minimal dataset/example for testing

[gabriellovate]

Dear Richard (I believe you are the only developer, right?), I've been trying to run RNAnue on the provided container unsuccessfully.

• I have set up a params.cfg file, and I am running the container via apptainer (previously called singularity):

  apptainer exec --bind /data/results/RNAnue:/mnt/output/ --bind /data/reads:/mnt/data/reads --bind /data/cfg_files:/mnt/cfg_files --bind /data/genomes:/mnt/data/genomes rnanue_latest.sif /RNAnue/build/RNAnue allign  --config /mnt/cfg_files/RNAnue/params.cfg

• my params.cfg file looks a bit like this:

  
  ### GENERAL
  readtype = SE # paired-end (PE) or single-end (SE)

absolute path of dirs containing the raw reads (additional dir for each library)

trtms = /mnt/data/reads outdir = /mnt/output

threads = 48 # number of threads quality = 20 # lower limit for the average quality (Phred Quality Score) of the reads mapquality = 20 # lower limit for the average quality (Phred Quality Score) of the alignment minlen = 20 # minimum length of the reads splicing = 0 # include splicing (=1) or not (=0)

ALIGNMENT (forwarded to segemehl.x)

dbref = /mnt/data/genomes/genome.fasta accuracy = 90 # min percentage of matches per read in semi-global alignment minfragsco = 15 # min score of a spliced fragment minfraglen = 15 # min length of a spliced fragment minsplicecov = 80 # min coverage for spliced transcripts exclclipping = 0 # exclude soft clipping from

SPLIT READ CALLING

sitelenratio = 0.0 cmplmin = 0.0 # complementarity cutoff - consider only split reads that exceed cmplmin nrgmax = 0 # hybridization energy cutoff - consider only split reads that fall beneath nrgmax

CLUSTERING

clust = 1 # clustering of the split reads can either be omitted (=0) or included (=1) clustdist = 0 # minimum distance between clusters

ANALYIS

specify the annotations of the organism of interest (optional)

features = /Users/riasc/Documents/work/projects/RNAnue/build/ecoli_BL21_DE3.gff # GFF3 feature file

OUTPUT

stats = 1 # produce a statistics of the libraries outcnt = 1 # (additionally) produce a count table as output outjgf = 1 # (additionally) produce a JSON graph file for visualization

- I get the following error message (which I can't quite debug on my own):

RNAnue v0.1.0 - Detect RNA-RNA interactions from Direct-Duplex-Detection (DDD) data. reads the data to align skipping preprocessing terminate called after throwing an instance of 'boost::wrapexcept' what(): boost::bad_any_cast: failed conversion using boost::any_cast Aborted

Would you be able to help me run the tool? Maybe you could provide a minimal dataset for testing?

[gabriellovate]

Hi @riasc I tried using the new image, but it seems it was prepared as an arm64 image instead of x64:

FATAL:  rnanue_latest.sif: the image's architecture (arm64) could not run on the host's (amd64)

[gabriellovate]

Do you think you could push an x64 image to docker hub?

[riasc]

Hi, sorry for the late reply. It has been a hit chaotic these days. Sorry, that's my bad. Yes, I will work on that and push it to docker. Thanks

[gabriellovate]

No problem, I appreciate the support

[Ikarto]

Dear Richard, I am experiencing same issue using singularity build from docker image of [v0.2] for amd64 platform. I am obtaining same error as an user above:

RNAnue v0.2.0 - Detect RNA-RNA interactions from Direct-Duplex-Detection (DDD) data.
[2024-05-30 12:33:57] Create directory to store the results (specified via --outdir)
[2024-05-30 12:33:57] The directory "/data/output/" already exists
[2024-05-30 12:33:57] The directory "/data/output/preproc" already exists
[2024-05-30 12:33:57] The directory "/data/output/tmp" already exists
terminate called after throwing an instance of 'boost::wrapexcept<boost::bad_any_cast>'
  what():  boost::bad_any_cast: failed conversion using boost::any_cast
Aborted```

[riasc]

Thanks for reporting this. I will look into it.

[riasc]

Since the initial issue for this was a minimal example (which is available via test) I'm closing this now. Thanks