Unable to get the complete results of craft, but Im able to run the beRBP tools individually

SREERAMIISERB commented 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 :

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.

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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 | | 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

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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='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 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 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

SREERAMIISERB commented 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

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 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 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 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 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

annadalmolin commented 11 months ago

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

annadalmolin / CRAFT

Unable to get the complete results of craft, but Im able to run the beRBP tools individually #8

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)

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)