Unable to get the complete results of craft, but Im able to run the beRBP tools individually #8
Description
Respected professor
As of now im just replicating your paper and file results and then I will produce results from my own data. In my root directory I have made a subdirectory called data in which I have made three files :
list_backsplice.txt :
4:143543509-143543972 +
11:33286413-33287511 +
15:64499292-64500166 +
path_files.txt :
/data/input/Homo_sapiens.GRCh38.104.gtf
/data/input/Homo_sapiens.GRCh38.dna.primary_assembly.fa
params.txt :
MRO
hsa
HG38
score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10
score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10, voteFrac_RBP=0.3
Now I have made input subdirectory within data, which has the fasta file, gtf file, and the index files respectively:
HG38.00.idx HG38.02.idx HG38.nhr HG38.nsq Homo_sapiens.GRCh38.104.gtf
HG38.01.idx HG38.fa HG38.nin HG38.shd Homo_sapiens.GRCh38.dna.primary_assembly.fa
Now when im running the craft using your command "sudo docker run -it -v $(pwd):/data annadalmolin/craft:v1.0" Im getting all the directories of sequence_extraction/, functional_predictions/, graphical_output/ with the respective folders inside it which are empty. Alongwith that Im getting the following errors :
mv: cannot stat '/data/sequence_extraction/backsplice_sequence_1.fa': No such file or directory
mv: cannot stat '/data/sequence_extraction/backsplice_sequence_1.txt': No such file or directory
mv: cannot stat '/data/sequence_extraction/backsplice_circRNA_length_1.txt': No such file or directory
cat: backsplice_circRNA_length_1.txt: No such file or directory
mv: cannot stat '/data/input/backsplice_gene_name.txt': No such file or directory
cat: ../backsplice_sequence_1.fa: No such file or directory
cat: ../backsplice_sequence_1.fa: No such file or directory
cat: ../backsplice_sequence_1.fa: No such file or directory
MiRNA binding site prediction analysis completed.
cat: ../backsplice_sequence_1.fa: No such file or directory
cp: cannot stat '../backsplice_sequence_1.txt': No such file or directory
cat: ../backsplice_circRNA_length_1.txt: No such file or directory
cat: ORF_backsplice2.bed: No such file or directory
rm: cannot remove 'ORF_backsplice2.bed': No such file or directory
cat: result.txt: No such file or directory
cat: result.txt: No such file or directory
rm: cannot remove 'result.txt': No such file or directory
cat: result_list_CDS_30.txt: No such file or directory
cat: result_list_ORF_30.txt: No such file or directory
ORF prediction analysis completed.
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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rmarkdown::render('/data/.scripts/functional_predictions_single_circRNA.Rmd', output_file='functional_predictions_single_circRNA.html', output_dir='.', params = list(circ='4:143543509-143543972', score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10))
processing file: functional_predictions_single_circRNA.Rmd
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inline R code fragments
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label: setup (with options)
List of 1
$ include: logi FALSE
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ordinary text without R code
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label: libraries (with options)
List of 2
$ echo : logi FALSE
$ include: logi FALSE
Bioconductor version '3.14' is out-of-date; the current release version '3.17'
is available with R version '4.3'; see https://bioconductor.org/install
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'data.table'
The following objects are masked from 'package:dplyr':
between, first, last
Loading required package: viridisLite
Attaching package: 'reshape2'
The following objects are masked from 'package:data.table':
dcast, melt
Failed to create bus connection: No such file or directory
-- Attaching packages -------------------------------------------------------------------------------------------- tidyverse 1.3.1 --
v tidyr 1.1.4 v stringr 1.4.0
v readr 2.1.1 v forcats 0.5.1
v purrr 0.3.4
-- Conflicts ----------------------------------------------------------------------------------------------- tidyverse_conflicts() --
x data.table::between() masks dplyr::between()
x dplyr::filter() masks stats::filter()
x data.table::first() masks dplyr::first()
x dplyr::lag() masks stats::lag()
x data.table::last() masks dplyr::last()
x purrr::transpose() masks data.table::transpose()
You have loaded plyr after dplyr - this is likely to cause problems.
If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
library(plyr); library(dplyr)
Attaching package: 'plyr'
The following object is masked from 'package:purrr':
compact
The following objects are masked from 'package:dplyr':
arrange, count, desc, failwith, id, mutate, rename, summarise,
summarize
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
rmarkdown::render('/data/.scripts/functional_predictions_single_circRNA.Rmd', output_file='functional_predictions_single_circRNA.html', output_dir='.', params = list(circ='11:33286413-33287511', score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10))
processing file: functional_predictions_single_circRNA.Rmd
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inline R code fragments
|. | 1%
label: setup (with options)
List of 1
$ include: logi FALSE
|. | 2%
ordinary text without R code
|.. | 2%
label: libraries (with options)
List of 2
$ echo : logi FALSE
$ include: logi FALSE
Bioconductor version '3.14' is out-of-date; the current release version '3.17'
is available with R version '4.3'; see https://bioconductor.org/install
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'data.table'
The following objects are masked from 'package:dplyr':
between, first, last
Loading required package: viridisLite
Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
rmarkdown::render('/data/.scripts/functional_predictions_single_circRNA.Rmd', output_file='functional_predictions_single_circRNA.html', output_dir='.', params = list(circ='15:64499292-64500166', score_miRNA=125, energy_miRNA=-25, dGduplex_miRNA=-22, dGopen_miRNA=-10))
processing file: functional_predictions_single_circRNA.Rmd
| | 1%
inline R code fragments
|. | 1%
label: setup (with options)
List of 1
$ include: logi FALSE
|. | 2%
ordinary text without R code
|.. | 2%
label: libraries (with options)
List of 2
$ echo : logi FALSE
$ include: logi FALSE
Bioconductor version '3.14' is out-of-date; the current release version '3.17'
is available with R version '4.3'; see https://bioconductor.org/install
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Attaching package: 'data.table'
The following objects are masked from 'package:dplyr':
between, first, last
Loading required package: viridisLite
Attaching package: 'reshape2'
The following objects are masked from 'package:data.table':
dcast, melt
Failed to create bus connection: No such file or directory
-- Attaching packages -------------------------------------------------------------------------------------------- tidyverse 1.3.1 --
v tidyr 1.1.4 v stringr 1.4.0
v readr 2.1.1 v forcats 0.5.1
v purrr 0.3.4
-- Conflicts ----------------------------------------------------------------------------------------------- tidyverse_conflicts() --
x data.table::between() masks dplyr::between()
x dplyr::filter() masks stats::filter()
x data.table::first() masks dplyr::first()
x dplyr::lag() masks stats::lag()
x data.table::last() masks dplyr::last()
x purrr::transpose() masks data.table::transpose()
You have loaded plyr after dplyr - this is likely to cause problems.
If you need functions from both plyr and dplyr, please load plyr first, then dplyr:
library(plyr); library(dplyr)
Attaching package: 'plyr'
The following object is masked from 'package:purrr':
compact
The following objects are masked from 'package:dplyr':
arrange, count, desc, failwith, id, mutate, rename, summarise,
summarize
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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expand
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I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:glue':
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c
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:dplyr':
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c
Warning message:
In system("timedatectl", intern = TRUE) :
running command 'timedatectl' had status 1
Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Execution halted
These are also the errors that im encountering:
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
mv: cannot stat '/data/input/backsplice_gene_name.txt': No such file or directory
Madam could you please guide me with these