annadalmolin / craft Goto Github PK

@annadalmolin Hello, I failed to run the demo. I am in China. Do you have any special requirements on the network?

Hi,
CRAFT looks like very convenient tool for circRNA analysis. However I am not able to run even test example because of dome errors. I run the following command:
sudo docker run -u id -u -it -v $(pwd):/data annadalmolin/craft:v1.0
After running command I have the following errors:

cat: /data/path_files.txt: No such file or directory
cat: /data/path_files.txt: No such file or directory
cat: /data/list_backsplice.txt: No such file or directory

Input files are the copies of your examples.
My working directory is:
/media/marcin/data/lymphoma_circs/test
and structure of the files is:

.
└── data
    ├── input
    │   ├── backsplice_gene_name.txt
    │   ├── est.fa
    │   ├── est.fa.gz.md5
    │   ├── hg38.2bit
    │   ├── hg38.agp
    │   ├── hg38.chromAlias.bb
    │   ├── hg38.chromAlias.txt
    │   ├── hg38.chromAlias.txt.0
    │   ├── hg38.chromFaMasked.tar
    │   ├── hg38.chromFa.tar
    │   ├── hg38.chrom.sizes
    │   ├── hg38.fa
    │   ├── hg38.fa.align
    │   ├── hg38.fa.masked
    │   ├── hg38.fa.out
    │   ├── hg38.gc5Base.bw
    │   ├── hg38.gc5Base.wib
    │   ├── hg38.gc5Base.wig
    │   ├── hg38.gc5Base.wigVarStep
    │   ├── hg38.trf.bed
    │   ├── Homo_sapiens.GRCh38.104.gtf
    │   ├── Homo_sapiens.GRCh38.dna.primary_assembly.fa
    │   ├── md5sum.txt
    │   ├── mrna.fa
    │   ├── mrna.fa.gz.md5
    │   ├── README.txt
    │   ├── refMrna.fa
    │   ├── refMrna.fa.gz.md5
    │   ├── upstream1000.fa
    │   ├── upstream1000.fa.gz.md5
    │   ├── upstream2000.fa
    │   ├── upstream2000.fa.gz.md5
    │   ├── upstream5000.fa
    │   ├── upstream5000.fa.gz.md5
    │   ├── xenoMrna.fa
    │   ├── xenoMrna.fa.gz.md5
    │   ├── xenoRefMrna.fa
    │   └── xenoRefMrna.fa.gz.md5
    ├── list_backsplice.txt
    ├── params.txt
    └── path_files.txt

Thanks for any help.

Marcin

Hello,

I was able to get CRAFT to complete when having it perform the sequence extraction for me. However, I am running into completion issues when providing CRAFT with the circRNA sequences.

When processing the individual circRNAs, I get this error for two of them.

  |...........................................................           |  84%
label: disease_association_RBP (with options) 
List of 2
 $ echo   : logi FALSE
 $ include: logi FALSE

Please wait we are processing your accessions ...

Error in file(file, ifelse(append, "a", "w")) :                               
  all connections are in use
Calls: <Anonymous> ... <Anonymous> -> signalCondition -> <Anonymous> -> cat -> file
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory

For the last circRNA prediction, I get this error in the same location, at 84%.

Please wait we are processing your accessions ...
Quitting from lines 2772-2830 (functional_predictions_single_circRNA.Rmd)     
Error: Can't subset columns that don't exist.
x Column `Involvement.in.disease` doesn't exist.
Backtrace:
     x
  1. +-rmarkdown::render(...)
  2. | \-knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  3. |   \-knitr:::process_file(text, output)
  4. |     +-base::withCallingHandlers(...)
  5. |     +-knitr:::process_group(group)
  6. |     \-knitr:::process_group.block(group)
  7. |       \-knitr:::call_block(x)
  8. |         \-knitr:::block_exec(params)
  9. |           \-knitr:::eng_r(options)
 10. |             +-knitr:::in_dir(...)
 11. |             \-knitr:::evaluate(...)
 12. |               \-evaluate::evaluate(...)
 13. |                 \-evaluate:::evaluate_call(...)
 14. |                   +-evaluate:::timing_fn(...)
 15. |                   +-base:::handle(...)
 16. |                   +-base::withCallingHandlers(...)
 17. |                   +-base::withVisible(eval(expr, envir, enclos))
 18. |                   \-base::eval(expr, envir, enclos)
 19. |                     \-base::eval(expr, envir, enclos)
 20. \-UniprotR::Get.diseases(PathologyObj)
 21.   +-dplyr::select(Pathology_object, "Involvement.in.disease")
 22.   \-dplyr:::select.data.frame(Pathology_object, "Involvement.in.disease")
 23.     \-tidyselect::eval_select(expr(c(...)), .data)
 24.       \-tidyselect:::eval_select_impl(...)
 25.         +-tidyselect:::with_subscript_errors(...)
 26.         | +-base::tryCatch(...)
 27.         | | \-base:::tryCatchList(expr, classes, parentenv, handlers)
 28.         | |   \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 29.         | |     \-base:::doTryCatch(return(expr), name, parentenv, handler)
 30.         | \-tidyselect:::instrument_base_errors(expr)
 31.         |   \-base::withCallingHandlers(...)
 32.         \-tidyselect:::vars_select_eval(...)
 33.           \-tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 34.             \-tidyselect:::eval_c(expr, data_mask, context_mask)
 35.               \-tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 36.                 \-tidyselect:::walk_data_tree(new, data_mask, context_mask)
 37.                   \-tidyselect:::as_indices_sel_impl(...)
 38.                     \-tidyselect:::as_indices_impl(x, vars, strict = strict)
 39.                       \-tidyselect:::chr_as_locations(x, vars)
 40.                         \-vctrs::vec_as_location(x, n = length(vars), names = vars)
 41.                           \-(function () ...
 42.                             \-vctrs:::stop_subscript_oob(...)
 43.                               \-vctrs:::stop_subscript(...)
There were 50 or more warnings (use warnings() to see the first 50)

Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory

The final prediction generating thefunctional_predictions_all_circRNA.htmland functional_predictions_all_circRNA.knit.md finishes completely with no errors.

I also get this error at the beginning of the run about permission denied to access .mature_hsa.fa. I checked my input files and I don't have this file in my inputs.

Putative sequence/s already extracted or provided by the user.
/scripts/pipeline_predictions.sh: line 102: /data/input/.mature_hsa.fa: Permission denied
MiRNA binding site prediction analysis already performed.
RBP binding site prediction analysis already performed.

Any help would be greatly appreciated. Thank you for your time.

Best,

Megan

Hello,

I am trying to use CRAFT to predict miRNA binding sites for three circular RNA, one of which comes from the mitochondrial chromosome. I am able to successfully finish predictions for two of the three circular RNA but not for the mitochondrial one. CRAFT hangs for a long time (10+ hours) at this point:

|...............................                                       |  45%
  ordinary text without R code

  |................................                                      |  46%
label: validated_TG (with options) 
List of 2
 $ echo   : logi FALSE
 $ include: logi FALSE

And then eventually ends up giving this error:

Quitting from lines 842-907 (functional_predictions_all_circRNAs.Rmd)
Error in function (type, msg, asError = TRUE)  :
  Could not resolve host: multimir.org
Calls: <Anonymous> ... submit_request -> <Anonymous> -> .postForm -> <Anonymous> -> fun
In addition: Warning messages:
1: package(s) not installed when version(s) same as current; use `force = TRUE` to
  re-install: 'grid'
2: In read.table(file_gene_names, header = T, sep = "\t") :
  incomplete final line found by readTableHeader on '/data/functional_predictions/backsplice_gene_name.txt'

Execution halted

Here is my backsplice_gene_name.txt input file:

circ_id	gene_names
1:16891302-16893846	NBPF1
5:89791493-89802491	POLR3G
MT:9533-9756	MT-CO3

Is it an issue to use sequences from the mitochondrial chromosome with CRAFT?

Thank you for your time.

Best,
Megan

Hello,
The CRAFT software is a power tools for me.
However, I got the following error messages when I want to use fasta file from GENCODE, which is used to find my circRNA.
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
I have changed the list_backsplice.txt and backsplice_gene_name.txt from 1 to chr1, to adapt my fasta file.
But the error still here.

I don't know whether I MUST use the genome file from Ensembl for CRAFT.
Can you give me some helps?

Thanks in advance.

Regards,
Kingatsu

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
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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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I, expand.grid, unname
Attaching package: 'IRanges'

The following object is masked from 'package:glue':

trim
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desc
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reduce
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shift
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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

Im a root user, in which i have a directory called test, inside which i have another directory called input. T he contents of the directories are as follows:

1.) root
1.A.) test/ :
a) list_backsplice.txt : 4:143543509-143543972 +
11:33286413-33287511 +
15:64499292-64500166 +
b) params.txt : MO
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.

c) path_files.txt :
/data/input/HG38.gtf
/data/input/Homo_sapiens.GRCh38.dna.primary_assembly.fa

1.B) input/ :

a) AGO2_binding_sites.bed
b) backsplice_gene_name.txt
c) hg38.02.idx
d) hg38.nin
e) hg38.nto
f) HG38.gtf
g) bigWigToWig
h) hg38.fa
i) hg38.not
j)hg38.shd
k)Homo_sapiens.GRCh38.104.gtf
l) hg38.00.idx
m) hg38.ndb
n) hg38.nsq
o) Homo_sapiens.GRCh38.dna.primary_assembly.fa
p) hg38.01.idx
q) hg38.nhr
r) hg38.ntf

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 :)

Hello and thanks for the tool, the link to beRBP instructions for genome indexing are not anymore available...could you indicate alternative sources or tools needed to produce them?

Thank you in advance
Eva

Hello,

Is it possible to produce the figures in the graphical_output folder in any other format than .png? Specifically, I'm trying to produce them as .eps files.

Thank you for your time.

Best,
Megan

Hi Anna,

Thank you very much for this nice tool.

But I really came across some problems when using it.
The system is MacOS

Here's the structure of my working directory data/
.
├── input
│   ├── Mus_musculus.GRCm39.104.gtf
│   ├── Mus_musculus.GRCm39.dna.primary_assembly.fa
│   ├── backsplice_gene_name.txt
│   ├── mm39.00.idx
│   ├── mm39.01.idx
│   ├── mm39.fa
│   ├── mm39.ndb
│   ├── mm39.nhr
│   ├── mm39.nin
│   ├── mm39.njs
│   ├── mm39.not
│   ├── mm39.nsq
│   ├── mm39.ntf
│   ├── mm39.nto
│   └── mm39.shd
├── list_backsplice.txt
├── params.txt
└── path_files.txt

my command is:
docker run -it -v $(pwd):/data annadalmolin/craft:v1.0

the path_files.txt:
/Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.104.gtf
/Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.dna.primary_assembly.fa

the params.txt:
MRO
mmu
.
.
mm39
.
orgdb="org.Mm.eg.db", meshdb="MeSH.Mmu.eg.db", symbol2eg="org.Mm.egSYMBOL2EG", eg2uniprot="org.Mm.egUNIPROT", org="mmusculus"
orgdb="org.Mm.eg.db", symbol2eg="org.Mm.egSYMBOL2EG", eg2uniprot="org.Mm.egUNIPROT"

reported error:
grep: /Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.104.gtf: No such file or directory
grep: /Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.104.gtf: No such file or directory
cat: /Users/lily/tool/craft/data/input/Mus_musculus.GRCm39.dna.primary_assembly.fa: No such file or directory
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
Error: The genome file annotation_chr.genome has no valid entries. Exiting.
rm: cannot remove 'backsplice_sequence_bed*': No such file or directory
rm: cannot remove 'circ_id.txt': No such file or directory
rm: cannot remove 'circ_length.txt': No such file or directory
rm: cannot remove 'out_region*': No such file or directory
rm: cannot remove 'region_to_extract_for_?.bed': No such file or directory
rm: cannot remove 'region_to_extract_rev_?.bed': No such file or directory
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
is not a valid option. Try with one of the followings: M, R, O, MR, MO, RO, MRO.

Looking forward to your response. Thank you!

Hi,

I am interested in using the CRAFT tool for running functional prediction on long circRNA (3k-30k nt). The tool works perfectly fine for smaller circRNA, however it takes really long to do the same for long circRNA and the job eventually runs out of time before the prediction can be finished. I am only running miRNA prediction as I am only interested in the disease associations of these circRNA. I have tried setting high scores, however that leads to either some circRNA taking forever or some circRNA not having any miRNA output. Given the wide range of the length I am working in, I am not sure what would be the best solution here and I would really appreciate it if you could provide some input on what would be the best parameters to analyze circRNA this long.

Best Regards,
Avleen