CRAFT cannot detect input data #2

annadalmolin / CRAFT

CRAFT is a computational pipeline that predicts circRNA sequence and molecular interactions with miRNAs and RBPs, along with their coding potential. CRAFT provides a comprehensive graphical visualization of the results, links to several knowledge databases, extensive functional enrichment analysis and combination of predictions for different circRNAs. CRAFT is a useful tool to help the user explore the potential regulatory networks involving the circRNAs of interest and generate hypotheses about the cooperation of circRNAs into the regulation of biological processes.

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Hi, I have an issue running an analysis. I prepared the necessary files in the following directory structure:

. └── test ├── input │ ├── backsplice_gene_name.txt │ ├── hg38.fa │ ├── hg38.ndb │ ├── hg38.nhr │ ├── hg38.nin │ ├── hg38.njs │ ├── hg38.not │ ├── hg38.nsq │ ├── hg38.ntf │ ├── hg38.nto │ ├── hg38.shd │ ├── Homo_sapiens.GRCh38.dna.primary_assembly.fa │ ├── Homo_sapiens.GRCh38.104.gtf │ ├── hg38.00.idx │ ├── hg38.01.idx │ ├── hg38.02.idx ├── list_backsplice.txt ├── params.txt └── path_files.txt

which lies inside C:\test. Then I paste the command: docker run -it -v C:\test :/data annadalmolin/craft:v1.0 to WIndows command prompt, but then I get an error:

Quitting from lines 90-153 (functional_predictions_all_circRNAs.Rmd) Error in read.table(file_parameters, header = F) : no lines available in input Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> read.table In addition: Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'grid'

As far as I understand, it cannot detect input data or/and some packages in R are not appropriate version. But maybe I just should run it in Linux or directly in Docker? I'm new to bioinformatics, so I might be making some basic mistakes. I find your analysis process so cool though, I would really like to make it work :)

Hi, thank you for using CRAFT!

The error given in output means that CRAFT wasn't able to find input files. The directory structure seems correct, but the command line is wrong.

Try docker run -it -v C:\test:/data annadalmolin/craft:v1.0 and run it inside the test/ directory.

Best, Anna

Il giorno mar 11 lug 2023 alle ore 18:19 AnaTrobec @.***> ha scritto:

Hi, I have an issue running an analysis. I prepared the necessary files in the following directory structure: . └── test ├── list_backsplice.txt ├── params.txt └── path_files.txt ├── input ├── backsplice_gene_name.txt ├── hg38.fa ├── hg38.ndb ├── hg38.nhr ├── hg38.nin ├── hg38.njs ├── hg38.not ├── hg38.nsq ├── hg38.ntf ├── hg38.nto ├── hg38.shd ├── Homo_sapiens.GRCh38.dna.primary_assembly.fa ├── Homo_sapiens.GRCh38.104.gtf ├── hg38.00.idx ├── hg38.01.idx ├── hg38.02.idx

which lies inside the path: C:\test. Then I paste the command: docker run -it -v C:\test :/data annadalmolin/craft:v1.0 to WIndows command prompt, but then I get an error:

Quitting from lines 90-153 (functional_predictions_all_circRNAs.Rmd) Error in read.table(file_parameters, header = F) : no lines available in input Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> read.table In addition: Warning message: package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'grid'

As far as I understand, it cannot detect input data or/and some packages in R are not appropriate version. But maybe I just should run it in Linux or directly in Docker? I'm new to bioinformatics, so I might be making some basic mistakes. I find your analysis process so cool though, I would really like to make it work :)

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annadalmolin / CRAFT

CRAFT cannot detect input data #2 #7