mrb20045 / casilico Goto Github PK

Hi,
I am reaching out to discuss the analysis results generated by your bioinformatics software. The results are currently accessible through individual web pages, each corresponding to specific analysis outputs.

While the web interface provides a convenient way to view individual results, I am facing a challenge with efficiently downloading these results for further offline analysis or archiving. My workflow would greatly benefit from a feature that allows for batch downloading of these web-based results.

Could you please advise if there is an existing functionality within the software that supports this use case?

We are very happy with your tool. It was easy to use with the examples provided. It was also very fast with the offline offtarget analysis with the blast database.

I was wondering if it is possible to define an existing blast database to make the tool even faster (no need to build the database)? When I use the LocalFasta option and define a reference which has a blast database it does not try to use this database.

Thanks in advance!

Hi,
I am encountering a similar issue to the https://github.com/mrb20045/CaSilico/issues/3
Error in plot.window(...) : need finite 'xlim' values
Interestingly, this issue does not occur on a Windows system; the code executes without any errors there.
To address this issue on Linux, I added the following lines to my script to ensure the software continues running even if this error occurs:
run_CaSilico_with_error <- function(file_path) {
tryCatch({
run_CaSilico(file_path)
}, error = function(e) {
if (grepl("Error in plot.window", e$message)) {
message("Plotting error ignored: ", e$message)
} else {
stop(e)
}
})
}

However, despite this attempt, the software fails to produce the final output files, such as Spacers_Information.Html and Off_Targets_Information.Html.

Could you please provide guidance on how to resolve this issue? Any assistance would be greatly appreciated.

Thank you.

Hi,
Im using Rstudio server from a docker image (rocker/rstudio), im trying to run the first example code inside de package help page, but im getting the following error:
Error in plot.window(...) : need finite 'xlim' values

The first step in the workflow seems to be ok, even i get the output folder with the alignments and subfolders, but somehow the plot is failing.

this are the final lines of the output i am getting:

final_structure
ggguugauuguugacaccagagauguggaagagcgcgugcacgucaugcgcaaaaccaagcuugcacccaccguggcacacgguguguuuaacccugaauuugggccugccgccuuguccaacaaggacccgcgccugaacgaagguguuguccucgacgaagucaucuucuccaaacacaagggagacaccaagaugucugaggaggacaaagcgcuguuccgccgcugcgcugcugacuacgcgucgcgccugcacagcgugcuggggacagcaaaugccccacugagcaucuaugaggccaucaagggcgucgacggacucgacgccauggagccugacaccgcgcccggccuccccugggcccuccaggggaagcgccgcggcgcgcucaucgacuucgagaacggcacugucggacccgagguugaggcugcccugaagcucauggagaaaagagaguacaaguuugcuugucaaaccuuccugaaggacgagauucgcccgauggagaaaguacgugccggcaagacucgcauugucgacgucuugccuguugaacacauucucuacaccaggaugaugauuggcagauuuugugcacaaaugcacucaaacaacggaccgcaaauuggcucggcggucgguugcaacccugauguugauuggcaaagauuuggcacacauuuugcccaguacaaaaacgugugggacguggacuauucggccuuugaugcuaaccacugcagugacgccaugaacaucauguuugaggagguguuccgcacggaauuugguuuccacccgaacgcugaguggauucugaagacucucgugaacacggaacacgccuacgagaacaagcgcaucacuguugaaggcggaaugccgucugguuguuccgcaacaagcaucaucaacacaauuuugaacaacaucuacgugcucuacgcccugcguagacacuaugagggaguugagcuggacaccuacaccaugaucuccuacggagacgacaucgugguggcaagugauuacgauuuggacuuugaggcucucaagccucacuuuaaaucucuuggucaaaccaucacuccagcugacaaaagcgacaaagguuuuguucuuggucacuccauuaccgaugucacuuuccucaaaagacacuuccacauggauuauggaacuggguuuuacaaaccugugauggcuucgaagacccucgaggcuauccucuccuuugcacgccgugggaccauacaggagaaguugaucuccguggcaggacucgccguccacucuggaccugacgaguaccggcgucucuucgagcccuuccagggccucuuugagauuccaagcuacagaucacuuuaccugcguugggugaacgccgugugcggugacgc
(((((((...))))).))......(((.(((.(((((((.....))))))).........))).))).((((...(((((((((((.....((((.......((((..(((.((((((...))))))....((((((......))))))(((((((.....((.((((((((((.........))))).....))))).))...)))))))....(((((((((((((((.((.((((((.....)))).))..)).))))).))..))))))))..((((........)))).....((((..((...((((((((.....))))))))...))))))((...(((((((((((((((((((.....))))))).)).)))).)))))).)).(((((((((.(..((((...))))..).)))))))))))).)))).....(((((((..(((.(((((...(((((((((.((((...(.(((((..((.(((...))).))..(((((((.((....((.(((((((((((......))).)))))))).)).....)).)))))))...))))).).)))).))))))))).(((((....))))).....((((.((((((...........)))))).))))((((......))))..((.(((....))).))........(((((((.((((..(((((((((.((((((...((((....(((((((.......(((((((((((((((...)))))(((((((..((((((((((((((.(((((..(((((.((.....)).)))))..)))))...)).))))....)))))))).))).)))).....)))..))))))).....((((((((((....)).))))))))....)))))))((((.......)))).((((.(((.((((.(((((((...)))))))...)))).))).))))((((((((((...(((((((((((((...))))).....))))))))....))).....((((((((...(((((((....))))))).))))))))...((((...))))....)))))))(((((((.(......).)))))))..(((.....)))...)))).))).((((.....)))).))))))))))))..)).))..)))))))...(((....)))(((((((((((......)))))))))))))))).))).....)))))))......((((.(((((.(((((..(((((.((((((((.(((((...)))))..).))))).))((.(((((...(((((((...)))).)))...))))).))..))))))))))))))).))))....))))..))))))))))))))).... (-542.40)
[1] "no sequences to match"
[1] "default ranges used"
[1] "no sequences to match"
[[1]]
[1] "Gap between bound NTs is less than 2"
[1] "no sequences to match"
Error in plot.window(...) : need finite 'xlim' values

Any idea what could be?