In [1]:

    

import sys; print(sys.version)
import os
import glob
import subprocess
import multiprocessing

import numpy as np; print('numpy', np.__version__)
import pandas as pd; print('pandas',pd.__version__)
import allel; print('allel', allel.__version__)
import zarr; print('zarr', zarr.__version__)

from IPython.display import display, HTML


    

    




3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38) 
[GCC 7.3.0]
numpy 1.16.2
pandas 0.24.1
allel 1.2.0
zarr 2.2.0

In [2]:

    

INFN = '/home/travc/proj/100Acol/100Acol_pflit.vcf.gz'
OUTFN = INFN+'.zarr'

# Below will probably not need to be changed
FIELDS = [
    'samples',
    'variants/CHROM',
    'variants/POS',
    'variants/REF',
    'variants/ALT',
    'variants/QUAL',
    'variants/TYPE',
#     'variants/NUMALT',
    'variants/numalt',
    'variants/AN',
    'variants/AC',
    'variants/AF',
    'variants/DP',
#     'variants/ANN',
    'calldata/DP',
    'calldata/GT',
         ]
EXCLUDE_FIELDS = None

# # ALTERNATIVE:
# # All the fields from the VCF (overkill leads to very big archive)
# FIELDS = '*' 
# EXCLUDE_FIELDS = ['variants/NUMALT'] # allel will calculate a numalt (lower case) on the fly

TABIX_EXEC = 'tabix'

print("Using tabix executable '{}' {} '{}'\n{}".format(TABIX_EXEC, u"\u2192", 
        subprocess.check_output(['which', 'tabix']).decode('utf-8').rstrip(),
        subprocess.check_output([TABIX_EXEC, '--version']).decode('utf-8')))


    

    




Using tabix executable 'tabix' → '/usr/local/bin/tabix'
tabix (htslib) 1.9
Copyright (C) 2018 Genome Research Ltd.

In [3]:

    

# get list of chroms
chroms = subprocess.check_output([TABIX_EXEC,'-l',INFN], 
                                 universal_newlines=True).strip().split('\n')
display(chroms)


    

    






['2L', '3L', 'X', '3R', '2R', 'UNKN', 'Y_unplaced', 'Mt']

In [4]:

    

# Create zarr archive with a group for each chrom
num_procs = multiprocessing.cpu_count()-1

transformers = None
if 'ANN' in FIELDS:
    transformers=allel.ANNTransformer()

def vcf_to_zarr_func(ch):
    allel.vcf_to_zarr(INFN, OUTFN,
                      region=ch,
                      group=ch,
                      log=sys.stderr,
                      fields=FIELDS,
                      exclude_fields=EXCLUDE_FIELDS,
                      tabix=TABIX_EXEC,
                      transformers=transformers)
    
with multiprocessing.Pool(num_procs) as pool:
    pool.map(vcf_to_zarr_func, chroms, chunksize=1)


    

    




[vcf_to_zarr] 953 rows in 0.09s; chunk in 0.09s (10117 rows/s)
[vcf_to_zarr] all done (6323 rows/s)
[vcf_to_zarr] 5983 rows in 0.18s; chunk in 0.18s (33430 rows/s)
[vcf_to_zarr] all done (25993 rows/s)
[vcf_to_zarr] 65536 rows in 1.74s; chunk in 1.74s (37738 rows/s); X:581702
[vcf_to_zarr] 65536 rows in 1.94s; chunk in 1.94s (33731 rows/s); 2R:743477
[vcf_to_zarr] 65536 rows in 2.07s; chunk in 2.07s (31735 rows/s); 3L:1776199
[vcf_to_zarr] 65536 rows in 2.05s; chunk in 2.05s (31921 rows/s); UNKN:1308985
[vcf_to_zarr] 65536 rows in 2.18s; chunk in 2.18s (30068 rows/s); 3R:728941
[vcf_to_zarr] 65536 rows in 2.18s; chunk in 2.18s (30040 rows/s); 2L:1758907
[vcf_to_zarr] 131072 rows in 3.26s; chunk in 1.52s (43121 rows/s); X:965276
[vcf_to_zarr] 131072 rows in 3.85s; chunk in 1.91s (34356 rows/s); 2R:1097260
[vcf_to_zarr] 131072 rows in 4.13s; chunk in 1.95s (33545 rows/s); 3R:1100020
[vcf_to_zarr] 131072 rows in 4.28s; chunk in 2.22s (29482 rows/s); UNKN:2805992
[vcf_to_zarr] 131072 rows in 4.29s; chunk in 2.11s (31072 rows/s); 2L:3188931
[vcf_to_zarr] 131072 rows in 4.42s; chunk in 2.36s (27820 rows/s); 3L:2995268
[vcf_to_zarr] 196608 rows in 4.87s; chunk in 1.62s (40568 rows/s); X:1372772
[vcf_to_zarr] 196608 rows in 5.97s; chunk in 1.84s (35636 rows/s); 3R:1466113
[vcf_to_zarr] 196608 rows in 5.99s; chunk in 2.14s (30672 rows/s); 2R:1498666
[vcf_to_zarr] 196608 rows in 6.37s; chunk in 2.08s (31462 rows/s); 2L:3741239
[vcf_to_zarr] 196608 rows in 6.51s; chunk in 2.23s (29354 rows/s); UNKN:4671987
[vcf_to_zarr] 262144 rows in 6.52s; chunk in 1.65s (39815 rows/s); X:1750941
[vcf_to_zarr] 196608 rows in 6.79s; chunk in 2.37s (27662 rows/s); 3L:4199240
[vcf_to_zarr] 262144 rows in 7.72s; chunk in 1.75s (37504 rows/s); 3R:1773907
[vcf_to_zarr] 262144 rows in 7.90s; chunk in 1.91s (34292 rows/s); 2R:1888547
[vcf_to_zarr] 262144 rows in 8.22s; chunk in 1.84s (35539 rows/s); 2L:4398102
[vcf_to_zarr] 327680 rows in 8.29s; chunk in 1.77s (36944 rows/s); X:2172956
[vcf_to_zarr] 262144 rows in 8.49s; chunk in 1.98s (33144 rows/s); UNKN:6065515
[vcf_to_zarr] 262144 rows in 8.93s; chunk in 2.15s (30552 rows/s); 3L:5507662
[vcf_to_zarr] 327680 rows in 9.55s; chunk in 1.83s (35840 rows/s); 3R:2093090
[vcf_to_zarr] 327680 rows in 9.78s; chunk in 1.88s (34795 rows/s); 2R:2265261
[vcf_to_zarr] 393216 rows in 10.01s; chunk in 1.72s (38197 rows/s); X:2538741
[vcf_to_zarr] 327680 rows in 10.29s; chunk in 2.07s (31587 rows/s); 2L:4980133
[vcf_to_zarr] 327680 rows in 10.64s; chunk in 2.16s (30404 rows/s); UNKN:7809763
[vcf_to_zarr] 327680 rows in 11.08s; chunk in 2.15s (30484 rows/s); 3L:6567822
[vcf_to_zarr] 393216 rows in 11.38s; chunk in 1.83s (35768 rows/s); 3R:2439744
[vcf_to_zarr] 458752 rows in 11.53s; chunk in 1.52s (43094 rows/s); X:2897492
[vcf_to_zarr] 393216 rows in 11.61s; chunk in 1.83s (35872 rows/s); 2R:2654778
[vcf_to_zarr] 393216 rows in 12.30s; chunk in 2.00s (32716 rows/s); 2L:5721220
[vcf_to_zarr] 393216 rows in 12.72s; chunk in 2.08s (31506 rows/s); UNKN:9286357
[vcf_to_zarr] 458752 rows in 13.17s; chunk in 1.79s (36544 rows/s); 3R:2808611
[vcf_to_zarr] 393216 rows in 13.23s; chunk in 2.15s (30491 rows/s); 3L:7552213
[vcf_to_zarr] 524288 rows in 13.38s; chunk in 1.86s (35328 rows/s); X:3360838
[vcf_to_zarr] 458752 rows in 13.44s; chunk in 1.83s (35826 rows/s); 2R:3014646
[vcf_to_zarr] 458752 rows in 14.17s; chunk in 1.87s (34961 rows/s); 2L:6312011
[vcf_to_zarr] 458752 rows in 14.84s; chunk in 2.12s (30973 rows/s); UNKN:10839976
[vcf_to_zarr] 524288 rows in 14.94s; chunk in 1.77s (37046 rows/s); 3R:3177343
[vcf_to_zarr] 589824 rows in 15.18s; chunk in 1.80s (36505 rows/s); X:3724744
[vcf_to_zarr] 458752 rows in 15.36s; chunk in 2.13s (30779 rows/s); 3L:8414412
[vcf_to_zarr] 524288 rows in 15.36s; chunk in 1.92s (34095 rows/s); 2R:3407080
[vcf_to_zarr] 524288 rows in 16.35s; chunk in 2.18s (30042 rows/s); 2L:6867080
[vcf_to_zarr] 589824 rows in 16.79s; chunk in 1.84s (35540 rows/s); 3R:3592383
[vcf_to_zarr] 655360 rows in 16.90s; chunk in 1.73s (37967 rows/s); X:4060215
[vcf_to_zarr] 524288 rows in 16.96s; chunk in 2.12s (30871 rows/s); UNKN:12967411
[vcf_to_zarr] 589824 rows in 17.15s; chunk in 1.79s (36697 rows/s); 2R:3752398
[vcf_to_zarr] 524288 rows in 17.51s; chunk in 2.15s (30478 rows/s); 3L:9071556
[vcf_to_zarr] 589824 rows in 18.27s; chunk in 1.92s (34202 rows/s); 2L:7459185
[vcf_to_zarr] 720896 rows in 18.48s; chunk in 1.57s (41612 rows/s); X:4421850
[vcf_to_zarr] 655360 rows in 18.79s; chunk in 2.00s (32730 rows/s); 3R:3948357
[vcf_to_zarr] 589824 rows in 18.99s; chunk in 2.03s (32236 rows/s); UNKN:15023027
[vcf_to_zarr] 655360 rows in 19.05s; chunk in 1.90s (34459 rows/s); 2R:4102454
[vcf_to_zarr] 589824 rows in 19.39s; chunk in 1.88s (34934 rows/s); 3L:9797245
[vcf_to_zarr] 786432 rows in 20.13s; chunk in 1.65s (39740 rows/s); X:4781071
[vcf_to_zarr] 655360 rows in 20.26s; chunk in 2.00s (32836 rows/s); 2L:7989943
[vcf_to_zarr] 720896 rows in 20.55s; chunk in 1.77s (37129 rows/s); 3R:4283931
[vcf_to_zarr] 720896 rows in 20.80s; chunk in 1.75s (37386 rows/s); 2R:4481622
[vcf_to_zarr] 655360 rows in 21.06s; chunk in 2.06s (31749 rows/s); UNKN:16757489
[vcf_to_zarr] 655360 rows in 21.51s; chunk in 2.12s (30965 rows/s); 3L:10491546
[vcf_to_zarr] 851968 rows in 21.99s; chunk in 1.86s (35179 rows/s); X:5155918
[vcf_to_zarr] 720896 rows in 22.13s; chunk in 1.87s (35065 rows/s); 2L:8592648
[vcf_to_zarr] 786432 rows in 22.32s; chunk in 1.77s (37086 rows/s); 3R:4611779
[vcf_to_zarr] 786432 rows in 22.62s; chunk in 1.82s (35934 rows/s); 2R:4865040
[vcf_to_zarr] 720896 rows in 22.93s; chunk in 1.87s (35020 rows/s); UNKN:18850034
[vcf_to_zarr] 720896 rows in 23.55s; chunk in 2.05s (31989 rows/s); 3L:11054838
[vcf_to_zarr] 917504 rows in 23.62s; chunk in 1.63s (40290 rows/s); X:5507700
[vcf_to_zarr] 851968 rows in 23.89s; chunk in 1.57s (41808 rows/s); 3R:4953432
[vcf_to_zarr] 786432 rows in 24.16s; chunk in 2.02s (32388 rows/s); 2L:9044742
[vcf_to_zarr] 851968 rows in 24.36s; chunk in 1.73s (37807 rows/s); 2R:5266387
[vcf_to_zarr] 786432 rows in 24.97s; chunk in 2.04s (32067 rows/s); UNKN:21684571
[vcf_to_zarr] 983040 rows in 25.53s; chunk in 1.91s (34249 rows/s); X:5906370
[vcf_to_zarr] 786432 rows in 25.61s; chunk in 2.06s (31857 rows/s); 3L:11740856
[vcf_to_zarr] 917504 rows in 25.65s; chunk in 1.76s (37201 rows/s); 3R:5278806
[vcf_to_zarr] 917504 rows in 26.14s; chunk in 1.78s (36832 rows/s); 2R:5642822
[vcf_to_zarr] 851968 rows in 26.16s; chunk in 2.00s (32693 rows/s); 2L:9544124
[vcf_to_zarr] 851968 rows in 27.07s; chunk in 2.10s (31230 rows/s); UNKN:22901844
[vcf_to_zarr] 1048576 rows in 27.19s; chunk in 1.65s (39598 rows/s); X:6266245
[vcf_to_zarr] 983040 rows in 27.57s; chunk in 1.92s (34082 rows/s); 3R:5613097
[vcf_to_zarr] 851968 rows in 27.60s; chunk in 1.99s (32989 rows/s); 3L:12191518
[vcf_to_zarr] 983040 rows in 28.13s; chunk in 1.99s (32882 rows/s); 2R:6026451
[vcf_to_zarr] 917504 rows in 28.21s; chunk in 2.05s (31932 rows/s); 2L:10002511
[vcf_to_zarr] 1114112 rows in 28.67s; chunk in 1.48s (44202 rows/s); X:6604196
[vcf_to_zarr] 917504 rows in 29.08s; chunk in 2.00s (32696 rows/s); UNKN:24340880
[vcf_to_zarr] 1048576 rows in 29.40s; chunk in 1.83s (35886 rows/s); 3R:5951592
[vcf_to_zarr] 917504 rows in 29.50s; chunk in 1.90s (34549 rows/s); 3L:12608842
[vcf_to_zarr] 1048576 rows in 30.02s; chunk in 1.89s (34711 rows/s); 2R:6390983
[vcf_to_zarr] 983040 rows in 30.24s; chunk in 2.03s (32296 rows/s); 2L:10420749
[vcf_to_zarr] 1179648 rows in 30.24s; chunk in 1.57s (41635 rows/s); X:6941643
[vcf_to_zarr] 983040 rows in 31.04s; chunk in 1.97s (33334 rows/s); UNKN:25851279
[vcf_to_zarr] 1114112 rows in 31.14s; chunk in 1.75s (37550 rows/s); 3R:6281462
[vcf_to_zarr] 983040 rows in 31.24s; chunk in 1.74s (37654 rows/s); 3L:12994503
[vcf_to_zarr] 1114112 rows in 31.85s; chunk in 1.84s (35710 rows/s); 2R:6754217
[vcf_to_zarr] 1245184 rows in 31.97s; chunk in 1.73s (37887 rows/s); X:7306773
[vcf_to_zarr] 1048576 rows in 32.11s; chunk in 1.87s (35017 rows/s); 2L:10787178
[vcf_to_zarr] 1179648 rows in 32.81s; chunk in 1.67s (39291 rows/s); 3R:6617350
[vcf_to_zarr] 1048576 rows in 33.05s; chunk in 2.01s (32654 rows/s); UNKN:27530148
[vcf_to_zarr] 1048576 rows in 33.36s; chunk in 2.12s (30848 rows/s); 3L:13370362
[vcf_to_zarr] 1179648 rows in 33.58s; chunk in 1.73s (37988 rows/s); 2R:7139422
[vcf_to_zarr] 1310720 rows in 33.64s; chunk in 1.67s (39332 rows/s); X:7712630
[vcf_to_zarr] 1114112 rows in 34.01s; chunk in 1.90s (34561 rows/s); 2L:11190318
[vcf_to_zarr] 1245184 rows in 34.68s; chunk in 1.87s (35074 rows/s); 3R:6882876
[vcf_to_zarr] 1114112 rows in 34.97s; chunk in 1.93s (34038 rows/s); UNKN:29141107
[vcf_to_zarr] 1114112 rows in 35.00s; chunk in 1.64s (39859 rows/s); 3L:13753569
[vcf_to_zarr] 1376256 rows in 35.43s; chunk in 1.79s (36611 rows/s); X:8163556
[vcf_to_zarr] 1245184 rows in 35.61s; chunk in 2.03s (32306 rows/s); 2R:7577086
[vcf_to_zarr] 1179648 rows in 35.86s; chunk in 1.85s (35425 rows/s); 2L:11638760
[vcf_to_zarr] 1310720 rows in 36.56s; chunk in 1.88s (34927 rows/s); 3R:7218696
[vcf_to_zarr] 1179648 rows in 37.04s; chunk in 2.03s (32247 rows/s); 3L:14154601
[vcf_to_zarr] 1179648 rows in 37.07s; chunk in 2.10s (31202 rows/s); UNKN:30872398
[vcf_to_zarr] 1441792 rows in 37.22s; chunk in 1.79s (36654 rows/s); X:8498555
[vcf_to_zarr] 1310720 rows in 37.81s; chunk in 2.20s (29728 rows/s); 2R:8001041
[vcf_to_zarr] 1245184 rows in 37.96s; chunk in 2.10s (31212 rows/s); 2L:12032953
[vcf_to_zarr] 1376256 rows in 38.31s; chunk in 1.75s (37502 rows/s); 3R:7545879
[vcf_to_zarr] 1245184 rows in 38.86s; chunk in 1.83s (35880 rows/s); 3L:14507329
[vcf_to_zarr] 1245184 rows in 38.95s; chunk in 1.88s (34855 rows/s); UNKN:32786612
[vcf_to_zarr] 1507328 rows in 38.97s; chunk in 1.76s (37285 rows/s); X:8876536
[vcf_to_zarr] 1376256 rows in 39.83s; chunk in 2.02s (32391 rows/s); 2R:8406515
[vcf_to_zarr] 1310720 rows in 39.92s; chunk in 1.96s (33370 rows/s); 2L:12440168
[vcf_to_zarr] 1441792 rows in 40.08s; chunk in 1.77s (36958 rows/s); 3R:7937423
[vcf_to_zarr] 1572864 rows in 40.63s; chunk in 1.65s (39651 rows/s); X:9231602
[vcf_to_zarr] 1310720 rows in 40.80s; chunk in 1.94s (33762 rows/s); 3L:14898271
[vcf_to_zarr] 1310720 rows in 40.80s; chunk in 1.84s (35595 rows/s); UNKN:35006642
[vcf_to_zarr] 1507328 rows in 41.76s; chunk in 1.68s (39006 rows/s); 3R:8268824
[vcf_to_zarr] 1441792 rows in 41.80s; chunk in 1.97s (33328 rows/s); 2R:8817870
[vcf_to_zarr] 1376256 rows in 41.96s; chunk in 2.03s (32248 rows/s); 2L:12798683
[vcf_to_zarr] 1638400 rows in 42.35s; chunk in 1.72s (38110 rows/s); X:9628277
[vcf_to_zarr] 1376256 rows in 42.67s; chunk in 1.86s (35163 rows/s); 3L:15293849
[vcf_to_zarr] 1376256 rows in 42.78s; chunk in 1.99s (33007 rows/s); UNKN:37402734
[vcf_to_zarr] 1441792 rows in 43.71s; chunk in 1.76s (37331 rows/s); 2L:13185578
[vcf_to_zarr] 1507328 rows in 43.73s; chunk in 1.93s (33970 rows/s); 2R:9196574
[vcf_to_zarr] 1572864 rows in 43.75s; chunk in 1.99s (32970 rows/s); 3R:8589698
[vcf_to_zarr] 1703936 rows in 44.09s; chunk in 1.74s (37618 rows/s); X:10022886
[vcf_to_zarr] 1441792 rows in 44.54s; chunk in 1.87s (35068 rows/s); 3L:15716543
[vcf_to_zarr] 1441792 rows in 44.78s; chunk in 2.00s (32776 rows/s); UNKN:39987569
[vcf_to_zarr] 1638400 rows in 45.52s; chunk in 1.77s (36938 rows/s); 3R:8907074
[vcf_to_zarr] 1572864 rows in 45.54s; chunk in 1.81s (36139 rows/s); 2R:9578034
[vcf_to_zarr] 1507328 rows in 45.74s; chunk in 2.03s (32299 rows/s); 2L:13694438
[vcf_to_zarr] 1769472 rows in 45.92s; chunk in 1.83s (35735 rows/s); X:10377236
[vcf_to_zarr] 1507328 rows in 46.38s; chunk in 1.84s (35539 rows/s); 3L:16153608
[vcf_to_zarr] 1495563 rows in 46.48s; chunk in 1.70s (31593 rows/s)
[vcf_to_zarr] all done (32106 rows/s)
[vcf_to_zarr] 1638400 rows in 47.29s; chunk in 1.75s (37546 rows/s); 2R:10143277
[vcf_to_zarr] 1703936 rows in 47.40s; chunk in 1.88s (34844 rows/s); 3R:9252907
[vcf_to_zarr] 1572864 rows in 47.63s; chunk in 1.89s (34750 rows/s); 2L:14106023
[vcf_to_zarr] 1835008 rows in 47.62s; chunk in 1.70s (38529 rows/s); X:10736172
[vcf_to_zarr] 1572864 rows in 48.22s; chunk in 1.84s (35571 rows/s); 3L:16574821
[vcf_to_zarr] 1703936 rows in 49.00s; chunk in 1.71s (38357 rows/s); 2R:10536865
[vcf_to_zarr] 1769472 rows in 49.23s; chunk in 1.83s (35755 rows/s); 3R:9576630
[vcf_to_zarr] 1900544 rows in 49.40s; chunk in 1.77s (36923 rows/s); X:11072876
[vcf_to_zarr] 1638400 rows in 49.51s; chunk in 1.88s (34824 rows/s); 2L:14445663
[vcf_to_zarr] 1638400 rows in 49.95s; chunk in 1.72s (37998 rows/s); 3L:16908667
[vcf_to_zarr] 1835008 rows in 50.78s; chunk in 1.54s (42477 rows/s); 3R:9949522
[vcf_to_zarr] 1769472 rows in 50.85s; chunk in 1.85s (35464 rows/s); 2R:10922179
[vcf_to_zarr] 1966080 rows in 51.07s; chunk in 1.67s (39321 rows/s); X:11527714
[vcf_to_zarr] 1703936 rows in 51.25s; chunk in 1.74s (37613 rows/s); 2L:14795477
[vcf_to_zarr] 1703936 rows in 51.75s; chunk in 1.80s (36455 rows/s); 3L:17233657
[vcf_to_zarr] 1900544 rows in 52.62s; chunk in 1.84s (35625 rows/s); 3R:10294378
[vcf_to_zarr] 1835008 rows in 52.61s; chunk in 1.77s (37095 rows/s); 2R:11291119
[vcf_to_zarr] 2031616 rows in 52.73s; chunk in 1.66s (39455 rows/s); X:11959513
[vcf_to_zarr] 1769472 rows in 52.87s; chunk in 1.62s (40466 rows/s); 2L:15131528
[vcf_to_zarr] 1769472 rows in 53.40s; chunk in 1.65s (39618 rows/s); 3L:17565730
[vcf_to_zarr] 1966080 rows in 54.31s; chunk in 1.69s (38738 rows/s); 3R:10648148
[vcf_to_zarr] 1900544 rows in 54.35s; chunk in 1.74s (37718 rows/s); 2R:11661003
[vcf_to_zarr] 2097152 rows in 54.58s; chunk in 1.85s (35375 rows/s); X:12328286
[vcf_to_zarr] 1835008 rows in 54.68s; chunk in 1.81s (36265 rows/s); 2L:15473113
[vcf_to_zarr] 1835008 rows in 54.88s; chunk in 1.48s (44265 rows/s); 3L:17932355
[vcf_to_zarr] 1966080 rows in 56.10s; chunk in 1.75s (37491 rows/s); 2R:12070931
[vcf_to_zarr] 2031616 rows in 56.20s; chunk in 1.89s (34641 rows/s); 3R:11009011
[vcf_to_zarr] 2162688 rows in 56.30s; chunk in 1.72s (37992 rows/s); X:12730528
[vcf_to_zarr] 1900544 rows in 56.32s; chunk in 1.64s (39949 rows/s); 2L:15824427
[vcf_to_zarr] 1900544 rows in 56.42s; chunk in 1.54s (42460 rows/s); 3L:18304697
[vcf_to_zarr] 2031616 rows in 57.71s; chunk in 1.61s (40667 rows/s); 2R:12430922
[vcf_to_zarr] 2228224 rows in 57.82s; chunk in 1.52s (43196 rows/s); X:13129132
[vcf_to_zarr] 2097152 rows in 57.86s; chunk in 1.66s (39565 rows/s); 3R:11363654
[vcf_to_zarr] 1966080 rows in 58.09s; chunk in 1.67s (39269 rows/s); 3L:18632041
[vcf_to_zarr] 1966080 rows in 58.29s; chunk in 1.98s (33142 rows/s); 2L:16236934
[vcf_to_zarr] 2097152 rows in 59.56s; chunk in 1.85s (35376 rows/s); 2R:12761779
[vcf_to_zarr] 2293760 rows in 59.60s; chunk in 1.77s (36925 rows/s); X:13537173
[vcf_to_zarr] 2162688 rows in 59.61s; chunk in 1.76s (37316 rows/s); 3R:11647513
[vcf_to_zarr] 2031616 rows in 59.91s; chunk in 1.81s (36140 rows/s); 3L:18965357
[vcf_to_zarr] 2031616 rows in 60.08s; chunk in 1.79s (36616 rows/s); 2L:16560105
[vcf_to_zarr] 2162688 rows in 61.22s; chunk in 1.66s (39514 rows/s); 2R:13142114
[vcf_to_zarr] 2228224 rows in 61.28s; chunk in 1.67s (39285 rows/s); 3R:11931646
[vcf_to_zarr] 2359296 rows in 61.61s; chunk in 2.01s (32623 rows/s); X:13961241
[vcf_to_zarr] 2097152 rows in 61.69s; chunk in 1.78s (36735 rows/s); 3L:19316595
[vcf_to_zarr] 2097152 rows in 61.82s; chunk in 1.73s (37816 rows/s); 2L:16910926
[vcf_to_zarr] 2293760 rows in 62.73s; chunk in 1.45s (45237 rows/s); 3R:12219590
[vcf_to_zarr] 2228224 rows in 62.90s; chunk in 1.68s (38947 rows/s); 2R:13493998
[vcf_to_zarr] 2162688 rows in 63.31s; chunk in 1.62s (40485 rows/s); 3L:19652577
[vcf_to_zarr] 2424832 rows in 63.31s; chunk in 1.71s (38399 rows/s); X:14401007
[vcf_to_zarr] 2162688 rows in 63.64s; chunk in 1.83s (35863 rows/s); 2L:17286955
[vcf_to_zarr] 2359296 rows in 64.18s; chunk in 1.45s (45127 rows/s); 3R:12545361
[vcf_to_zarr] 2293760 rows in 64.67s; chunk in 1.77s (37088 rows/s); 2R:13874058
[vcf_to_zarr] 2228224 rows in 65.02s; chunk in 1.71s (38229 rows/s); 3L:19991391
[vcf_to_zarr] 2228224 rows in 65.28s; chunk in 1.64s (39988 rows/s); 2L:17632874
[vcf_to_zarr] 2490368 rows in 65.48s; chunk in 2.16s (30288 rows/s); X:14917721
[vcf_to_zarr] 2424832 rows in 65.64s; chunk in 1.46s (44890 rows/s); 3R:12791701
[vcf_to_zarr] 2359296 rows in 66.33s; chunk in 1.66s (39582 rows/s); 2R:14252583
[vcf_to_zarr] 2293760 rows in 66.69s; chunk in 1.66s (39408 rows/s); 3L:20392681
[vcf_to_zarr] 2293760 rows in 66.81s; chunk in 1.53s (42849 rows/s); 2L:17971853
[vcf_to_zarr] 2490368 rows in 67.20s; chunk in 1.55s (42180 rows/s); 3R:13046765
[vcf_to_zarr] 2555904 rows in 67.38s; chunk in 1.91s (34348 rows/s); X:15869377
[vcf_to_zarr] 2424832 rows in 68.01s; chunk in 1.68s (38904 rows/s); 2R:14591508
[vcf_to_zarr] 2359296 rows in 68.39s; chunk in 1.70s (38497 rows/s); 3L:20726907
[vcf_to_zarr] 2359296 rows in 68.39s; chunk in 1.57s (41652 rows/s); 2L:18337435
[vcf_to_zarr] 2555904 rows in 68.75s; chunk in 1.55s (42255 rows/s); 3R:13326598
[vcf_to_zarr] 2621440 rows in 69.24s; chunk in 1.86s (35234 rows/s); X:16476305
[vcf_to_zarr] 2490368 rows in 69.72s; chunk in 1.71s (38349 rows/s); 2R:14940805
[vcf_to_zarr] 2424832 rows in 70.22s; chunk in 1.83s (35846 rows/s); 3L:21049483
[vcf_to_zarr] 2424832 rows in 70.32s; chunk in 1.93s (33895 rows/s); 2L:18723641
[vcf_to_zarr] 2621440 rows in 70.53s; chunk in 1.79s (36687 rows/s); 3R:13628242
[vcf_to_zarr] 2555904 rows in 71.30s; chunk in 1.58s (41486 rows/s); 2R:15302946
[vcf_to_zarr] 2686976 rows in 71.53s; chunk in 2.29s (28614 rows/s); X:17178339
[vcf_to_zarr] 2490368 rows in 71.84s; chunk in 1.62s (40400 rows/s); 3L:21348098
[vcf_to_zarr] 2490368 rows in 71.90s; chunk in 1.58s (41507 rows/s); 2L:19087367
[vcf_to_zarr] 2686976 rows in 72.29s; chunk in 1.76s (37341 rows/s); 3R:13931165
[vcf_to_zarr] 2621440 rows in 73.13s; chunk in 1.83s (35834 rows/s); 2R:15648390
[vcf_to_zarr] 2752512 rows in 73.37s; chunk in 1.83s (35789 rows/s); X:17919981
[vcf_to_zarr] 2555904 rows in 73.54s; chunk in 1.70s (38626 rows/s); 3L:21661581
[vcf_to_zarr] 2555904 rows in 73.82s; chunk in 1.92s (34094 rows/s); 2L:19482398
[vcf_to_zarr] 2752512 rows in 73.84s; chunk in 1.55s (42173 rows/s); 3R:14203468
[vcf_to_zarr] 2686976 rows in 74.84s; chunk in 1.71s (38309 rows/s); 2R:16019221
[vcf_to_zarr] 2621440 rows in 75.09s; chunk in 1.55s (42283 rows/s); 3L:22017375
[vcf_to_zarr] 2818048 rows in 75.48s; chunk in 2.12s (30977 rows/s); X:18655107
[vcf_to_zarr] 2621440 rows in 75.56s; chunk in 1.74s (37755 rows/s); 2L:19803629
[vcf_to_zarr] 2818048 rows in 75.59s; chunk in 1.75s (37489 rows/s); 3R:14502299
[vcf_to_zarr] 2752512 rows in 76.53s; chunk in 1.69s (38851 rows/s); 2R:16383578
[vcf_to_zarr] 2686976 rows in 76.75s; chunk in 1.67s (39267 rows/s); 3L:22316212
[vcf_to_zarr] 2883584 rows in 77.18s; chunk in 1.59s (41193 rows/s); 3R:14819205
[vcf_to_zarr] 2686976 rows in 77.37s; chunk in 1.81s (36177 rows/s); 2L:20121987
[vcf_to_zarr] 2883584 rows in 77.58s; chunk in 2.09s (31286 rows/s); X:19631766
[vcf_to_zarr] 2818048 rows in 78.20s; chunk in 1.68s (39034 rows/s); 2R:16764671
[vcf_to_zarr] 2752512 rows in 78.40s; chunk in 1.65s (39761 rows/s); 3L:22599127
[vcf_to_zarr] 2949120 rows in 78.64s; chunk in 1.46s (44840 rows/s); 3R:15091154
[vcf_to_zarr] 2752512 rows in 79.20s; chunk in 1.83s (35744 rows/s); 2L:20482092
[vcf_to_zarr] 2949120 rows in 79.80s; chunk in 2.23s (29409 rows/s); X:21499279
[vcf_to_zarr] 2883584 rows in 79.83s; chunk in 1.62s (40392 rows/s); 2R:17121280
[vcf_to_zarr] 2818048 rows in 80.12s; chunk in 1.72s (38181 rows/s); 3L:22886136
[vcf_to_zarr] 3014656 rows in 80.27s; chunk in 1.62s (40352 rows/s); 3R:15381723
[vcf_to_zarr] 2818048 rows in 80.73s; chunk in 1.53s (42771 rows/s); 2L:20852881
[vcf_to_zarr] 2949120 rows in 81.60s; chunk in 1.78s (36875 rows/s); 2R:17516898
[vcf_to_zarr] 2883584 rows in 81.89s; chunk in 1.77s (37018 rows/s); 3L:23207611
[vcf_to_zarr] 3080192 rows in 82.03s; chunk in 1.76s (37175 rows/s); 3R:15671209
[vcf_to_zarr] 3014656 rows in 82.23s; chunk in 2.43s (27006 rows/s); X:23401954
[vcf_to_zarr] 2883584 rows in 82.32s; chunk in 1.58s (41398 rows/s); 2L:21155322
[vcf_to_zarr] 3014656 rows in 83.34s; chunk in 1.74s (37760 rows/s); 2R:17930612
[vcf_to_zarr] 3049427 rows in 83.40s; chunk in 1.17s (29647 rows/s)
[vcf_to_zarr] all done (36537 rows/s)
[vcf_to_zarr] 2949120 rows in 83.49s; chunk in 1.60s (40894 rows/s); 3L:23710000
[vcf_to_zarr] 3145728 rows in 83.62s; chunk in 1.59s (41287 rows/s); 3R:15930367
[vcf_to_zarr] 2949120 rows in 84.01s; chunk in 1.69s (38737 rows/s); 2L:21481219
[vcf_to_zarr] 3080192 rows in 84.94s; chunk in 1.60s (41033 rows/s); 2R:18298211
[vcf_to_zarr] 3211264 rows in 85.04s; chunk in 1.42s (46133 rows/s); 3R:16230192
[vcf_to_zarr] 3014656 rows in 85.11s; chunk in 1.62s (40395 rows/s); 3L:24090999
[vcf_to_zarr] 3014656 rows in 85.43s; chunk in 1.42s (46245 rows/s); 2L:21799148
[vcf_to_zarr] 3080192 rows in 86.64s; chunk in 1.52s (43032 rows/s); 3L:24431024
[vcf_to_zarr] 3145728 rows in 86.63s; chunk in 1.69s (38734 rows/s); 2R:18722580
[vcf_to_zarr] 3276800 rows in 86.64s; chunk in 1.61s (40782 rows/s); 3R:16490830
[vcf_to_zarr] 3080192 rows in 86.85s; chunk in 1.42s (46073 rows/s); 2L:22125556
[vcf_to_zarr] 3342336 rows in 88.09s; chunk in 1.45s (45213 rows/s); 3R:16748351
[vcf_to_zarr] 3145728 rows in 88.19s; chunk in 1.55s (42263 rows/s); 3L:24863805
[vcf_to_zarr] 3211264 rows in 88.23s; chunk in 1.60s (40924 rows/s); 2R:19097543
[vcf_to_zarr] 3145728 rows in 88.34s; chunk in 1.49s (43896 rows/s); 2L:22443968
[vcf_to_zarr] 3407872 rows in 89.61s; chunk in 1.52s (43233 rows/s); 3R:17059224
[vcf_to_zarr] 3211264 rows in 89.73s; chunk in 1.54s (42477 rows/s); 3L:25191242
[vcf_to_zarr] 3211264 rows in 89.80s; chunk in 1.46s (44954 rows/s); 2L:22861034
[vcf_to_zarr] 3276800 rows in 89.80s; chunk in 1.57s (41734 rows/s); 2R:19443892
[vcf_to_zarr] 3276800 rows in 91.23s; chunk in 1.43s (45722 rows/s); 2L:23163164
[vcf_to_zarr] 3473408 rows in 91.29s; chunk in 1.68s (38901 rows/s); 3R:17346772
[vcf_to_zarr] 3342336 rows in 91.37s; chunk in 1.57s (41741 rows/s); 2R:19829126
[vcf_to_zarr] 3276800 rows in 91.52s; chunk in 1.79s (36692 rows/s); 3L:25549399
[vcf_to_zarr] 3342336 rows in 92.72s; chunk in 1.49s (43936 rows/s); 2L:23470227
[vcf_to_zarr] 3538944 rows in 92.93s; chunk in 1.64s (40013 rows/s); 3R:17645208
[vcf_to_zarr] 3407872 rows in 93.02s; chunk in 1.65s (39608 rows/s); 2R:20186566
[vcf_to_zarr] 3342336 rows in 93.13s; chunk in 1.62s (40573 rows/s); 3L:25861529
[vcf_to_zarr] 3407872 rows in 94.15s; chunk in 1.43s (45854 rows/s); 2L:23800301
[vcf_to_zarr] 3604480 rows in 94.44s; chunk in 1.51s (43484 rows/s); 3R:17923855
[vcf_to_zarr] 3473408 rows in 94.60s; chunk in 1.57s (41688 rows/s); 2R:20575910
[vcf_to_zarr] 3407872 rows in 94.70s; chunk in 1.57s (41668 rows/s); 3L:26154826
[vcf_to_zarr] 3473408 rows in 95.61s; chunk in 1.45s (45119 rows/s); 2L:24150581
[vcf_to_zarr] 3538944 rows in 96.08s; chunk in 1.48s (44247 rows/s); 2R:20927039
[vcf_to_zarr] 3670016 rows in 96.30s; chunk in 1.86s (35266 rows/s); 3R:18258756
[vcf_to_zarr] 3473408 rows in 96.37s; chunk in 1.67s (39303 rows/s); 3L:26448824
[vcf_to_zarr] 3538944 rows in 97.04s; chunk in 1.43s (45823 rows/s); 2L:24472338
[vcf_to_zarr] 3735552 rows in 97.77s; chunk in 1.47s (44454 rows/s); 3R:18540743
[vcf_to_zarr] 3604480 rows in 97.79s; chunk in 1.71s (38305 rows/s); 2R:21260859
[vcf_to_zarr] 3538944 rows in 97.86s; chunk in 1.48s (44176 rows/s); 3L:26768776
[vcf_to_zarr] 3604480 rows in 98.48s; chunk in 1.45s (45289 rows/s); 2L:24803212
[vcf_to_zarr] 3604480 rows in 99.34s; chunk in 1.49s (44044 rows/s); 3L:27168254
[vcf_to_zarr] 3801088 rows in 99.38s; chunk in 1.61s (40681 rows/s); 3R:19068597
[vcf_to_zarr] 3670016 rows in 99.46s; chunk in 1.67s (39299 rows/s); 2R:21596358
[vcf_to_zarr] 3670016 rows in 99.94s; chunk in 1.46s (45016 rows/s); 2L:25142703
[vcf_to_zarr] 3670016 rows in 100.85s; chunk in 1.51s (43525 rows/s); 3L:27461846
[vcf_to_zarr] 3866624 rows in 100.93s; chunk in 1.55s (42377 rows/s); 3R:19380202
[vcf_to_zarr] 3735552 rows in 100.97s; chunk in 1.52s (43250 rows/s); 2R:21958918
[vcf_to_zarr] 3735552 rows in 101.44s; chunk in 1.50s (43608 rows/s); 2L:25541625
[vcf_to_zarr] 3735552 rows in 102.68s; chunk in 1.83s (35805 rows/s); 3L:27764341
[vcf_to_zarr] 3932160 rows in 102.71s; chunk in 1.78s (36764 rows/s); 3R:19674124
[vcf_to_zarr] 3801088 rows in 102.73s; chunk in 1.76s (37216 rows/s); 2R:22359191
[vcf_to_zarr] 3801088 rows in 102.93s; chunk in 1.49s (43932 rows/s); 2L:25886855
[vcf_to_zarr] 3997696 rows in 104.18s; chunk in 1.47s (44716 rows/s); 3R:19942647
[vcf_to_zarr] 3801088 rows in 104.21s; chunk in 1.53s (42764 rows/s); 3L:28057690
[vcf_to_zarr] 3866624 rows in 104.33s; chunk in 1.59s (41089 rows/s); 2R:22704985
[vcf_to_zarr] 3866624 rows in 104.45s; chunk in 1.51s (43262 rows/s); 2L:26219878
[vcf_to_zarr] 4063232 rows in 105.56s; chunk in 1.39s (47264 rows/s); 3R:20226133
[vcf_to_zarr] 3866624 rows in 105.82s; chunk in 1.61s (40727 rows/s); 3L:28347608
[vcf_to_zarr] 3932160 rows in 105.91s; chunk in 1.46s (44772 rows/s); 2L:26515944
[vcf_to_zarr] 3932160 rows in 105.95s; chunk in 1.62s (40437 rows/s); 2R:23039759
[vcf_to_zarr] 4128768 rows in 107.24s; chunk in 1.67s (39143 rows/s); 3R:20533000
[vcf_to_zarr] 3997696 rows in 107.29s; chunk in 1.38s (47603 rows/s); 2L:26821079
[vcf_to_zarr] 3932160 rows in 107.56s; chunk in 1.74s (37771 rows/s); 3L:28664009
[vcf_to_zarr] 3997696 rows in 107.54s; chunk in 1.60s (41052 rows/s); 2R:23427576
[vcf_to_zarr] 4063232 rows in 108.72s; chunk in 1.43s (45696 rows/s); 2L:27149490
[vcf_to_zarr] 4194304 rows in 108.89s; chunk in 1.65s (39673 rows/s); 3R:20840579
[vcf_to_zarr] 3997696 rows in 109.00s; chunk in 1.44s (45524 rows/s); 3L:28945941
[vcf_to_zarr] 4063232 rows in 109.10s; chunk in 1.56s (42088 rows/s); 2R:23790355
[vcf_to_zarr] 4128768 rows in 110.22s; chunk in 1.50s (43724 rows/s); 2L:27451882
[vcf_to_zarr] 4259840 rows in 110.39s; chunk in 1.50s (43557 rows/s); 3R:21138997
[vcf_to_zarr] 4063232 rows in 110.50s; chunk in 1.50s (43643 rows/s); 3L:29241065
[vcf_to_zarr] 4128768 rows in 110.68s; chunk in 1.58s (41587 rows/s); 2R:24128653
[vcf_to_zarr] 4194304 rows in 111.63s; chunk in 1.41s (46605 rows/s); 2L:27757252
[vcf_to_zarr] 4325376 rows in 112.13s; chunk in 1.74s (37734 rows/s); 3R:21421687
[vcf_to_zarr] 4128768 rows in 112.24s; chunk in 1.74s (37664 rows/s); 3L:29527063
[vcf_to_zarr] 4194304 rows in 112.33s; chunk in 1.65s (39611 rows/s); 2R:24498353
[vcf_to_zarr] 4259840 rows in 113.29s; chunk in 1.67s (39355 rows/s); 2L:28039609
[vcf_to_zarr] 4390912 rows in 113.76s; chunk in 1.63s (40288 rows/s); 3R:21732427
[vcf_to_zarr] 4194304 rows in 113.85s; chunk in 1.61s (40608 rows/s); 3L:29805410
[vcf_to_zarr] 4259840 rows in 114.22s; chunk in 1.89s (34643 rows/s); 2R:24905480
[vcf_to_zarr] 4325376 rows in 114.74s; chunk in 1.44s (45365 rows/s); 2L:28358261
[vcf_to_zarr] 4456448 rows in 115.22s; chunk in 1.46s (44798 rows/s); 3R:22012534
[vcf_to_zarr] 4259840 rows in 115.42s; chunk in 1.57s (41681 rows/s); 3L:30099800
[vcf_to_zarr] 4325376 rows in 115.86s; chunk in 1.64s (39999 rows/s); 2R:25353308
[vcf_to_zarr] 4390912 rows in 116.46s; chunk in 1.72s (38085 rows/s); 2L:28697385
[vcf_to_zarr] 4521984 rows in 116.99s; chunk in 1.77s (37010 rows/s); 3R:22281611
[vcf_to_zarr] 4325376 rows in 117.33s; chunk in 1.91s (34339 rows/s); 3L:30413435
[vcf_to_zarr] 4390912 rows in 117.37s; chunk in 1.51s (43506 rows/s); 2R:25718425
[vcf_to_zarr] 4456448 rows in 117.90s; chunk in 1.44s (45415 rows/s); 2L:28983052
[vcf_to_zarr] 4587520 rows in 118.40s; chunk in 1.41s (46440 rows/s); 3R:22554166
[vcf_to_zarr] 4390912 rows in 118.78s; chunk in 1.45s (45104 rows/s); 3L:30726611
[vcf_to_zarr] 4456448 rows in 118.90s; chunk in 1.54s (42684 rows/s); 2R:26098455
[vcf_to_zarr] 4521984 rows in 119.40s; chunk in 1.50s (43662 rows/s); 2L:29282544
[vcf_to_zarr] 4653056 rows in 119.86s; chunk in 1.46s (44921 rows/s); 3R:22829659
[vcf_to_zarr] 4456448 rows in 120.33s; chunk in 1.54s (42475 rows/s); 3L:31032007
[vcf_to_zarr] 4521984 rows in 120.55s; chunk in 1.65s (39775 rows/s); 2R:26473802
[vcf_to_zarr] 4587520 rows in 121.00s; chunk in 1.60s (41045 rows/s); 2L:29591831
[vcf_to_zarr] 4718592 rows in 121.28s; chunk in 1.42s (46283 rows/s); 3R:23099703
[vcf_to_zarr] 4587520 rows in 122.11s; chunk in 1.55s (42190 rows/s); 2R:26863948
[vcf_to_zarr] 4521984 rows in 122.20s; chunk in 1.87s (34963 rows/s); 3L:31325411
[vcf_to_zarr] 4653056 rows in 122.42s; chunk in 1.42s (46133 rows/s); 2L:29901405
[vcf_to_zarr] 4784128 rows in 123.05s; chunk in 1.77s (37076 rows/s); 3R:23398512
[vcf_to_zarr] 4587520 rows in 123.93s; chunk in 1.73s (37864 rows/s); 3L:31634604
[vcf_to_zarr] 4653056 rows in 123.97s; chunk in 1.86s (35172 rows/s); 2R:27249123
[vcf_to_zarr] 4718592 rows in 123.98s; chunk in 1.56s (42108 rows/s); 2L:30350554
[vcf_to_zarr] 4849664 rows in 124.65s; chunk in 1.60s (40901 rows/s); 3R:23806008
[vcf_to_zarr] 4784128 rows in 125.44s; chunk in 1.47s (44723 rows/s); 2L:30688359
[vcf_to_zarr] 4653056 rows in 125.49s; chunk in 1.56s (41992 rows/s); 3L:31927517
[vcf_to_zarr] 4718592 rows in 125.74s; chunk in 1.77s (37062 rows/s); 2R:27666963
[vcf_to_zarr] 4915200 rows in 126.24s; chunk in 1.59s (41141 rows/s); 3R:24090690
[vcf_to_zarr] 4849664 rows in 126.84s; chunk in 1.40s (46720 rows/s); 2L:30977280
[vcf_to_zarr] 4718592 rows in 127.12s; chunk in 1.63s (40289 rows/s); 3L:32210333
[vcf_to_zarr] 4784128 rows in 127.37s; chunk in 1.63s (40112 rows/s); 2R:28079841
[vcf_to_zarr] 4980736 rows in 127.87s; chunk in 1.63s (40151 rows/s); 3R:24372010
[vcf_to_zarr] 4915200 rows in 128.25s; chunk in 1.40s (46645 rows/s); 2L:31258090
[vcf_to_zarr] 4784128 rows in 128.79s; chunk in 1.67s (39351 rows/s); 3L:32502138
[vcf_to_zarr] 4849664 rows in 129.00s; chunk in 1.63s (40241 rows/s); 2R:28531378
[vcf_to_zarr] 5046272 rows in 129.38s; chunk in 1.50s (43582 rows/s); 3R:24659296
[vcf_to_zarr] 4980736 rows in 129.71s; chunk in 1.46s (44854 rows/s); 2L:31539764
[vcf_to_zarr] 4849664 rows in 130.61s; chunk in 1.82s (35934 rows/s); 3L:32845396
[vcf_to_zarr] 4915200 rows in 130.67s; chunk in 1.67s (39282 rows/s); 2R:28960814
[vcf_to_zarr] 5111808 rows in 130.83s; chunk in 1.45s (45245 rows/s); 3R:24980597
[vcf_to_zarr] 5046272 rows in 131.15s; chunk in 1.44s (45652 rows/s); 2L:31879136
[vcf_to_zarr] 4980736 rows in 132.29s; chunk in 1.63s (40275 rows/s); 2R:29418860
[vcf_to_zarr] 4915200 rows in 132.46s; chunk in 1.85s (35332 rows/s); 3L:33181073
[vcf_to_zarr] 5111808 rows in 132.62s; chunk in 1.47s (44510 rows/s); 2L:32190676
[vcf_to_zarr] 5177344 rows in 132.64s; chunk in 1.82s (36012 rows/s); 3R:25288615
[vcf_to_zarr] 5046272 rows in 133.98s; chunk in 1.69s (38823 rows/s); 2R:29865558
[vcf_to_zarr] 4980736 rows in 134.19s; chunk in 1.72s (38077 rows/s); 3L:33512962
[vcf_to_zarr] 5177344 rows in 134.20s; chunk in 1.58s (41371 rows/s); 2L:32494588
[vcf_to_zarr] 5242880 rows in 134.25s; chunk in 1.61s (40828 rows/s); 3R:25636666
[vcf_to_zarr] 5242880 rows in 135.78s; chunk in 1.58s (41458 rows/s); 2L:32783491
[vcf_to_zarr] 5111808 rows in 135.78s; chunk in 1.80s (36396 rows/s); 2R:30278020
[vcf_to_zarr] 5046272 rows in 135.80s; chunk in 1.62s (40572 rows/s); 3L:33805326
[vcf_to_zarr] 5308416 rows in 135.90s; chunk in 1.65s (39746 rows/s); 3R:25952212
[vcf_to_zarr] 5308416 rows in 137.24s; chunk in 1.45s (45120 rows/s); 2L:33057896
[vcf_to_zarr] 5177344 rows in 137.32s; chunk in 1.54s (42537 rows/s); 2R:30656608
[vcf_to_zarr] 5111808 rows in 137.59s; chunk in 1.79s (36684 rows/s); 3L:34137020
[vcf_to_zarr] 5373952 rows in 137.62s; chunk in 1.72s (38105 rows/s); 3R:26264677
[vcf_to_zarr] 5373952 rows in 138.68s; chunk in 1.45s (45238 rows/s); 2L:33357481
[vcf_to_zarr] 5242880 rows in 138.96s; chunk in 1.63s (40160 rows/s); 2R:31083040
[vcf_to_zarr] 5177344 rows in 139.00s; chunk in 1.41s (46403 rows/s); 3L:34419638
[vcf_to_zarr] 5439488 rows in 139.20s; chunk in 1.58s (41413 rows/s); 3R:26603701
[vcf_to_zarr] 5439488 rows in 140.29s; chunk in 1.61s (40825 rows/s); 2L:33663793
[vcf_to_zarr] 5242880 rows in 140.55s; chunk in 1.55s (42346 rows/s); 3L:34749125
[vcf_to_zarr] 5308416 rows in 140.60s; chunk in 1.64s (39964 rows/s); 2R:31495323
[vcf_to_zarr] 5505024 rows in 140.81s; chunk in 1.61s (40732 rows/s); 3R:26959153
[vcf_to_zarr] 5505024 rows in 141.85s; chunk in 1.56s (42045 rows/s); 2L:33983212
[vcf_to_zarr] 5373952 rows in 142.27s; chunk in 1.68s (39079 rows/s); 2R:31898720
[vcf_to_zarr] 5308416 rows in 142.43s; chunk in 1.88s (34782 rows/s); 3L:35037062
[vcf_to_zarr] 5570560 rows in 142.55s; chunk in 1.74s (37567 rows/s); 3R:27281369
[vcf_to_zarr] 5570560 rows in 143.35s; chunk in 1.50s (43574 rows/s); 2L:34315234
[vcf_to_zarr] 5439488 rows in 143.88s; chunk in 1.61s (40789 rows/s); 2R:32339567
[vcf_to_zarr] 5373952 rows in 143.94s; chunk in 1.51s (43367 rows/s); 3L:35337062
[vcf_to_zarr] 5636096 rows in 144.13s; chunk in 1.57s (41659 rows/s); 3R:27608960
[vcf_to_zarr] 5636096 rows in 144.82s; chunk in 1.47s (44685 rows/s); 2L:34634091
[vcf_to_zarr] 5439488 rows in 145.56s; chunk in 1.62s (40529 rows/s); 3L:35657368
[vcf_to_zarr] 5505024 rows in 145.55s; chunk in 1.67s (39241 rows/s); 2R:32812615
[vcf_to_zarr] 5701632 rows in 145.81s; chunk in 1.68s (38945 rows/s); 3R:27917793
[vcf_to_zarr] 5701632 rows in 146.43s; chunk in 1.62s (40578 rows/s); 2L:34977152
[vcf_to_zarr] 5570560 rows in 147.12s; chunk in 1.57s (41671 rows/s); 2R:33296791
[vcf_to_zarr] 5505024 rows in 147.44s; chunk in 1.88s (34815 rows/s); 3L:36019348
[vcf_to_zarr] 5767168 rows in 147.69s; chunk in 1.88s (34940 rows/s); 3R:28308825
[vcf_to_zarr] 5767168 rows in 148.00s; chunk in 1.57s (41742 rows/s); 2L:35307862
[vcf_to_zarr] 5636096 rows in 148.66s; chunk in 1.54s (42592 rows/s); 2R:33709939
[vcf_to_zarr] 5570560 rows in 148.95s; chunk in 1.51s (43472 rows/s); 3L:36401245
[vcf_to_zarr] 5832704 rows in 149.43s; chunk in 1.74s (37647 rows/s); 3R:28738500
[vcf_to_zarr] 5832704 rows in 149.60s; chunk in 1.60s (41027 rows/s); 2L:35654107
[vcf_to_zarr] 5701632 rows in 150.28s; chunk in 1.62s (40394 rows/s); 2R:34170166
[vcf_to_zarr] 5636096 rows in 150.58s; chunk in 1.63s (40200 rows/s); 3L:36864486
[vcf_to_zarr] 5898240 rows in 151.08s; chunk in 1.48s (44230 rows/s); 2L:36009450
[vcf_to_zarr] 5898240 rows in 151.11s; chunk in 1.68s (39005 rows/s); 3R:29098872
[vcf_to_zarr] 5767168 rows in 151.85s; chunk in 1.57s (41797 rows/s); 2R:34617437
[vcf_to_zarr] 5701632 rows in 152.08s; chunk in 1.50s (43649 rows/s); 3L:37169435
[vcf_to_zarr] 5963776 rows in 152.62s; chunk in 1.53s (42735 rows/s); 2L:36332745
[vcf_to_zarr] 5963776 rows in 152.97s; chunk in 1.86s (35264 rows/s); 3R:29457272
[vcf_to_zarr] 5832704 rows in 153.47s; chunk in 1.62s (40500 rows/s); 2R:35071399
[vcf_to_zarr] 5767168 rows in 153.74s; chunk in 1.66s (39443 rows/s); 3L:37562702
[vcf_to_zarr] 6029312 rows in 154.04s; chunk in 1.43s (45951 rows/s); 2L:36670847
[vcf_to_zarr] 6029312 rows in 154.37s; chunk in 1.40s (46751 rows/s); 3R:29708380
[vcf_to_zarr] 5898240 rows in 155.15s; chunk in 1.68s (39079 rows/s); 2R:35509106
[vcf_to_zarr] 5832704 rows in 155.35s; chunk in 1.60s (40895 rows/s); 3L:37975177
[vcf_to_zarr] 6094848 rows in 155.54s; chunk in 1.50s (43751 rows/s); 2L:37004233
[vcf_to_zarr] 6094848 rows in 155.84s; chunk in 1.47s (44499 rows/s); 3R:29979480
[vcf_to_zarr] 5963776 rows in 157.05s; chunk in 1.91s (34356 rows/s); 2R:35945689
[vcf_to_zarr] 5898240 rows in 157.13s; chunk in 1.79s (36677 rows/s); 3L:38360323
[vcf_to_zarr] 6160384 rows in 157.21s; chunk in 1.67s (39242 rows/s); 2L:37458901
[vcf_to_zarr] 6160384 rows in 157.63s; chunk in 1.79s (36573 rows/s); 3R:30321604
[vcf_to_zarr] 6225920 rows in 158.70s; chunk in 1.49s (44040 rows/s); 2L:37777037
[vcf_to_zarr] 6029312 rows in 158.77s; chunk in 1.72s (38132 rows/s); 2R:36488538
[vcf_to_zarr] 5963776 rows in 158.80s; chunk in 1.67s (39272 rows/s); 3L:38752406
[vcf_to_zarr] 6225920 rows in 159.18s; chunk in 1.54s (42420 rows/s); 3R:30640457
[vcf_to_zarr] 6291456 rows in 160.22s; chunk in 1.52s (43120 rows/s); 2L:38109387
[vcf_to_zarr] 6029312 rows in 160.34s; chunk in 1.54s (42456 rows/s); 3L:39057933
[vcf_to_zarr] 6094848 rows in 160.45s; chunk in 1.67s (39152 rows/s); 2R:36952634
[vcf_to_zarr] 6291456 rows in 160.72s; chunk in 1.55s (42394 rows/s); 3R:30938085
[vcf_to_zarr] 6356992 rows in 161.66s; chunk in 1.44s (45410 rows/s); 2L:38446008
[vcf_to_zarr] 6094848 rows in 161.88s; chunk in 1.54s (42664 rows/s); 3L:39409319
[vcf_to_zarr] 6160384 rows in 162.21s; chunk in 1.76s (37184 rows/s); 2R:37452780
[vcf_to_zarr] 6356992 rows in 162.40s; chunk in 1.68s (39121 rows/s); 3R:31300790
[vcf_to_zarr] 6422528 rows in 163.20s; chunk in 1.54s (42541 rows/s); 2L:38790322
[vcf_to_zarr] 6160384 rows in 163.65s; chunk in 1.77s (37093 rows/s); 3L:39779939
[vcf_to_zarr] 6225920 rows in 163.89s; chunk in 1.68s (38895 rows/s); 2R:38028611
[vcf_to_zarr] 6422528 rows in 164.02s; chunk in 1.62s (40445 rows/s); 3R:31665876
[vcf_to_zarr] 6488064 rows in 164.88s; chunk in 1.67s (39171 rows/s); 2L:39091319
[vcf_to_zarr] 6225920 rows in 165.14s; chunk in 1.49s (43838 rows/s); 3L:40133984
[vcf_to_zarr] 6291456 rows in 165.61s; chunk in 1.72s (38110 rows/s); 2R:38562291
[vcf_to_zarr] 6488064 rows in 165.63s; chunk in 1.62s (40542 rows/s); 3R:32054713
[vcf_to_zarr] 6553600 rows in 166.41s; chunk in 1.53s (42721 rows/s); 2L:39424615
[vcf_to_zarr] 6291456 rows in 166.67s; chunk in 1.53s (42866 rows/s); 3L:40466673
[vcf_to_zarr] 6553600 rows in 167.13s; chunk in 1.50s (43768 rows/s); 3R:32426153
[vcf_to_zarr] 6356992 rows in 167.34s; chunk in 1.72s (38000 rows/s); 2R:39039536
[vcf_to_zarr] 6619136 rows in 167.98s; chunk in 1.57s (41703 rows/s); 2L:39736891
[vcf_to_zarr] 6356992 rows in 168.68s; chunk in 2.01s (32549 rows/s); 3L:40824013
[vcf_to_zarr] 6619136 rows in 168.78s; chunk in 1.65s (39689 rows/s); 3R:32841586
[vcf_to_zarr] 6422528 rows in 169.12s; chunk in 1.79s (36713 rows/s); 2R:39461250
[vcf_to_zarr] 6684672 rows in 169.51s; chunk in 1.53s (42912 rows/s); 2L:40065287
[vcf_to_zarr] 6684672 rows in 170.33s; chunk in 1.55s (42316 rows/s); 3R:33139813
[vcf_to_zarr] 6422528 rows in 170.46s; chunk in 1.77s (36956 rows/s); 3L:41260771
[vcf_to_zarr] 6488064 rows in 170.73s; chunk in 1.60s (40880 rows/s); 2R:39924213
[vcf_to_zarr] 6750208 rows in 171.01s; chunk in 1.50s (43712 rows/s); 2L:40406509
[vcf_to_zarr] 6750208 rows in 171.73s; chunk in 1.40s (46777 rows/s); 3R:33490273
[vcf_to_zarr] 6488064 rows in 172.24s; chunk in 1.78s (36834 rows/s); 3L:41758088
[vcf_to_zarr] 6553600 rows in 172.32s; chunk in 1.60s (41064 rows/s); 2R:40364408
[vcf_to_zarr] 6815744 rows in 172.58s; chunk in 1.57s (41761 rows/s); 2L:40722658
[vcf_to_zarr] 6499075 rows in 172.62s; chunk in 0.38s (29093 rows/s)
[vcf_to_zarr] all done (37639 rows/s)
[vcf_to_zarr] 6815744 rows in 173.40s; chunk in 1.66s (39405 rows/s); 3R:33784657
[vcf_to_zarr] 6619136 rows in 173.98s; chunk in 1.65s (39606 rows/s); 2R:40792813
[vcf_to_zarr] 6881280 rows in 174.03s; chunk in 1.46s (44972 rows/s); 2L:41053777
[vcf_to_zarr] 6881280 rows in 174.85s; chunk in 1.46s (45020 rows/s); 3R:34172574
[vcf_to_zarr] 6684672 rows in 175.54s; chunk in 1.56s (41880 rows/s); 2R:41294097
[vcf_to_zarr] 6946816 rows in 175.55s; chunk in 1.52s (43175 rows/s); 2L:41412301
[vcf_to_zarr] 6946816 rows in 176.28s; chunk in 1.42s (46014 rows/s); 3R:34517958
[vcf_to_zarr] 7012352 rows in 177.06s; chunk in 1.51s (43356 rows/s); 2L:41729861
[vcf_to_zarr] 6750208 rows in 177.08s; chunk in 1.54s (42662 rows/s); 2R:41787163
[vcf_to_zarr] 7012352 rows in 177.77s; chunk in 1.49s (43902 rows/s); 3R:34921583
[vcf_to_zarr] 7077888 rows in 178.57s; chunk in 1.51s (43532 rows/s); 2L:42041786
[vcf_to_zarr] 6815744 rows in 178.73s; chunk in 1.65s (39698 rows/s); 2R:42313307
[vcf_to_zarr] 7077888 rows in 179.55s; chunk in 1.79s (36698 rows/s); 3R:35283361
[vcf_to_zarr] 7143424 rows in 180.21s; chunk in 1.64s (39936 rows/s); 2L:42378081
[vcf_to_zarr] 6881280 rows in 180.49s; chunk in 1.76s (37205 rows/s); 2R:42837611
[vcf_to_zarr] 7143424 rows in 181.02s; chunk in 1.46s (44793 rows/s); 3R:35635571
[vcf_to_zarr] 7208960 rows in 181.74s; chunk in 1.53s (42882 rows/s); 2L:42688528
[vcf_to_zarr] 6946816 rows in 182.25s; chunk in 1.76s (37178 rows/s); 2R:43314444
[vcf_to_zarr] 7208960 rows in 182.42s; chunk in 1.40s (46730 rows/s); 3R:35998768
[vcf_to_zarr] 7274496 rows in 183.29s; chunk in 1.55s (42361 rows/s); 2L:43030202
[vcf_to_zarr] 7012352 rows in 183.98s; chunk in 1.73s (37877 rows/s); 2R:43950002
[vcf_to_zarr] 7274496 rows in 184.19s; chunk in 1.77s (37097 rows/s); 3R:36398016
[vcf_to_zarr] 7340032 rows in 184.85s; chunk in 1.57s (41787 rows/s); 2L:43352832
[vcf_to_zarr] 7077888 rows in 185.60s; chunk in 1.62s (40410 rows/s); 2R:44486650
[vcf_to_zarr] 7340032 rows in 185.77s; chunk in 1.58s (41488 rows/s); 3R:36837619
[vcf_to_zarr] 7405568 rows in 186.41s; chunk in 1.55s (42237 rows/s); 2L:43697091
[vcf_to_zarr] 7405568 rows in 187.28s; chunk in 1.52s (43206 rows/s); 3R:37198354
[vcf_to_zarr] 7143424 rows in 187.44s; chunk in 1.83s (35764 rows/s); 2R:45054974
[vcf_to_zarr] 7471104 rows in 187.86s; chunk in 1.45s (45153 rows/s); 2L:43999442
[vcf_to_zarr] 7208960 rows in 189.15s; chunk in 1.72s (38168 rows/s); 2R:45641780
[vcf_to_zarr] 7471104 rows in 189.22s; chunk in 1.94s (33810 rows/s); 3R:37661103
[vcf_to_zarr] 7536640 rows in 189.40s; chunk in 1.54s (42435 rows/s); 2L:44331032
[vcf_to_zarr] 7536640 rows in 190.89s; chunk in 1.67s (39215 rows/s); 3R:38023237
[vcf_to_zarr] 7274496 rows in 190.92s; chunk in 1.76s (37198 rows/s); 2R:46316054
[vcf_to_zarr] 7602176 rows in 190.93s; chunk in 1.53s (42822 rows/s); 2L:44676625
[vcf_to_zarr] 7667712 rows in 192.33s; chunk in 1.40s (46812 rows/s); 2L:45034093
[vcf_to_zarr] 7602176 rows in 192.64s; chunk in 1.74s (37586 rows/s); 3R:38485088
[vcf_to_zarr] 7340032 rows in 192.66s; chunk in 1.74s (37558 rows/s); 2R:46828921
[vcf_to_zarr] 7733248 rows in 193.83s; chunk in 1.50s (43592 rows/s); 2L:45355502
[vcf_to_zarr] 7405568 rows in 194.30s; chunk in 1.64s (40045 rows/s); 2R:47340396
[vcf_to_zarr] 7667712 rows in 194.51s; chunk in 1.87s (35041 rows/s); 3R:38900545
[vcf_to_zarr] 7798784 rows in 195.22s; chunk in 1.38s (47351 rows/s); 2L:45653332
[vcf_to_zarr] 7471104 rows in 196.09s; chunk in 1.79s (36638 rows/s); 2R:47884608
[vcf_to_zarr] 7733248 rows in 196.29s; chunk in 1.78s (36736 rows/s); 3R:39313751
[vcf_to_zarr] 7864320 rows in 196.65s; chunk in 1.43s (45755 rows/s); 2L:45982379
[vcf_to_zarr] 7536640 rows in 197.75s; chunk in 1.67s (39307 rows/s); 2R:48450288
[vcf_to_zarr] 7798784 rows in 197.87s; chunk in 1.58s (41391 rows/s); 3R:39692809
[vcf_to_zarr] 7929856 rows in 198.24s; chunk in 1.58s (41361 rows/s); 2L:46328193
[vcf_to_zarr] 7602176 rows in 199.45s; chunk in 1.70s (38545 rows/s); 2R:49067862
[vcf_to_zarr] 7864320 rows in 199.60s; chunk in 1.73s (37984 rows/s); 3R:40052947
[vcf_to_zarr] 7995392 rows in 199.73s; chunk in 1.50s (43806 rows/s); 2L:46670062
[vcf_to_zarr] 8060928 rows in 201.28s; chunk in 1.55s (42221 rows/s); 2L:47011911
[vcf_to_zarr] 7929856 rows in 201.37s; chunk in 1.77s (37025 rows/s); 3R:40427236
[vcf_to_zarr] 7667712 rows in 201.39s; chunk in 1.94s (33803 rows/s); 2R:49718014
[vcf_to_zarr] 8126464 rows in 202.72s; chunk in 1.44s (45553 rows/s); 2L:47329449
[vcf_to_zarr] 7995392 rows in 202.92s; chunk in 1.55s (42358 rows/s); 3R:40772436
[vcf_to_zarr] 7733248 rows in 203.10s; chunk in 1.71s (38402 rows/s); 2R:50241224
[vcf_to_zarr] 8192000 rows in 204.22s; chunk in 1.50s (43777 rows/s); 2L:47651701
[vcf_to_zarr] 8060928 rows in 204.68s; chunk in 1.76s (37208 rows/s); 3R:41132098
[vcf_to_zarr] 7798784 rows in 205.07s; chunk in 1.97s (33193 rows/s); 2R:50909527
[vcf_to_zarr] 8257536 rows in 205.71s; chunk in 1.49s (43856 rows/s); 2L:48006760
[vcf_to_zarr] 8126464 rows in 206.37s; chunk in 1.69s (38783 rows/s); 3R:41516708
[vcf_to_zarr] 7864320 rows in 206.79s; chunk in 1.72s (38092 rows/s); 2R:51556012
[vcf_to_zarr] 8323072 rows in 207.16s; chunk in 1.44s (45370 rows/s); 2L:48342299
[vcf_to_zarr] 8192000 rows in 208.07s; chunk in 1.70s (38481 rows/s); 3R:41998843
[vcf_to_zarr] 7929856 rows in 208.46s; chunk in 1.67s (39223 rows/s); 2R:52168243
[vcf_to_zarr] 8388608 rows in 208.69s; chunk in 1.53s (42796 rows/s); 2L:48687355
[vcf_to_zarr] 8257536 rows in 209.97s; chunk in 1.89s (34587 rows/s); 3R:42486008
[vcf_to_zarr] 8454144 rows in 210.21s; chunk in 1.52s (43169 rows/s); 2L:49045933
[vcf_to_zarr] 7995392 rows in 210.28s; chunk in 1.82s (36007 rows/s); 2R:52817429
[vcf_to_zarr] 8477477 rows in 210.95s; chunk in 0.74s (31494 rows/s)
[vcf_to_zarr] all done (40175 rows/s)
[vcf_to_zarr] 8323072 rows in 211.64s; chunk in 1.68s (39054 rows/s); 3R:42918778
[vcf_to_zarr] 8060928 rows in 212.04s; chunk in 1.76s (37233 rows/s); 2R:53437978
[vcf_to_zarr] 8388608 rows in 213.31s; chunk in 1.67s (39332 rows/s); 3R:43465051
[vcf_to_zarr] 8126464 rows in 213.85s; chunk in 1.80s (36366 rows/s); 2R:54094810
[vcf_to_zarr] 8454144 rows in 215.05s; chunk in 1.74s (37724 rows/s); 3R:43924909
[vcf_to_zarr] 8192000 rows in 215.51s; chunk in 1.66s (39420 rows/s); 2R:54832808
[vcf_to_zarr] 8519680 rows in 216.68s; chunk in 1.63s (40195 rows/s); 3R:44361232
[vcf_to_zarr] 8257536 rows in 217.22s; chunk in 1.71s (38282 rows/s); 2R:55501230
[vcf_to_zarr] 8585216 rows in 218.23s; chunk in 1.56s (42096 rows/s); 3R:44855408
[vcf_to_zarr] 8323072 rows in 219.03s; chunk in 1.80s (36323 rows/s); 2R:56142778
[vcf_to_zarr] 8650752 rows in 220.04s; chunk in 1.81s (36213 rows/s); 3R:45424639
[vcf_to_zarr] 8388608 rows in 220.71s; chunk in 1.68s (38990 rows/s); 2R:56746619
[vcf_to_zarr] 8716288 rows in 221.76s; chunk in 1.71s (38289 rows/s); 3R:46168325
[vcf_to_zarr] 8454144 rows in 222.43s; chunk in 1.72s (38092 rows/s); 2R:57412809
[vcf_to_zarr] 8781824 rows in 223.53s; chunk in 1.78s (36904 rows/s); 3R:46849457
[vcf_to_zarr] 8519680 rows in 224.32s; chunk in 1.90s (34537 rows/s); 2R:58158057
[vcf_to_zarr] 8847360 rows in 225.33s; chunk in 1.80s (36488 rows/s); 3R:47457150
[vcf_to_zarr] 8585216 rows in 226.15s; chunk in 1.82s (35963 rows/s); 2R:59176583
[vcf_to_zarr] 8912896 rows in 227.04s; chunk in 1.71s (38371 rows/s); 3R:48179337
[vcf_to_zarr] 8650752 rows in 227.96s; chunk in 1.81s (36174 rows/s); 2R:60480251
[vcf_to_zarr] 8978432 rows in 228.72s; chunk in 1.69s (38807 rows/s); 3R:48928677
[vcf_to_zarr] 8689068 rows in 229.22s; chunk in 1.26s (30402 rows/s)
[vcf_to_zarr] all done (37896 rows/s)
[vcf_to_zarr] 9043968 rows in 230.64s; chunk in 1.92s (34194 rows/s); 3R:49763649
[vcf_to_zarr] 9109504 rows in 232.41s; chunk in 1.77s (36935 rows/s); 3R:50433535
[vcf_to_zarr] 9175040 rows in 234.37s; chunk in 1.96s (33455 rows/s); 3R:51228367
[vcf_to_zarr] 9240576 rows in 236.22s; chunk in 1.84s (35585 rows/s); 3R:52221142
[vcf_to_zarr] 9274700 rows in 237.20s; chunk in 0.99s (34603 rows/s)
[vcf_to_zarr] all done (39089 rows/s)

In [ ]:

    




    

In [5]:

    

callset = zarr.open_group(OUTFN, mode='r')


    

In [7]:

    

%%time
callset['2L'].tree()


    

    




CPU times: user 997 µs, sys: 290 µs, total: 1.29 ms
Wall time: 789 µs






    
Out[7]:




2L
calldata
DP (8477477, 100) int16
GT (8477477, 100, 2) int8
samples (100,) object
variants
AC (8477477, 3) int32
AF (8477477, 3) float32
ALT (8477477, 3) object
AN (8477477,) int32
CHROM (8477477,) object
DP (8477477,) int32
POS (8477477,) int32
QUAL (8477477,) float32
REF (8477477,) object
TYPE (8477477, 3) object
numalt (8477477,) int32

In [6]:

    

t = callset


    

In [9]:

    

list(callset['2L/variants'].keys())


    

    
Out[9]:





['AC',
 'AF',
 'ALT',
 'AN',
 'CHROM',
 'DP',
 'POS',
 'QUAL',
 'REF',
 'TYPE',
 'numalt']

In [ ]: