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thierrygosselin / radiator

RADseq Data Exploration, Manipulation and Visualization using R
https://thierrygosselin.github.io/radiator/
GNU General Public License v3.0
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Error in .DynamicClusterCall(cl, length(cl), .fun = function(.proc_idx #188

Closed laiajulianamu closed 4 months ago

laiajulianamu commented 5 months ago

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

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[1] C:/Program Files/R/R-4.3.2/library

result.csv rstrataesult.csv

thierrygosselin commented 5 months ago

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)

laiajulianamu commented 5 months ago

Dear Thierry, Thank you so much for your response. Yes, I did check the the troubleshooting section and I added to my code the parallel.core =1. However, After that I am having another error

Step 1. Coverage visualization and helper table

Generating statistics Error in UseMethod("mutate") : no applicable method for 'mutate' applied to an object of class "list" In addition: There were 50 or more warnings (use warnings() to see the first 50) ✖ Writing files [61ms]

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. Thank you so muchchecked the troubleshooting section and added the parallel to my code, Laia

thierrygosselin commented 5 months ago

Send the real data by email I'll have a look

thierrygosselin commented 5 months ago

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...

thierrygosselin commented 5 months ago

First test with your data works

test <- radiator::read_dart(data = "SNPS1.csv", strata = "strata1.tsv")
Reading DArT file...                                                
Number of blacklisted samples: 0                                      
DArT SNP format: alleles absence/presence in 2 Rows
fstcore package v0.9.18
(OpenMP detected, using 56 threads)
Generating genotypes and calibrating REF/ALT alleles...
Number of markers recalibrated based on counts of allele: 11707
Generating GDS...
File written: radiator_20240514@1226.gds.rad                        

Number of chrom: 1
Number of locus: 45544
Number of SNPs: 76246
Number of strata: 6
Number of individuals: 479

Number of ind/strata:
PER = 47
MEX = 99
GAL = 216
COL = 32
GM = 11
ITW = 74

Number of duplicate id: 0

Computation time, overall: 102 sec
thierrygosselin commented 5 months ago

Using radiator::filter_rad I do get an error, I think it's link to using DArT SNP format other than count (which I no longer use, favouring counts). I'll have a look for a fix.

This should not take long

thierrygosselin commented 5 months ago

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: By the time I am ready to look at the dataset coverage, 100% of the time I have already discarded samples. The statistics provided by DArT becomes obviously biased because it's using the full dataset...

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

laiajulianamu commented 5 months ago

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 "...": filter_coverage

Thank you again

thierrygosselin commented 5 months ago

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.

Coverage statistics information for 2rows and 1row DArT format is ignored

radiator cannot generate coverage statistics from source
potential blacklisted individuals bias the statistics generated by DArT

request DArT count format from DArT

Coverate information is not available for this dataset, returning GDS...
thierrygosselin commented 5 months ago

Latest radiator version should fix your problem

thierrygosselin commented 5 months ago

For your info... For your dataset exploration here is the filters thresholds I used:

  1. reproducibility: I'm filtering based on the outlier statistics, it blacklist 5424 SNPs
  2. filter for common markers removes 469 SNPs
  3. blacklist samples based on missingness and outlier statistics, 32 samples are removed. At this step I don't remove samples based on heterozygosity. At the end I re-run monomorphic markers removal, this discard 3428 markers.
  4. Minor allele: I use the MAC stats and use 4 alternate alleles, 17282 SNPs are removed (you could also use MAF, but I prefer the count, MAC).
  5. filter genotyping rate based on 0.2 Max missing removes 16779 SNPs
  6. the SNP position on the read, I keep all (option 1, filter is off).
  7. filter based on SNP number on the locus. Based on your data and figures generated I do want to blacklist some locus, and I use my own threshold here. We will keep only locus with a Max of 2 SNPs. This result in blacklisting 2515 locus and 8604 SNPs
  8. filter based on short distance LD, I say yes, because the locus with 2 SNPs (about half the dataset) carries the same information and it bias stats. To filter those I'm using option 1 (based on Mac). So it keeps the SNP with max Mac which makes sense because more samples carries the info). 5049 SNPs are blacklisted. I don't filter for long distance LD with this de novo dataset.
  9. filter individuals based on heterozygosity. You really want to check the samples here because I think you might have 2 species mixed together or there was some wet lab problem (uneven tissue, too much DNA, mixed DNA, etc)... and the one that have really low heterozygosity is probably another specie if it's not correlated with missing data (small bubbles) and if the missing data is important it's usually poor DNA quality... Based on the thresholds (lower and upper) on the figures, 57 samples are removed. This sounds like a lot but if you re-run filter_rad without removing the samples with weird heterozygosity you end up creating false close-kin (it's the next filter that looks for duplicated samples, but provide the figure that shows distances). Removing those 57 samples really end up with a good dataset and highlight real relationships.

Removing

manhattan plot distance

Not removing manhattan plot distance

  1. filtering individuals based on duplicated genomes: I'm using the 0.25 threshold here. If you have remove the problematic samples in the previous filtering steps (heterozygosity), the figure shows 3 pairs of samples from the same population that are potential duplicates, check your lab note or naming, etc. Because they are from the same pop, you can keep 3 based on missingness (keeping the samples with less missing data). So this step, will remove an additional 3 samples.
  2. Hardy Weinberg Disequilibrium filtering depends on the analysis you will do after, this is why in the folder it keeps all the different dataset so you can check its impact e.g. in population discovery analysis. I used 3 pops as threshold to discard the markers (3 sampling sites/pops need to be in disequilibrium to discard the SNPs) and the mid p value chosen here is 0.001. This is a light filtering threshold that blacklist 770 SNPS.

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

thierrygosselin commented 5 months ago

radiator and dartR approaches

In case you are wondering some of the differences between radiator and dartR...

radiator

Quickly if you want to test the mixed genomes (individual heterozygosity) or duplicated genomes (duplicate samples and close kin detection) without any filters:

data <- radiator::read_dart(data = "SNPS1.csv", strata = "strata1.tsv")
 #103 sec on my computer
mix <- radiator::detect_mixed_genomes(data = data) 
#54 sec

individual heterozygosity boxplot individual heterozygosity manhattan plot

dup <- radiator::detect_duplicate_genomes(data = data)
#47 sec

manhattan plot distance violin plot distance

Using dartR

tictoc::tic()
data.gl <- dartR.base::gl.read.dart(filename = "SNPS1.csv", ind.metafile = "strata1_dartR.csv")
tictoc::toc()
# 167.62 sec elapsed
# longer to process and file is not saved...
tictoc::tic()
test.dartr.het <- dartR.base::gl.report.heterozygosity(x = data.gl, save2tmp = TRUE)
tictoc::toc()
# 104.738 sec elapsed

dartR_hetRplot

Conclusion for:

Hope this helps highlight the differences in the 2 packages

laiajulianamu commented 5 months ago

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 ######################## completed detect_mixed_genomes ######################## ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240515@1021 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240515@1021.tsv File written: random.seed (306779)
Calculating manhattan distances between individuals...
Error in .InitFile2(cmd = "Identity-By-State (IBS) analysis on genotypes:", : There is no SNP! In addition: There were 50 or more warnings (use warnings() to see the first 50)

thierrygosselin commented 5 months ago

Could you post the exact command that you used, I've ran the analysis 4-5 times on your data without problems first try this:

data <- radiator::read_dart(data = "SNPS1.csv", strata = "strata1.tsv")
mix <- radiator::detect_mixed_genomes(data = data) # don't remove individuals
dup <- radiator::detect_duplicate_genomes(data = data)

does it work?

laiajulianamu commented 5 months ago

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( data = "SNPS1.csv", strata = "stratayft.tsv", output = c("genind", "stockr", "genpop", "genlight"), parallel.core = 1 )

Below are the lines that you asked me to run: ###################### completed detect_duplicate_genomes ######################

data <- radiator::read_dart(data = "SNPS1.csv", strata = "stratayft.tsv") Reading DArT file...
Number of blacklisted samples: 0
DArT SNP format: alleles absence/presence in 2 Rows Generating genotypes and calibrating REF/ALT alleles... Number of markers recalibrated based on counts of allele: 11707 Generating GDS... File written: radiator_20240515@1113.gds.rad

Number of chrom: 1 Number of locus: 45544 Number of SNPs: 76246 Number of strata: 6 Number of individuals: 479

Number of ind/strata: PER = 47 MEX = 99 GAL = 216 COL = 32 GM = 11 ITW = 74

Number of duplicate id: 0

Computation time, overall: 90 sec

mix <- radiator::detect_mixed_genomes(data = data) # don't remove individuals ################################################################################ ######################## radiator::detect_mixed_genomes ######################## ################################################################################ Execution date@time: 20240515@1114 Folder created: 09_detect_mixed_genomes_20240515@1114 File written: radiator_detect_mixed_genomes_args_20240515@1114.tsv
Filters parameters file generated: filters_parameters_20240515@1114.tsv Error in dplyr::mutate(): ℹ In argument: MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\read_dart_20240515@1113\radiator_20240515@1113.gds.rad'. The process cannot access the file because it is being used by another process. Run rlang::last_trace() to see where the error occurred.

Computation time, overall: 10 sec ######################## completed detect_mixed_genomes ########################

dup <- radiator::detect_duplicate_genomes(data = data) ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240515@1115 Folder created: 10_detect_duplicate_genomes_20240515@1115 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240515@1115.tsv File written: random.seed (747612)
Filters parameters file generated: filters_parameters_20240515@1115.tsv Error in dplyr::mutate(): ℹ In argument: MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\read_dart_20240515@1113\radiator_20240515@1113.gds.rad'. The process cannot access the file because it is being used by another process. Run rlang::last_trace() to see where the error occurred.

Computation time, overall: 10 sec ###################### completed detect_duplicate_genomes ######################

thierrygosselin commented 5 months ago
  1. Start a new session of R and R studio (if using). The problem stems from using too many times the object I think. Start fresh.
  2. install the latest radiator
  3. try re-running the functions above
laiajulianamu commented 5 months ago

I restarted everything, but I am still having the same problem

data <- radiator::read_dart(data = "SNPS1.csv", strata = "stratayft.tsv") Reading DArT file... Number of blacklisted samples: 0
DArT SNP format: alleles absence/presence in 2 Rows fstcore package v0.9.18 (OpenMP detected, using 16 threads) Generating genotypes and calibrating REF/ALT alleles... Number of markers recalibrated based on counts of allele: 11707 Generating GDS... File written: radiator_20240515@1528.gds.rad

Number of chrom: 1 Number of locus: 45544 Number of SNPs: 76246 Number of strata: 6 Number of individuals: 479

Number of ind/strata: PER = 47 MEX = 99 GAL = 216 COL = 32 GM = 11 ITW = 74

Number of duplicate id: 0

Computation time, overall: 118 sec Warning message: package ‘fstcore’ was built under R version 4.3.3

mix <- radiator::detect_mixed_genomes(data = data) # don't remove individuals ################################################################################ ######################## radiator::detect_mixed_genomes ######################## ################################################################################ Execution date@time: 20240515@1530 Folder created: 12_detect_mixed_genomes_20240515@1530 File written: radiator_detect_mixed_genomes_args_20240515@1530.tsv
Filters parameters file generated: filters_parameters_20240515@1530.tsv Error in dplyr::mutate(): ℹ In argument: MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\read_dart_20240515@1528\radiator_20240515@1528.gds.rad'. The process cannot access the file because it is being used by another process. Run rlang::last_trace() to see where the error occurred.

Computation time, overall: 11 sec ######################## completed detect_mixed_genomes ########################

dup <- radiator::detect_duplicate_genomes(data = data) ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240515@1530 Folder created: 13_detect_duplicate_genomes_20240515@1530 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240515@1530.tsv File written: random.seed (622500)
Filters parameters file generated: filters_parameters_20240515@1530.tsv Error in dplyr::mutate(): ℹ In argument: MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\read_dart_20240515@1528\radiator_20240515@1528.gds.rad'. The process cannot access the file because it is being used by another process. Run rlang::last_trace() to see where the error occurred.

laiajulianamu commented 5 months ago

And I am still with the same error :( Computation time, overall: 200 sec ######################## completed detect_mixed_genomes ######################## ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240515@1552 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240515@1552.tsv File written: random.seed (891654)
Calculating manhattan distances between individuals...
Error in .InitFile2(cmd = "Identity-By-State (IBS) analysis on genotypes:", : There is no SNP! In addition: There were 50 or more warnings (use warnings() to see the first 50)

Computation time, overall: 1 sec ###################### completed detect_duplicate_genomes ######################

thierrygosselin commented 5 months ago

Write down below the output of this command: devtools::session_info()

laiajulianamu commented 5 months ago

devtools::session_info() ─ 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 2024-05-16 rstudio 2023.12.1+402 Ocean Storm (desktop) pandoc NA

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[1] C:/Program Files/R/R-4.3.2/library

laiajulianamu commented 5 months ago

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. Thank you so much, Laia

###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240531@1825 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240531@1825.tsv File written: random.seed (118851)
Calculating manhattan distances between individuals...
Error in .InitFile2(cmd = "Identity-By-State (IBS) analysis on genotypes:", : There is no SNP! In addition: There were 50 or more warnings (use warnings() to see the first 50)

Computation time, overall: 2 sec ###################### completed detect_duplicate_genomes ######################

Computation time, overall: 412 sec ############################# completed filter_rad #############################

thierrygosselin commented 4 months ago

Try the last version, re-open if problem still persist

laiajulianamu commented 4 months ago

Dear Thierry,

I am so sorry, but the problem persists. I tried with two different computers.

Computation time, overall: 21 sec ######################## completed detect_mixed_genomes ######################## ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240605@1634 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240605@1634.tsv File written: random.seed (16040)
Calculating manhattan distances between individuals...
Error in .InitFile2(cmd = "Identity-By-State (IBS) analysis on genotypes:", : There is no SNP! In addition: There were 50 or more warnings (use warnings() to see the first 50)

Computation time, overall: 1 sec ###################### completed detect_duplicate_genomes ######################

Computation time, overall: 307 sec ############################# completed filter_rad #############################

devtools::session_info() ─ 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 2024-06-05 rstudio 2024.04.1+748 Chocolate Cosmos (desktop) pandoc NA

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The code that you sent to me: data <- radiator::read_dart(data = "SNPS1.csv", strata = "stratayft.tsv") Reading DArT file...
Number of blacklisted samples: 0
DArT SNP format: alleles absence/presence in 2 Rows Generating genotypes and calibrating REF/ALT alleles... Number of markers recalibrated based on counts of allele: 11707 Generating GDS... File written: radiator_20240605@1636.gds.rad

Number of chrom: 1 Number of locus: 45544 Number of SNPs: 76246 Number of strata: 6 Number of individuals: 479

Number of ind/strata: PER = 47 MEX = 99 GAL = 216 COL = 32 GM = 11 ITW = 74

Number of duplicate id: 0

Computation time, overall: 112 sec

mix <- radiator::detect_mixed_genomes(data = data) (parallel.core = 1) # don't remove individuals ################################################################################ ######################## radiator::detect_mixed_genomes ######################## ################################################################################ Execution date@time: 20240605@1639 Folder created: 01_detect_mixed_genomes_20240605@1639 File written: radiator_detect_mixed_genomes_args_20240605@1639.tsv
Filters parameters file generated: filters_parameters_20240605@1639.tsv Error in dplyr::mutate(): ℹ In argument: MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\read_dart_20240605@1636\radiator_20240605@1636.gds.rad'. The process cannot access the file because it is being used by another process. Run rlang::last_trace() to see where the error occurred.

Computation time, overall: 10 sec ######################## completed detect_mixed_genomes ########################

dup <- radiator::detect_duplicate_genomes(data = data) ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240605@1639 Folder created: 02_detect_duplicate_genomes_20240605@1639 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240605@1639.tsv File written: random.seed (135945)
Filters parameters file generated: filters_parameters_20240605@1639.tsv Error in dplyr::mutate(): ℹ In argument: MISSING_PROP = round(...). Caused by error in .DynamicClusterCall(): ! One of the nodes produced an error: Can not open file 'C:\Users\User\Desktop\gen\read_dart_20240605@1636\radiator_20240605@1636.gds.rad'. The process cannot access the file because it is being used by another process. Run rlang::last_trace() to see where the error occurred.

Computation time, overall: 8 sec