Last class you submitted jobs to the cluster. Now it is time to log back in to check on your analyses.
Log in:
ssh yourusername@scc1.bu.eduNavigate to your project folder. Probably something like this:
cd /project/ct-shbioinf/yourusername/biodiversity
ls -lh
ls -lh figuresAre there new files in the main project folder and in the figures folder?
Files that start as “SDM_ENMeval.” contain information about the analyses you submitted last time.
In the cat command below remove the {} and replace with the job ID number at the end of your file.
cat SDM_ENMeval.o{SERIES OF NUMBERS}Does it look like your analysis finished properly?
If you have image files in the figures folder (ending in ‘.png’) the next step will be to copy those somewhere that they can be viewed. For this, use git commands: (enter your GitHub username and password when prompted)
git add figures
git commit -m 'update figures from sdm1.R'
git pushIF all has gone correctly until now it is time to update the analysis script to both be more flexible and to build more robust models with ENMeval through higher level model testing.
Download the new SDM analysis
This script:
Accepts a species name from the command line when called by the submit script
Performs ENMeval with more model feature classes and more RMvalues
Performs ‘block’ resampling for model testing rather than random kfolds. (block tests geographic transferability more)
Predicts models under two future climate scenarios (2.6 and 8.5 emissions scenarios) under the CCSM4 model. more here
Saves figure images for modern and two future scenarios
Saves raster objects to data files in the ‘data/’ folder.
Download the new submit script.
EDIT THE TAXON NAME ON THE RScript LINE
Updates to the submit script include:
Memory management to request 16GB of memory per CPU core. This ensures that the queue puts these jobs on larger compute nodes.
Accepting species name as argment when calling RScript
Copy the two new scripts via git to the cluster and run as:
qsub submit_sdm2Create 10 submit scripts using the new SDM script for different species in the Stonehill Biodiversity iNaturalist project. Sign up for your species on the Slack #general channel.
Species to choose from:
library(rinat)
library(stringr)
projdata = get_inat_obs_project("stonehill-biodiversity",
type = "observations", raw=F)## 1035 Records
## 0-200-400-600-800-1000-1200tNames = unique(projdata$taxon.name) %>% str_extract("[A-z]+\\s[A-z]+")
binomials = na.omit(tNames) %>% sort()
#get full taxonomy
library(taxonomizr)
taxaNodes<-read.nodes.sql("/usr/share/data/taxonomizr/nodes.dmp")## nameNode.sqlite already contains table nodes. Delete file or set overwrite=TRUE to reloadtaxaNames<-read.names.sql("/usr/share/data/taxonomizr/names.dmp")## nameNode.sqlite already contains table names. Delete file or set overwrite=TRUE to reloadids<-getId(binomials, sqlFile=taxaNodes)
#taxlist displays the taxonomic names from each ID #
taxlist=getTaxonomy(ids, taxaNodes, taxaNames)
print(taxlist[order(taxlist[,'phylum']),c('phylum', 'species')])## phylum species
## 1655836 "Arthropoda" "Acanthocephala terminalis"
## 691622 "Arthropoda" "Acrolophus popeanella"
## 688356 "Arthropoda" "Acronicta americana"
## 115084 "Arthropoda" "Agapostemon virescens"
## 1088606 "Arthropoda" "Ammophila pictipennis"
## 214820 "Arthropoda" "Anax junius"
## 7120 "Arthropoda" "Antheraea polyphemus"
## 7460 "Arthropoda" "Apis mellifera"
## 663471 "Arthropoda" "Argia fumipennis"
## 1081945 "Arthropoda" "Basiaeschna janata"
## 132113 "Arthropoda" "Bombus impatiens"
## 240869 "Arthropoda" "Bombylius major"
## 1642215 "Arthropoda" "Callophrys niphon"
## 82598 "Arthropoda" "Campaea perlata"
## 42299 "Arthropoda" "Celastrina ladon"
## 37250 "Arthropoda" "Chortophaga viridifasciata"
## 37250 "Arthropoda" "Chortophaga viridifasciata"
## 572826 "Arthropoda" "Chrysoteuchia topiarius"
## 176362 "Arthropoda" "Cicindela sexguttata"
## 189344 "Arthropoda" "Cordulegaster maculata"
## 128943 "Arthropoda" "Cynomya cadaverina"
## 13037 "Arthropoda" "Danaus plexippus"
## 34621 "Arthropoda" "Dermacentor variabilis"
## 94999 "Arthropoda" "Ellychnia corrusca"
## 721901 "Arthropoda" "Elophila icciusalis"
## 79488 "Arthropoda" "Enallagma traviatum"
## 216861 "Arthropoda" "Ennomos subsignaria"
## 687090 "Arthropoda" "Epicallima argenticinctella"
## 70384 "Arthropoda" "Erythemis simplicicollis"
## 688625 "Arthropoda" "Glaphyria glaphyralis"
## 236401 "Arthropoda" "Graphocephala coccinea"
## 77576 "Arthropoda" "Halictus ligatus"
## 286706 "Arthropoda" "Halyomorpha halys"
## 115357 "Arthropoda" "Harmonia axyridis"
## 40095 "Arthropoda" "Hylephila phyleus"
## 214174 "Arthropoda" "Hypoprepia fucosa"
## 6945 "Arthropoda" "Ixodes scapularis"
## 39708 "Arthropoda" "Junonia coenia"
## 500506 "Arthropoda" "Leiobunum vittatum"
## 236887 "Arthropoda" "Leptoglossus occidentalis"
## 273679 "Arthropoda" "Lestes congener"
## 70392 "Arthropoda" "Libellula incesta"
## 124411 "Arthropoda" "Limenitis arthemis"
## 124411 "Arthropoda" "Limenitis arthemis"
## 282391 "Arthropoda" "Lycaena phlaeas"
## 683892 "Arthropoda" "Lygaeus kalmii"
## 13123 "Arthropoda" "Lymantria dispar"
## 214180 "Arthropoda" "Macaria pustularia"
## 1725467 "Arthropoda" "Machimus sadyates"
## 7507 "Arthropoda" "Mantis religiosa"
## 103640 "Arthropoda" "Melanoplus femurrubrum"
## 270817 "Arthropoda" "Microcentrum rhombifolium"
## 687109 "Arthropoda" "Microcrambus elegans"
## 642705 "Arthropoda" "Neoconocephalus retusus"
## 187181 "Arthropoda" "Neriene radiata"
## 171592 "Arthropoda" "Nymphalis antiopa"
## 1847369 "Arthropoda" "Olethreutes osmundana"
## 96861 "Arthropoda" "Oniscus asellus"
## 104452 "Arthropoda" "Operophtera brumata"
## 1592237 "Arthropoda" "Pantala hymenaea"
## 45779 "Arthropoda" "Papilio glaucus"
## 7146 "Arthropoda" "Papilio polyxenes"
## 721902 "Arthropoda" "Parapediasia teterrellus"
## 304576 "Arthropoda" "Phidippus audax"
## 115148 "Arthropoda" "Philoscia muscorum"
## 1425322 "Arthropoda" "Phyllopalpus pulchellus"
## 64459 "Arthropoda" "Pieris rapae"
## 763388 "Arthropoda" "Platycentropus radiatus"
## 153429 "Arthropoda" "Platycryptus undatus"
## 1666682 "Arthropoda" "Pococera asperatella"
## 30207 "Arthropoda" "Polistes fuscatus"
## 691597 "Arthropoda" "Polites peckius"
## 691673 "Arthropoda" "Prolimacodes badia"
## 687487 "Arthropoda" "Psaphida rolandi"
## 688492 "Arthropoda" "Pyreferra hesperidago"
## 214332 "Arthropoda" "Pyrrharctia isabella"
## 38060 "Arthropoda" "Schinia arcigera"
## 132600 "Arthropoda" "Scoliopteryx libatrix"
## 522708 "Arthropoda" "Sphinx kalmiae"
## 13698 "Arthropoda" "Strymon melinus"
## 451115 "Arthropoda" "Sympetrum internum"
## 400502 "Arthropoda" "Sympetrum vicinum"
## 406589 "Arthropoda" "Tenodera sinensis"
## 218773 "Arthropoda" "Thymelicus lineola"
## 1699004 "Arthropoda" "Tigrosa aspersa"
## 1890936 "Arthropoda" "Tipula furca"
## 312236 "Arthropoda" "Tipula oleracea"
## 1690403 "Arthropoda" "Tipula ultima"
## 1720764 "Arthropoda" "Trachelipus rathkii"
## 688605 "Arthropoda" "Udea rubigalis"
## 42275 "Arthropoda" "Vanessa atalanta"
## 171605 "Arthropoda" "Vanessa cardui"
## 1892751 "Arthropoda" "Xenox tigrinus"
## 28638 "Arthropoda" "Xylocopa virginica"
## 172615 "Ascomycota" "Flavoparmelia caperata"
## 1004486 "Basidiomycota" "Amanita flavorubens"
## 67710 "Basidiomycota" "Amanita gemmata"
## 41956 "Basidiomycota" "Amanita muscaria"
## 41956 "Basidiomycota" "Amanita muscaria"
## 71717 "Basidiomycota" "Coprinellus micaceus"
## 71694 "Basidiomycota" "Coprinopsis atramentaria"
## 181915 "Basidiomycota" "Lycoperdon marginatum"
## 355849 "Basidiomycota" "Phallus ravenelii"
## 40452 "Basidiomycota" "Trichaptum abietinum"
## 39638 "Chordata" "Agelaius phoeniceus"
## 8833 "Chordata" "Aix sponsa"
## 8839 "Chordata" "Anas platyrhynchos"
## 8389 "Chordata" "Anaxyrus americanus"
## 110620 "Chordata" "Ardea alba"
## 56072 "Chordata" "Ardea herodias"
## 8853 "Chordata" "Branta canadensis"
## 56263 "Chordata" "Buteo jamaicensis"
## 8475 "Chordata" "Chelydra serpentina"
## 8479 "Chordata" "Chrysemys picta"
## 8479 "Chordata" "Chrysemys picta"
## 8869 "Chordata" "Cygnus olor"
## 184451 "Chordata" "Esox niger"
## 134758 "Chordata" "Eurycea bislineata"
## 258930 "Chordata" "Lasiurus borealis"
## 270329 "Chordata" "Lepomis gibbosus"
## 13106 "Chordata" "Lepomis macrochirus"
## 279951 "Chordata" "Lophodytes cucullatus"
## 9995 "Chordata" "Marmota monax"
## 9103 "Chordata" "Meleagris gallopavo"
## 30548 "Chordata" "Mephitis mephitis"
## 27706 "Chordata" "Micropterus salmoides"
## 10058 "Chordata" "Microtus pennsylvanicus"
## 84834 "Chordata" "Molothrus ater"
## 9874 "Chordata" "Odocoileus virginianus"
## 48849 "Chordata" "Passer domesticus"
## 10041 "Chordata" "Peromyscus leucopus"
## 141976 "Chordata" "Plethodon cinereus"
## 48891 "Chordata" "Poecile atricapillus"
## 8182 "Chordata" "Pomoxis nigromaculatus"
## 189920 "Chordata" "Pseudacris crucifer"
## 30640 "Chordata" "Sciurus carolinensis"
## 40210 "Chordata" "Spizella passerina"
## 9988 "Chordata" "Sylvilagus floridanus"
## 45474 "Chordata" "Tamias striatus"
## 35019 "Chordata" "Thamnophis sirtalis"
## 35019 "Chordata" "Thamnophis sirtalis"
## 9188 "Chordata" "Turdus migratorius"
## 9627 "Chordata" "Vulpes vulpes"
## 47245 "Chordata" "Zenaida macroura"
## 28835 "Mollusca" "Cepaea nemoralis"
## 4025 "Streptophyta" "Acer platanoides"
## 45314 "Streptophyta" "Acer rubrum"
## 13329 "Streptophyta" "Achillea millefolium"
## 669136 "Streptophyta" "Artemisia pontica"
## 4220 "Streptophyta" "Artemisia vulgaris"
## 48545 "Streptophyta" "Asclepias syriaca"
## 50459 "Streptophyta" "Barbarea vulgaris"
## 121720 "Streptophyta" "Berberis thunbergii"
## 228874 "Streptophyta" "Berteroa incana"
## 3508 "Streptophyta" "Betula nigra"
## 3507 "Streptophyta" "Betula papyrifera"
## 216989 "Streptophyta" "Betula populifolia"
## 47519 "Streptophyta" "Calystegia sepium"
## 12991 "Streptophyta" "Carpinus caroliniana"
## 60418 "Streptophyta" "Carya ovata"
## 85181 "Streptophyta" "Celastrus orbiculatus"
## 43461 "Streptophyta" "Cephalanthus occidentalis"
## 262425 "Streptophyta" "Chelone glabra"
## 3559 "Streptophyta" "Chenopodium album"
## 93813 "Streptophyta" "Chimaphila maculata"
## 13427 "Streptophyta" "Cichorium intybus"
## 4744 "Streptophyta" "Commelina communis"
## 29742 "Streptophyta" "Comptonia peregrina"
## 4284 "Streptophyta" "Cornus racemosa"
## 4039 "Streptophyta" "Daucus carota"
## 62333 "Streptophyta" "Dendrolycopodium obscurum"
## 32088 "Streptophyta" "Dennstaedtia punctilobula"
## 645197 "Streptophyta" "Dianthus armeria"
## 13841 "Streptophyta" "Diphasiastrum digitatum"
## 32114 "Streptophyta" "Dryopteris cristata"
## 207841 "Streptophyta" "Dryopteris intermedia"
## 449839 "Streptophyta" "Dryopteris marginalis"
## 53751 "Streptophyta" "Echinacea purpurea"
## 43233 "Streptophyta" "Elaeagnus umbellata"
## 4307 "Streptophyta" "Euonymus alatus"
## 60423 "Streptophyta" "Fagus grandifolia"
## 106677 "Streptophyta" "Frangula alnus"
## 38872 "Streptophyta" "Fraxinus americana"
## 56036 "Streptophyta" "Fraxinus pennsylvanica"
## 28509 "Streptophyta" "Glechoma hederacea"
## 54874 "Streptophyta" "Gleditsia triacanthos"
## 4397 "Streptophyta" "Hamamelis virginiana"
## 185559 "Streptophyta" "Ilex verticillata"
## 55378 "Streptophyta" "Impatiens capensis"
## 16719 "Streptophyta" "Juglans nigra"
## 39584 "Streptophyta" "Juniperus virginiana"
## 45902 "Streptophyta" "Kalmia latifolia"
## 43171 "Streptophyta" "Linaria vulgaris"
## 4400 "Streptophyta" "Liquidambar styraciflua"
## 3415 "Streptophyta" "Liriodendron tulipifera"
## 76578 "Streptophyta" "Lobelia cardinalis"
## 13129 "Streptophyta" "Lythrum salicaria"
## 416391 "Streptophyta" "Maianthemum canadense"
## 50148 "Streptophyta" "Monotropa uniflora"
## 3498 "Streptophyta" "Morus alba"
## 4416 "Streptophyta" "Nuphar variegata"
## 4419 "Streptophyta" "Nymphaea odorata"
## 3942 "Streptophyta" "Oenothera biennis"
## 3281 "Streptophyta" "Onoclea sensibilis"
## 3284 "Streptophyta" "Osmundastrum cinnamomeum"
## 213833 "Streptophyta" "Oxalis stricta"
## 3607 "Streptophyta" "Parthenocissus quinquefolia"
## 487997 "Streptophyta" "Persicaria hydropiperoides"
## 137696 "Streptophyta" "Persicaria sagittata"
## 3527 "Streptophyta" "Phytolacca americana"
## 3348 "Streptophyta" "Pinus strobus"
## 39414 "Streptophyta" "Plantago lanceolata"
## 4403 "Streptophyta" "Platanus occidentalis"
## 3693 "Streptophyta" "Populus tremuloides"
## 3513 "Streptophyta" "Quercus alba"
## 3512 "Streptophyta" "Quercus rubra"
## 500452 "Streptophyta" "Quercus velutina"
## 488216 "Streptophyta" "Reynoutria japonica"
## 298662 "Streptophyta" "Rhus glabra"
## 255348 "Streptophyta" "Rhus typhina"
## 35938 "Streptophyta" "Robinia pseudoacacia"
## 74647 "Streptophyta" "Rosa multiflora"
## 46945 "Streptophyta" "Sassafras albidum"
## 212686 "Streptophyta" "Scorzoneroides autumnalis"
## 53861 "Streptophyta" "Securigera varia"
## 37657 "Streptophyta" "Silene latifolia"
## 299602 "Streptophyta" "Smilax herbacea"
## 45834 "Streptophyta" "Solanum dulcamara"
## 471148 "Streptophyta" "Solidago caesia"
## 511490 "Streptophyta" "Solidago rugosa"
## 526933 "Streptophyta" "Symphyotrichum lateriflorum"
## 556915 "Streptophyta" "Symphyotrichum racemosum"
## 128002 "Streptophyta" "Tanacetum vulgare"
## 50225 "Streptophyta" "Taraxacum officinale"
## 29618 "Streptophyta" "Thelypteris palustris"
## 66669 "Streptophyta" "Tilia americana"
## 43853 "Streptophyta" "Toxicodendron radicans"
## 57577 "Streptophyta" "Trifolium pratense"
## 3899 "Streptophyta" "Trifolium repens"
## 66173 "Streptophyta" "Tsuga canadensis"
## 4733 "Streptophyta" "Typha latifolia"
## 472369 "Streptophyta" "Vaccinium angustifolium"
## 69266 "Streptophyta" "Vaccinium corymbosum"
## 39388 "Streptophyta" "Verbascum thapsus"
## 4205 "Streptophyta" "Viburnum acerifolium"
## 60093 "Streptophyta" "Vinca minor"
## 55960 "Streptophyta" "Yucca filamentosa"
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