ICGRC Omics API Demo (using batch offline WGS7DS data, and GloerfeltTarp2023 samples for cannabinoid GWAS)

About this notebook Semi-offline mode using pre-downloaded SNPs WGS7DS, gene annotatons for GWAS of cannabinoid traits from GloerfeltTarp2023 using shared IPK samples

%matplotlib inline
%load_ext autoreload
   
import os
import requests
from IPython.display import display, Image, FileLink
#from jupyter_datatables import init_datatables_mode
#from ipydatagrid import DataGrid
from itables import init_notebook_mode
init_notebook_mode(all_interactive=True)
#init_notebook_mode(connected=True)
import itables.options as itablesopt
# display table options
#itablesopt.lengthMenu = [2, 5, 10, 20, 50, 100, 200, 500]
#itablesopt.maxBytes = 10000 , 0 to disable
#itablesopt.maxRows
#itablesopt.maxColumns

#%load_ext jupyter_require
#%requirejs d3 https://d3js.org/d3.v5.min
#init_datatables_mode()

%autoreload 2
import omics_api
from omics_api import *

# Flags to emable example
others=False
PLOT_PHEN=True
WGCNA=others
GWAS=others
MATRIXEQT=others
VERBOSE=True
MERGE=others
REQUERY_URL=False

CHECK_BE=False  # check and correct batch effect
# imputation strategy from https://doi.org/10.1038/s41598-023-30084-2
IMPUTE_M1=False # global mean
IMPUTE_M2=False # batch mean


DEBUGGNG=False

# strict setting
#maxp=1e-5

# threshold settings
maxpgwas=1e-20
maxpeqtl=1e-5
maxpwgcna=1e-5
mincorwgcna=0.7
cortopnwgcna=None
gstopnwgcna=None

top_dfgwas=[]
top_dfwgcna=[]
top_dfeqtl=[]
myunit='percent_of_dw'
#SHOW_ALL
#SHOW_DEBUG
#SHOW_ERRORONLY



if DEBUGGNG:
    setVariables(loglevel=getSetting('SHOW_DEBUG'),keep_unit=myunit)
else:
    setVariables(loglevel=getSetting('SHOW_ERRORONLY'),keep_unit=myunit)
#setVariables(loglevel=getSetting('SHOW_ERRORONLY'))

"set variables: \nkeep_unit=percent_of_dw\nr_path=Rscript\nplink_path=plink\nLOG_LEVEL=1\nunit_converter={('percent_of_dw', 'ug_per_gdw'): 10000.0, ('ug_per_gdw', 'percent_of_dw'): 0.0001}"

Multiple data sources

This demo plots dstribution of datasets from multiple sources

Avalable options for phenotypes

api_url = ["https://icgrc.info/api/user/phenotype/all?phends=GloerfeltTarp2023&with_stdunits=1"]
label_url=['GloerfeltTarp2023']
label2color=dict()
label2color['Azman2023']='red'
label2color['Booth2020']='blue'
label2color['GloerfeltTarp2023']='green'
label2color['Zager2019']='orange'
label2color['BZphenotypes']='yellow'

keep_unit='percent_of_dw'
#keep_unit='ug_per_gdw'
n_bins=10

icnt=0
dfs=[]
dfs_imputed_m2=[]
phenall=set()
keep_samples=set()
keep_phenotypes=set()
if PLOT_PHEN:
	for iurl in api_url:
		print(label_url[icnt])
		df_raw= read_url(iurl, label_url[icnt],requery=REQUERY_URL)
	
		if VERBOSE and icnt==0:
			display('in original units')
			display(drop_allnazero_rowcol(df_raw.loc[df_raw['datatype'].str.startswith('3 PHEN')]))

		(c_converted_phenunits, c_converted_phenunits_values)=convert_units_to(df_raw,to_unit='percent_of_dw')
		phenall.update(set(get_phenotypes(c_converted_phenunits_values)))
		plot_histograms(c_converted_phenunits_values, 'changed_to_' + keep_unit, label_url[icnt]) #,label2color=label2color)
	
		if VERBOSE and icnt==0:
	
			display('coverted to ' +  keep_unit)
			display(drop_allnazero_rowcol(c_converted_phenunits.loc[c_converted_phenunits['datatype'].str.startswith('3 PHEN')]))
	
			display('coverted to (values only) ' +  keep_unit)
			display(drop_allnazero_rowcol(c_converted_phenunits_values.loc[c_converted_phenunits_values['datatype'].str.startswith('3 PHEN')]))
		
		dfs.append(c_converted_phenunits_values)
        
		if IMPUTE_M2:
			(df_corrected,dummy)=check_batcheffects(c_converted_phenunits_values, label_url[icnt], TYPE_PHEN, whiten=True, batch_id='phenotype_dataset',on_missing='mean',correct_BE=False) #properties=['phenotype_dataset']) #properties=['NCBI BioProject'])
			dfs_imputed_m2.append(df_corrected)
		icnt+=1

GloerfeltTarp2023

'in original units'

	datatype	property	SAMN30166821	SAMN30166822	SAMN30166823	SAMN30166824	SAMN30166825	SAMN30166826	SAMN30166827	SAMN30166828	SAMN30166829	SAMN30166830	SAMN30166831	SAMN30166832	SAMN30166872	SAMN30166873	SAMN30166874	SAMN30166875	SAMN30166876	SAMN30166877	SAMN30166878	SAMN30166879	SAMN30166880	SAMN30166881	SAMN30166882	SAMN30166883	SAMN30166884	SAMN30166885	SAMN30166886	SAMN30166887	SAMN30166888	SAMN30166889	SAMN30166890	SAMN30166891	SAMN30166892	SAMN30166893	SAMN30166894	SAMN30166895	SAMN30166896	SAMN30166897	SAMN30166898	SAMN30166899	SAMN30166900	SAMN30166901	SAMN30166902	SAMN30166903	SAMN30166904	SAMN30166905	SAMN30166906	SAMN30166907	SAMN30166908	SAMN30166909	SAMN30166910	SAMN30166911	SAMN30166912	SAMN30166913	SAMN30166914	SAMN30166915	SAMN30166916	SAMN30166917	SAMN30166918	SAMN30166919	SAMN30166920	SAMN30166921	SAMN30166922	SAMN30166923	SAMN30166924	SAMN30166925	SAMN30166926	SAMN30166931	SAMN30166933	SAMN30166934	SAMN30166937	SAMN30166938	SAMN30166939	SAMN30166940	SAMN30166941	SAMN30166942	SAMN30166944	SAMN30166946	SAMN30166949	SAMN30166950	SAMN30166951	SAMN30166952	SAMN30166954	SAMN30166955
Loading... (need help?)

'Sample shared by phenotype datasets: SAMN30166828 : (GloerfeltTarp2023,GloerfeltTarp2023); SAMN30166829 : (GloerfeltTarp2023,GloerfeltTarp2023); SAMN30166877 : (GloerfeltTarp2023,GloerfeltTarp2023); SAMN30166878 : (GloerfeltTarp2023,GloerfeltTarp2023); '

'Sample shared by multiple stocks: SAMN30166828 : (SC1900003,SC1900065); SAMN30166829 : (SC1900003,SC1900065); SAMN30166877 : (SC1900008,SC1900059); SAMN30166878 : (SC1900008,SC1900059); '

'Samples with multiple phenotye units: SAMN30166828 : (percent_of_dw,percent_of_dw); SAMN30166829 : (percent_of_dw,percent_of_dw); SAMN30166877 : (percent_of_dw,percent_of_dw); SAMN30166878 : (percent_of_dw,percent_of_dw); '

'coverted to percent_of_dw'

	datatype	property	SAMN30166821	SAMN30166822	SAMN30166823	SAMN30166824	SAMN30166825	SAMN30166826	SAMN30166827	SAMN30166828	SAMN30166829	SAMN30166830	SAMN30166831	SAMN30166832	SAMN30166872	SAMN30166873	SAMN30166874	SAMN30166875	SAMN30166876	SAMN30166877	SAMN30166878	SAMN30166879	SAMN30166880	SAMN30166881	SAMN30166882	SAMN30166883	SAMN30166884	SAMN30166885	SAMN30166886	SAMN30166887	SAMN30166888	SAMN30166889	SAMN30166890	SAMN30166891	SAMN30166892	SAMN30166893	SAMN30166894	SAMN30166895	SAMN30166896	SAMN30166897	SAMN30166898	SAMN30166899	SAMN30166900	SAMN30166901	SAMN30166902	SAMN30166903	SAMN30166904	SAMN30166905	SAMN30166906	SAMN30166907	SAMN30166908	SAMN30166909	SAMN30166910	SAMN30166911	SAMN30166912	SAMN30166913	SAMN30166914	SAMN30166915	SAMN30166916	SAMN30166917	SAMN30166918	SAMN30166919	SAMN30166920	SAMN30166921	SAMN30166922	SAMN30166923	SAMN30166924	SAMN30166925	SAMN30166926	SAMN30166931	SAMN30166933	SAMN30166934	SAMN30166937	SAMN30166938	SAMN30166939	SAMN30166940	SAMN30166941	SAMN30166942	SAMN30166944	SAMN30166946	SAMN30166949	SAMN30166950	SAMN30166951	SAMN30166952	SAMN30166954	SAMN30166955
Loading... (need help?)

'coverted to (values only) percent_of_dw'

	datatype	property	SAMN30166821	SAMN30166822	SAMN30166823	SAMN30166824	SAMN30166825	SAMN30166826	SAMN30166827	SAMN30166828	SAMN30166829	SAMN30166830	SAMN30166831	SAMN30166832	SAMN30166872	SAMN30166873	SAMN30166874	SAMN30166875	SAMN30166876	SAMN30166877	SAMN30166878	SAMN30166879	SAMN30166880	SAMN30166881	SAMN30166882	SAMN30166883	SAMN30166884	SAMN30166885	SAMN30166886	SAMN30166887	SAMN30166888	SAMN30166889	SAMN30166890	SAMN30166891	SAMN30166892	SAMN30166893	SAMN30166894	SAMN30166895	SAMN30166896	SAMN30166897	SAMN30166898	SAMN30166899	SAMN30166900	SAMN30166901	SAMN30166902	SAMN30166903	SAMN30166904	SAMN30166905	SAMN30166906	SAMN30166907	SAMN30166908	SAMN30166909	SAMN30166910	SAMN30166911	SAMN30166912	SAMN30166913	SAMN30166914	SAMN30166915	SAMN30166916	SAMN30166917	SAMN30166918	SAMN30166919	SAMN30166920	SAMN30166921	SAMN30166922	SAMN30166923	SAMN30166924	SAMN30166925	SAMN30166926	SAMN30166931	SAMN30166933	SAMN30166934	SAMN30166937	SAMN30166938	SAMN30166939	SAMN30166940	SAMN30166941	SAMN30166942	SAMN30166944	SAMN30166946	SAMN30166949	SAMN30166950	SAMN30166951	SAMN30166952	SAMN30166954	SAMN30166955
Loading... (need help?)

if PLOT_PHEN:
    phenminmaxbin=None
    plot_histograms_multi(dfs, keep_unit,label_url,phenminmaxbin,label2color=label2color,nbins=n_bins,heatmap=True)

Path (generated 1_-3415761884218997149_phenotypes_percent_of_dw.png) doesn't exist. It may still be in the process of being generated, or you may have the incorrect path.

'file dont exists generated 1_-3415761884218997149_phenotypes_percent_of_dw.png'

Path (generated 1_-3415761884218997149_phenotypes_percent_of_dw_density.png) doesn't exist. It may still be in the process of being generated, or you may have the incorrect path.

'file dont exists generated 1_-3415761884218997149_phenotypes_percent_of_dw_density.png'

<Figure size 2000x2000 with 0 Axes>

Click here to download: GloerfeltTarp2023.phen2samplesrc-by_sample_dataset.txt

'generated GloerfeltTarp2023.phen2samplesrc-by_sample_dataset.txt'

<Figure size 640x480 with 0 Axes>

Click here to download: GloerfeltTarp2023.phensrc2sample-by_trait_dataset.txt

'generated GloerfeltTarp2023.phensrc2sample-by_trait_dataset.txt'

Click here to download: GloerfeltTarp2023.phensrc2sample-by_dataset_trait.txt

'generated GloerfeltTarp2023.phensrc2sample-by_dataset_trait.txt'

<Figure size 640x480 with 0 Axes>

Metabolite SNP Association (semi-mGWAS)

This demonstration uses traits/metabolite associaton with SNPs using plink --assoc feature. This generates the Manhattan Plot for each trait on the genomic location of genes that satify the functional annotation or accession constraints. The result is the list of top SNP-Trait pairs according to the set number or p-value cutoff.

Requirements

• R
• Python package: qqman
• plink

import datetime

DATADIR='data'
#PLINKFILE=DATADIR + '/cs10-21trichomes-all-gatkgenotype-allsnps-samn-plink-nofam'
PLINKFILE=DATADIR + '/cs10-merge-wgs7ds-21trich-plink'

GENEFILE=DATADIR+'/gene_cs10.tsv'
#pd.read_csv('https://icgrc.info/api/user/gene/list?annot=cs10',sep="\t").to_csv(GENEFILE,sep="\t",index=False)

# GENELOCFILE is derived from GENEFILE using only gene_id\tcontig\tfmin\tfmax
GENELOCFILE=DATADIR+'/cs10xm_exp.genesloc.tsv'

GWAS=True
if GWAS:
	snpds='7ds'
	phends=['GloerfeltTarp2023']
	geneslabel='all'
	ref='cs10'
	label_gwas=[]
	url_gwas=[]
	for i in range(len(phends)):
		label_gwas.append('gwas_7ds_allsnps_cs10_' + phends[i] + '_' + geneslabel)
		url_gwas.append("https://icgrc.info/api/user/phenotype/list?ref=" + ref + "&snpds=" + snpds + "&tablelimit=10000000000&limit=2000000&fmissing_lt=0.7&maf_gt=0.2&upstream=1000&phends=" + phends[i] + "&with_stdunits=1")

phenall=set()
icnt=0
df_gwas=[]
# collect available phenotypes then make selection
if GWAS:
	print('STARTED GWAS ' + str(datetime.datetime.now()))
	for iurl in url_gwas:
		ilabel=label_gwas[icnt]
		df_raw= read_url(iurl, ilabel,requery=False)
		(c_converted_phenunits, c_converted_phenunits_values)=convert_units_to(df_raw,to_unit=myunit)
		df_gwas.append(c_converted_phenunits_values)
		phenall.update(set(get_phenotypes(c_converted_phenunits_values)))

# select all traits
selectionid=list(range(1,len(phenall)+1))
selection=select_options(phenall, waitInput=False, selected=selectionid)

STARTED GWAS 2023-12-07 20:09:53.532065

'Sample shared by phenotype datasets: SAMN30166828 : (GloerfeltTarp2023,GloerfeltTarp2023); SAMN30166829 : (GloerfeltTarp2023,GloerfeltTarp2023); SAMN30166877 : (GloerfeltTarp2023,GloerfeltTarp2023); SAMN30166878 : (GloerfeltTarp2023,GloerfeltTarp2023); '

'Sample shared by multiple stocks: SAMN30166828 : (SC1900003,SC1900065); SAMN30166829 : (SC1900003,SC1900065); SAMN30166877 : (SC1900008,SC1900059); SAMN30166878 : (SC1900008,SC1900059); '

'Samples with multiple phenotye units: SAMN30166828 : (percent_of_dw,percent_of_dw); SAMN30166829 : (percent_of_dw,percent_of_dw); SAMN30166877 : (percent_of_dw,percent_of_dw); SAMN30166878 : (percent_of_dw,percent_of_dw); '

'[13] tetrahydrocannabivarinic acid'

"pre-selected ['Delta9-tetrahydrocannabinol', 'Delta9-tetrahydrocannabinolic acid', 'Total_cannabinoids', 'cannabichromene', 'cannabidiol', 'cannabidiolic acid', 'cannabidivarin', 'cannabidivarinic acid', 'cannabigerol', 'cannabigerolic acid', 'cannabinol', 'tetrahydrocannabivarin', 'tetrahydrocannabivarinic acid']"

maxpgwas=1e-15
recalc=True
pfilter=1e-4
top_dfgwas=[]
if GWAS:
	idf=0
	for df in df_gwas:
		dfgwas=do_gwas(df, label_gwas[idf],myunit,phenotypes=selection,rerunplink=False,recalc=recalc,maxp=maxpgwas,plink_file=PLINKFILE, plotgwasi=False,pfilter=pfilter) #,assocmethod='linear')
		top_dfgwas.append(dfgwas)
		idf+=1

common samples of 3 PHEN with data/cs10-merge-wgs7ds-21trich-plink = 84	{'SAMN30166877', 'SAMN30166899', 'SAMN30166923', 'SAMN30166950', 'SAMN30166890', 'SAMN30166937', 'SAMN30166919', 'SAMN30166874', 'SAMN30166880', 'SAMN30166908', 'SAMN30166822', 'SAMN30166903', 'SAMN30166885', 'SAMN30166951', 'SAMN30166916', 'SAMN30166949', 'SAMN30166934', 'SAMN30166826', 'SAMN30166905', 'SAMN30166925', 'SAMN30166889', 'SAMN30166901', 'SAMN30166893', 'SAMN30166907', 'SAMN30166823', 'SAMN30166920', 'SAMN30166897', 'SAMN30166912', 'SAMN30166895', 'SAMN30166939', 'SAMN30166904', 'SAMN30166828', 'SAMN30166876', 'SAMN30166911', 'SAMN30166931', 'SAMN30166913', 'SAMN30166933', 'SAMN30166900', 'SAMN30166825', 'SAMN30166888', 'SAMN30166952', 'SAMN30166884', 'SAMN30166954', 'SAMN30166940', 'SAMN30166906', 'SAMN30166941', 'SAMN30166946', 'SAMN30166926', 'SAMN30166883', 'SAMN30166824', 'SAMN30166942', 'SAMN30166896', 'SAMN30166910', 'SAMN30166827', 'SAMN30166909', 'SAMN30166938', 'SAMN30166922', 'SAMN30166831', 'SAMN30166821', 'SAMN30166944', 'SAMN30166898', 'SAMN30166887', 'SAMN30166882', 'SAMN30166894', 'SAMN30166886', 'SAMN30166955', 'SAMN30166873', 'SAMN30166830', 'SAMN30166891', 'SAMN30166902', 'SAMN30166915', 'SAMN30166921', 'SAMN30166917', 'SAMN30166924', 'SAMN30166879', 'SAMN30166914', 'SAMN30166872', 'SAMN30166881', 'SAMN30166878', 'SAMN30166892', 'SAMN30166832', 'SAMN30166829', 'SAMN30166875', 'SAMN30166918'}

'do_gwas_fromplink0 using gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

rm: cannot remove ‘*.qassoc.done’: No such file or directory

'GWAS cannabidivarinic_acid'

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

'prep=cannabidivarinic_acid'

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

'GWAS cannabidiolic_acid'

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

'prep=cannabidiolic_acid'

PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
80 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%26%27%28%29%30%31%32%33%34%35%36%37%38%39%40%41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%56%57%58%59%60%61%62%63%64%65%66%67%68%69%70%71%72%73%74%75%76%77%78%79%80%81%82%83%84%85%86%87%88%89%90%91%92%93%94%95%96%97%98%99% done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 0%1%2%3%4%5%6%7%8%9%10%11%12%13%14%15%16%17%18%19%20%21%22%23%24%25%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

26%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

27%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

28%29%30%31%32%33%34%35%36%37%38%

'GWAS tetrahydrocannabivarin'

39%

'keep_unit=percent_of_dw'

40%41%

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

'prep=tetrahydrocannabivarin'

42434445464748495051525354555657585960616263646566676869707172%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 27771011121314151675171819202122232476252627282930317732333435363738397840414243444579464748495051528053545556575859816061626364658266676869707172738374757677788479808182838485868587888990919293948695969798998 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 081829394959697989991098119912131415done.
16171819202122232425262728293031323334353637%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

38%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

39%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

40%41%42%43%44%45%46%47%48%49%50%

'GWAS cannabidivarin'

51%

'keep_unit=percent_of_dw'

52%53%

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

'prep=cannabidivarin'

5455565758596061626364656667686970717273747576777879808182%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
51 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 0868101112131485151617181920212286232425262728293031873233343536373839884041424344454689474849505152539054555657585960619162636465666792686970717273747593767778798081948283848586878889909591929394959697969899979 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 096done.
1011121314151617181920212223242526272829303132333435363738%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

39%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

40%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

41%42%43%44%45%46%47%48%49%50%51%52%53%54%55%

'GWAS tetrahydrocannabivarinic_acid'

56%

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

57%

'prep=tetrahydrocannabivarinic_acid'

585960616263646566676869707172737475767778798081828384858687888990919293949596%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
76 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 0949891011121314151617181920212223242526272829303132333435363738done.
3940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 1011121314151617181920%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

21%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

22%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

232425262728293031323334%

'GWAS Delta9-tetrahydrocannabinolic_acid'

35%

'keep_unit=percent_of_dw'

36%

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

'prep=Delta9-tetrahydrocannabinolic_acid'

373839404142434445464748495051525354555657585960616263646566%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
76 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 06861011121314151669171819202122237024252627282971303132333435363772383940414243444573464748495051745253545556575859756061626364656667766869707172737475777677787980818278838485868788798990919293949580969798998182838 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 08182838485969798910941195129613971498159916171819done.
2021222324252627%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

28%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

29%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

3031323334353637383940%

'GWAS Delta9-tetrahydrocannabinol'

41%

'keep_unit=percent_of_dw'

42%

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

43%

'prep=Delta9-tetrahydrocannabinol'

444546474849505152535455565758596061626364656667686970717273%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 571011121375141516171819202176222324252627287729303132333435367837383940414279434445464748498050515253545581565758596061628263646566676883697071727374847576777879808182858384858687888986909192939495969798879988899 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
...91%09193929394959691011done.
121314151617181920212223242526272829%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

30%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

31%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

3233343536373839404142%

'GWAS cannabichromene'

43%44%

'keep_unit=percent_of_dw'

45%

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

46%

'prep=cannabichromene'

4748495051525354555657585960616263646566676869707172%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 471011741213141516171819207521222324252627282976303132333435363777383940414243444578464748495051527953545556575859806061626364656681676869707172738274757677787980838182838485868487888990919293948595969798998 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 0818283949596979101195129613971498159916171819done.
20212223242526272829303132333435363738%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

39%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

4041424344454647484950%

'GWAS cannabigerolic_acid'

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

51%

'prep=cannabigerolic_acid'

525354555657585960616263646566676869707172737475767778798081%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
80 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 2878101112841314151617181920852122232425262728862930313233343536378738394041424344884546474849505189525354555657589059606162636465916667686970719272737475767778937980818283848586878889909192939495969798999 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 09192939499done.
1011121314151617181920212223242526272829303132%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

33%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

34%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

3536373839404142434445%

'GWAS cannabinol'

46%

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

47%

'prep=cannabinol'

484950515253545556575859606162636465666768697071727374757677%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 47971011121314151680171819202122238124252627282982303132333435363783383940414284434445464748495085515253545556575886596061626364656667876869707172737475887677787980818289838485868788899090919293949596919798999 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
...93%09192939598910done.
111213141516171819202122232425262728293031%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

32%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

3334353637383940414243%

'GWAS cannabigerol'

44%

'keep_unit=percent_of_dw'

45%

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

46%

'prep=cannabigerol'

47484950515253545556575859606162636465666768697071727374%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
82 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 67101112131476151617181920212277232425262728293078313233343536377938394041424380444546474849505181525354555657825859606162636483656667686970847172737475767778798580818283848586878688899091929394959687979899888 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 091919393959697989991011121314done.
151617181920212223242526272829%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

30%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

31%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

32333435363738394041%

'GWAS cannabidiol'

42%

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

4344%

'prep=cannabidiol'

454647484950515253545556575859606162636465666768697071727374%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 4710111276131415161718192077212223242526272878293031323334793536373839404180424344454647488149505152535455825657585960616283636465666784686970717273747576857778798081828384868586878889909192879394959697989988899 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 09192939395969798910111213done.
14151617181920212223242526%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

27%

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

28293031323334353637%

'GWAS Total_cannabinoids'

38%

'keep_unit=percent_of_dw'

'plinklabel=gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all'

39%

'prep=Total_cannabinoids'

4041424344454647484950515253545556575859606162636465666768%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 261070111213141516711718192021222324722526272829303132733334353637383974404142434445464775484950515253545576565758596061626377646566676869707178727374757677797879808182838480858687888990919281939495969798829983848 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 0818283849596979899910961197129813991415161718done.
19202122%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

' output rediretion in command: plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

23%

'plink --bfile data/cs10-merge-wgs7ds-21trich-plink  --assoc counts --pheno  phen_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt --out assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts --pfilter 0.0001 --allow-extra-chr --allow-no-sex && touch  assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.done &> assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc.out  &'

2425262728293031323334%

'waiting for gwas runs'

35%

'0 mins. 11/13 done.'

36373839404142434445464748495051525354555657585960616263%PLINK v1.90b6.12 64-bit (28 Oct 2019)          www.cog-genomics.org/plink/1.9/
(C) 2005-2019 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.log.
Options in effect:
  --allow-extra-chr
  --allow-no-sex
  --assoc counts
  --bfile data/cs10-merge-wgs7ds-21trich-plink
  --out assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts
  --pfilter 0.0001
  --pheno phen_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.txt

332375 MB RAM detected; reserving 166187 MB for main workspace.
490142 variants loaded from .bim file.
413 people (0 males, 0 females, 413 ambiguous) loaded from .fam.
Ambiguous sex IDs written to
assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.nosex
.
84 phenotype values present after --pheno.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 413 founders and 0 nonfounders present.
Calculating allele frequencies... 269610111213141516661718192021222367242526272829303132683334353637383940694142434445464748704950515253547155565758596061627263646566676869707371727374757674777879808182838485758687888990919293769495969798997 done.
Total genotyping rate is 0.47454.
490142 variants and 413 people pass filters and QC.
Phenotype data is quantitative.
Writing QT --assoc report to
assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc
... 071728381858387888981088118912901391149215931694179518961997209821992223242526done.
27282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899done.

'0.5 mins. 13/13 done.'

'All gwas plink done'

"qqman_plots=['cannabidivarinic_acid', 'cannabidiolic_acid', 'tetrahydrocannabivarin', 'cannabidivarin', 'tetrahydrocannabivarinic_acid', 'Delta9-tetrahydrocannabinolic_acid', 'Delta9-tetrahydrocannabinol', 'cannabichromene', 'cannabigerolic_acid', 'cannabinol', 'cannabigerol', 'cannabidiol', 'Total_cannabinoids']"

'image generated gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all_gwasmp_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.png'

Click here to download: gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all_gwasmp_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.png

'Added file assoc_Delta9-tetrahydrocannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_Delta9-tetrahydrocannabinolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_Total_cannabinoids_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabichromene_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabidiol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabidiolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabidivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabidivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabigerol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabigerolic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_cannabinol_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_tetrahydrocannabivarin_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

'Added file assoc_tetrahydrocannabivarinic_acid_percent_of_dw_gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.qassoc.counts.qassoc'

top snp-trait gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.gwas.top.tsv

Click here to download: gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.gwas.top.tsv

trait	CHR	snps	BP	NMISS	BETA	SE	R2	T	pvalue
Loading... (need help?)

display(top_dfgwas[0])

	trait	CHR	snps	BP	NMISS	BETA	SE	R2	T	pvalue
Loading... (need help?)

df_genes=pd.read_csv(GENEFILE,sep="\t")

df_snpgenes=do_snpgenes(top_dfgwas[0], df_genes,label_gwas[0]+'.tsv',snpcolumn='snps',other_columns=['trait','pvalue'],requery=True,how='left')
display(df_snpgenes)

"getting genes for snps (332, 12)  ['trait', 'CHR', 'snps', 'BP', 'NMISS', 'BETA', 'SE', 'R2', 'T', 'pvalue', 'contig', 'pos']"

"getting gene data (33639, 9)  ['gene', 'contig', 'fmin', 'fmax', 'strand', 'locus', 'gb_keyword', 'go_term', 'interpro_value']"

"df_snpgne (385, 21) ['trait', 'CHR', 'snps', 'BP', 'NMISS', 'BETA', 'SE', 'R2', 'T', 'pvalue', 'contig', 'pos', 'gene', 'contig', 'fmin', 'fmax', 'strand', 'locus', 'gb_keyword', 'go_term', 'interpro_value']"

Click here to download: gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.tsv

'generated gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all.tsv'

trait	pvalue	snps	snpgenes	locus	note	goterm	iprterm
Loading... (need help?)

tgzdownloads('gwas_7ds_allsnps_cs10_GloerfeltTarp2023_all', txt=True, img=True)