CRAFT cannot detect input data #2

[AnaTrobec]

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 :)

[annadalmolin]

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 :) — Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AWKFLFJGWMT5E7TLTQQ2P4TXPV4JNANCNFSM6AAAAAA2GH6VGY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>