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lvclark / polyRAD

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝
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"ExpectedHindHe" not found while all other functions of polyRAD work #14

Closed CornilleAmandine closed 3 years ago

CornilleAmandine commented 3 years ago

Hello I have followed the tutorial and succeeded in running the command lines but I have got a error message for this step:

"ExpectedHindHe(mydata, inbreeding = 0.94, ploidy = 2, reps = 10) Error in ExpectedHindHe(mydata, inbreeding = 0.94, ploidy = 2, reps = 10) : impossible to find the function"

I have tried several times on several Rstudio. Could you please help me ? Thanks! my best Amandine

lvclark commented 3 years ago

The ExpectedHindHe function is not on CRAN yet. You'll have to install from GitHub with devtools::install_github("lvclark/polyRAD").

CornilleAmandine commented 3 years ago

Super thanks a lot!! But I have installed as you said and I still have the same error.... Do you know what could be the origin? Thanks!! my best, Amandine

On Wed, 30 Dec 2020 at 20:18, Lindsay Clark notifications@github.com wrote:

The ExpectedHindHe function is not on CRAN yet. You'll have to install from GitHub with devtools::install_github("lvclark/polyRAD").

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-752729789, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYSW5P4MQGT42224LZTSXN4JHANCNFSM4VOSNENQ .

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Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

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lvclark commented 3 years ago

Are you certain it installed without error? Run sessionInfo() to make sure you have polyRAD 1.3 and not 1.2.

CornilleAmandine commented 3 years ago

I have run

polyRAD_1.3 is on :

sessionInfo()R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /usr/local/public/R-4.0.2/lib64/R/lib/libRblas.so LAPACK: /usr/local/public/R-4.0.2/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 [5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] nnet_7.3-14 abc.data_1.0 reshape2_1.4.4 forcats_0.5.0 [5] stringr_1.4.0 purrr_0.3.4 readr_1.4.0 tidyr_1.1.2 [9] tibble_3.0.4 ggplot2_3.3.2 tidyverse_1.3.0 dplyr_1.0.2 [13] abcrf_1.8.1 vcfR_1.12.0 VariantAnnotation_1.34.0 Rsamtools_2.4.0 [17] Biostrings_2.56.0 XVector_0.28.0 SummarizedExperiment_1.18.2 DelayedArray_0.14.1 [21] matrixStats_0.57.0 Biobase_2.48.0 GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 [25] IRanges_2.22.2 S4Vectors_0.26.1 BiocGenerics_0.34.0 polyRAD_1.3

loaded via a namespace (and not attached): [1] colorspace_2.0-0 ellipsis_0.3.1 rprojroot_2.0.2 fs_1.5.0 [5] rstudioapi_0.13 farver_2.0.3 remotes_2.2.0 bit64_4.0.5 [9] AnnotationDbi_1.50.3 fansi_0.4.1 lubridate_1.7.9.2 ranger_0.12.1 [13] xml2_1.3.2 codetools_0.2-18 splines_4.0.2 doParallel_1.0.16 [17] pkgload_1.1.0 jsonlite_1.7.2 broom_0.7.3 cluster_2.1.0 [21] dbplyr_2.0.0 compiler_4.0.2 httr_1.4.2 backports_1.2.1 [25] assertthat_0.2.1 Matrix_1.3-0 cli_2.2.0 prettyunits_1.1.1 [29] tools_4.0.2 gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.3 [33] rappdirs_0.3.1 fastmatch_1.1-0 Rcpp_1.0.5 cellranger_1.1.0 [37] vctrs_0.3.5 ape_5.4-1 nlme_3.1-151 rtracklayer_1.48.0 [41] iterators_1.0.13 pinfsc50_1.2.0 ps_1.5.0 rvest_0.3.6 [45] testthat_3.0.1 lifecycle_0.2.0 devtools_2.3.2 XML_3.99-0.5 [49] zlibbioc_1.34.0 MASS_7.3-53 scales_1.1.1 BSgenome_1.56.0 [53] hms_0.5.3 curl_4.3 memoise_1.1.0 biomaRt_2.44.4 [57] stringi_1.5.3 RSQLite_2.2.1 desc_1.2.0 foreach_1.5.1 [61] permute_0.9-5 GenomicFeatures_1.40.1 pkgbuild_1.2.0 BiocParallel_1.22.0 [65] rlang_0.4.9 pkgconfig_2.0.3 bitops_1.0-6 lattice_0.20-41 [69] labeling_0.4.2 GenomicAlignments_1.24.0 bit_4.0.4 processx_3.4.5 [73] tidyselect_1.1.0 plyr_1.8.6 magrittr_2.0.1 R6_2.5.0 [77] generics_0.1.0 DBI_1.1.0 pillar_1.4.7 haven_2.3.1 [81] withr_2.3.0 mgcv_1.8-33 RCurl_1.98-1.2 modelr_0.1.8 [85] crayon_1.3.4 BiocFileCache_1.12.1 progress_1.2.2 usethis_2.0.0 [89] readxl_1.3.1 grid_4.0.2 blob_1.2.1 callr_3.5.1 [93] vegan_2.5-7 reprex_0.3.0 digest_0.6.27 openssl_1.4.3 [97] munsell_0.5.0 viridisLite_0.3.0 sessioninfo_1.1.1 askpass_1.1

On Wed, 30 Dec 2020 at 21:12, Lindsay Clark notifications@github.com wrote:

Are you certain it installed without error? Run sessionInfo() to make sure you have polyRAD 1.3 and not 1.2.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-752744146, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYRWH3ZHPC4UBLI4W7LSXOCSRANCNFSM4VOSNENQ .

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

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lvclark commented 3 years ago

I just did a fresh install of R 4.0.3 on my home computer and installed polyRAD from GitHub, and could not reproduce your problem.

CornilleAmandine commented 3 years ago

Thanks a lot! I am going to try again, I don't why it still doesn't work. my best, Amandine

On Mon, 4 Jan 2021 at 15:16, Lindsay Clark notifications@github.com wrote:

I just did a fresh install of R 4.0.3 on my home computer and installed polyRAD from GitHub, and could not reproduce your problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-753998983, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYRYLQEGKYXTW3Y262LSYHESTANCNFSM4VOSNENQ .

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Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

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lvclark commented 3 years ago

I've put version 1.3 on CRAN now, so you can install from there if GitHub isn't working for you.

CornilleAmandine commented 3 years ago

Super thanks a lot I am going to try now. my best, Amandine

On Wed, 6 Jan 2021 at 17:29, Lindsay Clark notifications@github.com wrote:

I've put version 1.3 on CRAN now, so you can install from there if GitHub isn't working for you.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-755408326, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYUTA3UIWPIVDGHY4NDSYSFYDANCNFSM4VOSNENQ .

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

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CornilleAmandine commented 3 years ago

It works now !!! Thanks a lot!!!! my best, Amandine

On Wed, 6 Jan 2021 at 17:30, Amandine Cornille amandine.cornille@gmail.com wrote:

Super thanks a lot I am going to try now. my best, Amandine

On Wed, 6 Jan 2021 at 17:29, Lindsay Clark notifications@github.com wrote:

I've put version 1.3 on CRAN now, so you can install from there if GitHub isn't working for you.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-755408326, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYUTA3UIWPIVDGHY4NDSYSFYDANCNFSM4VOSNENQ .

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

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CornilleAmandine commented 3 years ago

Hi Lindsay, I don't know if it is normal, but the first rep is stuck like that since 6 hours (see attached a screenshot)... My data is big, 160 genomes with 30M SNPs... Thanks!! my best, Amandine

On Wed, 6 Jan 2021 at 23:44, Amandine Cornille amandine.cornille@gmail.com wrote:

It works now !!! Thanks a lot!!!! my best, Amandine

On Wed, 6 Jan 2021 at 17:30, Amandine Cornille < amandine.cornille@gmail.com> wrote:

Super thanks a lot I am going to try now. my best, Amandine

On Wed, 6 Jan 2021 at 17:29, Lindsay Clark notifications@github.com wrote:

I've put version 1.3 on CRAN now, so you can install from there if GitHub isn't working for you.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-755408326, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYUTA3UIWPIVDGHY4NDSYSFYDANCNFSM4VOSNENQ .

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

Tout message que j’envoie en dehors des heures de travail réglementaires ne nécessite aucune réponse immédiate

lvclark commented 3 years ago

Hi Amandine,

I didn't get the screenshot since the email came through GitHub. However, 30M SNPs is far more than I have ever tried to process at once with polyRAD, so I am not surprised that it would take so long. One thing you can do is split it into smaller datasets and then do genotype calling on them in parallel on a computing cluster or cloud computing. One option for this is to import the whole dataset, then use SplitByChromosome to save it into a series of individual R workspaces. Another option is to subset the data before or during import; see the final example on the VCF2RADdata help page.

Best, Lindsay

CornilleAmandine commented 3 years ago

Okdoki! Thanks a lot!!

On Thu, 7 Jan 2021 at 16:07, Lindsay Clark notifications@github.com wrote:

Hi Amandine,

I didn't get the screenshot since the email came through GitHub. However, 30M SNPs is far more than I have ever tried to process at once with polyRAD, so I am not surprised that it would take so long. One thing you can do is split it into smaller datasets and then do genotype calling on them in parallel on a computing cluster or cloud computing. One option for this is to import the whole dataset, then use SplitByChromosome to save it into a series of individual R workspaces. Another option is to subset the data before or during import; see the final example on the VCF2RADdata help page.

Best, Lindsay

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lvclark/polyRAD/issues/14#issuecomment-756172606, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQO7LYRLB4L7OBIS7RBYVZ3SYXEZVANCNFSM4VOSNENQ .

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Chargée de Recherche CNRS Génétique Quantitative et Évolution - Le Moulon Université Paris-Saclay - INRAE - CNRS - AgroParisTech Ferme du Moulon 91190 Gif-sur-Yvette France phone : +33 6 72 44 85 55 phone : +33 1 69 33 23 52

Twitter: @CornilleAmand Google Scholar profile : https://scholar.google.com/citations?user=EqIE2h8AAAAJ&hl=fr Personal page : http://moulon.inrae.fr/personnes/acornille/ Group page: http://moulon.inrae.fr/en/equipes/atip/

On the ESEB-STN network on the ecological genomics of coevolution: https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/ecological-genomics-of-coevolutionary-interactions/ On the wild apple orchard project: https://www.ideev.universite-paris-saclay.fr/en/the-orchard https://www.ideev.universite-paris-saclay.fr/index.php?option=com_content&view=article&id=321:orchard&catid=80&lang=en&Itemid=297

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