Open SREERAMIISERB opened 1 year ago
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 : 1) list_backsplice.txt : 4:143543509-143543972 + 11:33286413-33287511 + 15:64499292-64500166 +
2) path_files.txt :
/data/input/Homo_sapiens.GRCh38.104.gtf /data/input/Homo_sapiens.GRCh38.dna.primary_assembly.fa
3) 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
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)
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='4:143543509-143543972', 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
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 | | 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
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
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'
The following object is masked from 'package:plyr':
rename
The following object is masked from 'package:tidyr':
expand
The following objects are masked from 'package:data.table':
first, second
The following objects are masked from 'package:dplyr':
first, rename
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:glue':
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The following object is masked from 'package:plyr':
desc
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reduce
The following object is masked from 'package:data.table':
shift
The following objects are masked from 'package:dplyr':
collapse, desc, slice
c Attaching package: 'AnnotationDbi'
The following object is masked from 'package:dplyr':
select
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
Hi Seeram, the error simply means that the path for the input files told to CRAFT is wrong.
Try to delate output directories, put input files in the correct directory (check it, because due to the analysis, some of them change directory), and then re-run the analysis from inside the data/ directory.
Best, Anna
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)
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='4:143543509-143543972', 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 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 | | 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
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'
The following object is masked from 'package:plyr':
rename The following object is masked from 'package:tidyr':
expand The following objects are masked from 'package:data.table':
first, second The following objects are masked from 'package:dplyr':
first, rename The following objects are masked from 'package:base':
I, expand.grid, unname Attaching package: 'IRanges'
The following object is masked from 'package:glue':
trim The following object is masked from 'package:plyr':
desc The following object is masked from 'package:purrr':
reduce The following object is masked from 'package:data.table':
shift The following objects are masked from 'package:dplyr':
collapse, desc, slice c Attaching package: 'AnnotationDbi'
The following object is masked from 'package:dplyr':
select 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