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Error in .DynamicClusterCall(cl, length(cl), .fun = function(.proc_idx #188
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Dear Laia, did you check the troubleshooting section ? I think this error is documented. I'm unable to run the data you sent (even if the strata csv is converted to tsv) |
Dear Thierry, Step 1. Coverage visualization and helper table Generating statistics I already updated tidyverse following some suggestion from google butI am still traped in this point. Sadly I was not able to upload my data base because it has more than 178 MB. |
Send the real data by email |
Don't share full dataset to the public If not possible try making a smaller dataset that generate the same error so that I can reproduce With my dataset I don't have any... |
First test with your data works
|
Using This should not take long |
Ok so I see the problem, it's during the coverage filter, when using DArT data without counts, the coverage information is based on average and the dataset provided by DArT. I don't filter coverage when using 1 row and 2 rows provided by DArT, for several reasons that were mentioned during the workshop you attended. Simplify: I don't like that so I prefer not to filter it and advertise the idea to 1. get the FQ files for good bookkeeping 2. get the count files... I will still fix the issue not to throw an error |
Dear Thierry, Thank you so much. Yes, I understand that I should avoid the coverage filter, however, when I tried to exclude (using filter_coverage = FALSE), the code did not run exclueded it. Unknowned arguments identified inside "...": Thank you again |
In the earlier days I was trying to accommodate all format, now I'm more picky. I had plan to re-integrate the coverage statistics generated by DArT for 1row and 2rows format but I slept on it and I really thing it's almost 100% of the time biased with the dataset that I have seen, for the single reason that samples will eventually get blacklisted (removed) and the stats becomes biased. Request DArT count file the next time. Now the function will bypass the coverage for those files.
|
* Fix issue #188 related to coverage in DArT 1row and 2rows format
Latest radiator version should fix your problem |
For your info... For your dataset exploration here is the filters thresholds I used:
Removing
At the end of this first filtering exploration you have 18 427 SNPs and 387 samples Hope this helps, re-open an issue if you are still having problems |
radiator and dartR approachesIn case you are wondering some of the differences between radiator and dartR... radiatorQuickly if you want to test the mixed genomes (individual heterozygosity) or duplicated genomes (duplicate samples and close kin detection) without any filters:
Using dartR
Conclusion for:
Hope this helps highlight the differences in the 2 packages |
Dear Thierry, It is awesome, thank you so much; I also ran dartR and am seeing the differences. Sadly, I am struggling with a new error with the radiator righ now; it sounds like it is related with SNPrate. Computation time, overall: 241 sec |
Could you post the exact command that you used, I've ran the analysis 4-5 times on your data without problems
does it work? |
I am running the command below following all your instructions. However, I was not able to finish with the two last filters. data <- radiator::filter_rad( Below are the lines that you asked me to run:
Number of chrom: 1 Number of ind/strata: Number of duplicate id: 0 Computation time, overall: 90 sec
Computation time, overall: 10 sec
Computation time, overall: 10 sec |
|
I restarted everything, but I am still having the same problem data <- radiator::read_dart(data = "SNPS1.csv", strata = "stratayft.tsv") Number of chrom: 1 Number of ind/strata: Number of duplicate id: 0 Computation time, overall: 118 sec
Computation time, overall: 11 sec
|
And I am still with the same error :( Computation time, overall: 1 sec |
Write down below the output of this command: |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── [1] C:/Program Files/R/R-4.3.2/library |
Dear Thierry, I hope you are doing great. I wonder if you have updates about my last bug. I am still having the same problem, and I definitely want to use Radiator for my data analyses. ###################### radiator::detect_duplicate_genomes ###################### Computation time, overall: 2 sec Computation time, overall: 412 sec |
Try the last version, re-open if problem still persist |
Dear Thierry, I am so sorry, but the problem persists. I tried with two different computers. Computation time, overall: 21 sec Computation time, overall: 1 sec Computation time, overall: 307 sec devtools::session_info() ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── The code that you sent to me: Number of chrom: 1 Number of ind/strata: Number of duplicate id: 0 Computation time, overall: 112 sec
Computation time, overall: 10 sec
Computation time, overall: 8 sec |
data <- radiator::filter_rad(
data = "SNPS1.csv",
strata = "stratayft.tsv"
)
Step 1. Minor Allele Statistics visualization and helper table
depth info not available, switching to count
Error in .DynamicClusterCall(cl, length(cl), .fun = function(.proc_idx, :
One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\filter_rad_20240513@2143\01_radiator\radiator_20240513@2143.gds.rad'. The process cannot access the file because it is being used by another process.
In addition: There were 50 or more warnings (use warnings() to see the first 50)
✖ Calculating Minor Allele statistics [15.2s]
Computation time, overall: 16 sec
############################# completed filter_ma ##############################
Computation time, overall: 172 sec
############################# completed filter_rad #############################
Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.2 (2023-10-31 ucrt)
os Windows 11 x64 (build 22631)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.utf8
ctype English_United States.utf8
tz America/Chicago
date 2024-05-13
rstudio 2023.12.1+402 Ocean Storm (desktop)
pandoc NA
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
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[1] C:/Program Files/R/R-4.3.2/library
result.csv
rstrataesult.csv
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