detect_duplicate_genomes

laiajulianamu commented 2 months ago

Dear Thierry,

I am running my dataset on a Mac, but for some reason, the process stops at the duplicate genome filter.

Execution date@time: 20240905@1842 File written: radiator_detect_mixed_genomes_args_20240905@1842.tsv
Calculating heterozygosity statistics
Generating plots

The greatest value of a picture is when it forces us to notice what we never expected to see.

John W. Tukey. Exploratory Data Analysis. 1977.

Inspect plots and tables in folder created... Do you want to exclude individuals based on heterozygosity ? (y/n): y Enter the min value for ind.heterozygosity.threshold argument (0 turns off): 0.80 Enter the max value for ind.heterozygosity.threshold argument (1 turns off): 0.98 Filter individual's heterozygosity: 649 individual(s) blacklisted ################################### RESULTS #################################### Detect mixed genomes: 0.8 0.98 Number of individuals / strata / chrom / locus / SNP: Before: 649 / 6 / 1 / 21089 / 21089 Blacklisted: 649 / 6 / 0 / 0 / 0 After: 0 / 0 / 1 / 21089 / 21089

Filter monomorphic markers Number of individuals / strata / chrom / locus / SNP: Blacklisted: 0 / 0 / 0 / 0 / 0

Computation time, overall: 22 sec ######################## completed detect_mixed_genomes ######################## ################################################################################ ###################### radiator::detect_duplicate_genomes ###################### ################################################################################ Execution date@time: 20240905@1842 Function call and arguments stored in a file File written: radiator_detect_duplicate_genomes_args_20240905@1842.tsv File written: random.seed (791874)
Calculating manhattan distances between individuals...
Error in .InitFile2(cmd = "Identity-By-State (IBS) analysis on genotypes:", : There is no SNP! In addition: Warning messages: 1: There was 1 warning in dplyr::mutate(). ℹ In argument: WHITELISTED_MARKERS = purrr::map_int(...). Caused by warning: ! Using one column matrices in filter() was deprecated in dplyr 1.1.0. ℹ Please use one dimensional logical vectors instead. ℹ The deprecated feature was likely used in the radiator package. Please report the issue at https://github.com/thierrygosselin/radiator/issues. This warning is displayed once every 8 hours. Call lifecycle::last_lifecycle_warnings() to see where this warning was generated. 2: Removed 2 rows containing missing values or values outside the scale range (geom_hline()). 3: Removed 2 rows containing missing values or values outside the scale range (geom_hline()). 4: In min(x, na.rm = TRUE) : no non-missing arguments to min; returning Inf 5: In max(x, na.rm = TRUE) : no non-missing arguments to max; returning -Inf

Computation time, overall: 0 sec ###################### completed detect_duplicate_genomes ######################

Computation time, overall: 567 sec ############################# completed filter_rad #############################

Session info ──────────────────────────────────────────────────────────────── setting value version R version 4.4.1 (2024-06-14) os macOS Sonoma 14.6.1 system x86_64, darwin20 ui RStudio language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz America/Guayaquil date 2024-09-05 rstudio 2024.04.2+764 Chocolate Cosmos (desktop) pandoc NA

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[1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library

thierrygosselin commented 3 weeks ago

Dear Laia,

Read carefully the message you sent above.
Look at the values you have chosen for the radiator_detect_mixed_genomes.
It's normal that radiator stop at the next step, because you have filtered out all the samples... it cannot run the duplicate individuals analysis...

Detect mixed genomes: 0.8 0.98
Number of individuals / strata / chrom / locus / SNP:
Before: 649 / 6 / 1 / 21089 / 21089
Blacklisted: 649 / 6 / 0 / 0 / 0
After: 0 / 0 / 1 / 21089 / 21089

I highly doubt that you have lower and upper values requiring 0.80 and 0.98 respectively.

Consequently, here are 2 advices:

Read the documentation for these 2 functions here:

Carefully read what's written while radiator is running. It's usually printing useful information.

laiajulianamu commented 2 weeks ago

Dear Thierry,

Thank you so much for everything. I learned a lot and ran it successfully. You can’t imagine how much I appreciate it. Best, Laia

On Fri, 8 Nov 2024 at 00:28, Thierry Gosselin @.***> wrote:

Dear Laia,

Read carefully the message you sent above.

Look at the values you have chosen for the radiator_detect_mixed_genomes.

It's normal that radiator stop at the next step, because you have filtered out all the samples... it cannot run the duplicate individuals analysis...

Detect mixed genomes: 0.8 0.98 Number of individuals / strata / chrom / locus / SNP: Before: 649 / 6 / 1 / 21089 / 21089 Blacklisted: 649 / 6 / 0 / 0 / 0 After: 0 / 0 / 1 / 21089 / 21089

I highly doubt that you have lower and upper values requiring 0.80 and 0.98 respectively.

Consequently, here are 2 advices:

Read the documentation for these 2 functions here:

-

detect_duplicate_genomes https://thierrygosselin.github.io/radiator/reference/detect_duplicate_genomes.html

detect_mixed_genomes https://thierrygosselin.github.io/radiator/reference/detect_mixed_genomes.html

Carefully read what's written while radiator is running. It's usually printing useful information.

— Reply to this email directly, view it on GitHub https://github.com/thierrygosselin/radiator/issues/192#issuecomment-2463878752, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALV6WJLINU4DNRVJPMUD4PLZ7RKYBAVCNFSM6AAAAABO3V6JOCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINRTHA3TQNZVGI . You are receiving this because you authored the thread.Message ID: @.***>

thierrygosselin / radiator

detect_duplicate_genomes #192

detect_duplicate_genomes https://thierrygosselin.github.io/radiator/reference/detect_duplicate_genomes.html