level outputs

README.md

output from:

for i in 0 1 2 3 4 5;
do
   ../../sourmash/sourmash search_mxt 15genome.catlas.5.mxt *.sig -l $i \
       > /tmp/level${i}.txt
done

You'll need:

• 15genome.gxt and 15genome.mxt from spacegraphcats/examples/.
• the 15genome*.sig files in spacegraphcats/data/.
• the 'search_mxt' branch of sourmash
• the minhash branch of khmer and the master branch of spacegraphcats

Then build an r=5 catlas,

 spacegraphcats/build-catlas.py 15genome 5

and run the command at the top.

level0.txt

# running sourmash subcommand: search_mxt
reading gxtfile for level 0
read 12794 nodes
reading mxt file
loading ../data/15genome.fa.1.sig
loading ../data/15genome.fa.10.sig
loading ../data/15genome.fa.11.sig
loading ../data/15genome.fa.12.sig
loading ../data/15genome.fa.13.sig
loading ../data/15genome.fa.14.sig
loading ../data/15genome.fa.15.sig
loading ../data/15genome.fa.2.sig
loading ../data/15genome.fa.3.sig
loading ../data/15genome.fa.4.sig
loading ../data/15genome.fa.5.sig
loading ../data/15genome.fa.6.sig
loading ../data/15genome.fa.7.sig
loading ../data/15genome.fa.8.sig
loading ../data/15genome.fa.9.sig
sig: Acidobacterium_capsulatum_ATCC_51196
0.024 0.006 16546
0.026 0.002 15023
0.043 0.002 20100
0.125 0.002 15062
sum: 0.378
---
sig: Caldibescii_DSM_6725
0.200 0.002 20940
0.200 0.002 21666
0.200 0.002 21997
0.200 0.002 24694
sum: 5.180
---
sig: Chlorobiumlimicola_DSM_245
0.200 0.002 22150
0.200 0.002 22388
0.200 0.002 23665
0.200 0.002 24357
sum: 3.084
---
sig: Chlorobiumphaeobacteroides_DSM_266
0.200 0.002 13744
0.200 0.002 17575
0.200 0.002 23544
0.200 0.002 24563
sum: 2.232
---
sig: Chlorobiumphaeovibrioides_DSM_265
0.111 0.002 19902
0.167 0.002 12074
0.200 0.002 17450
0.200 0.002 18618
sum: 1.039
---
sig: Chlorobiumtepidum_TLS
0.050 0.002 21318
0.053 0.008 20167
0.077 0.002 13459
0.200 0.002 24087
sum: 1.036
---
sig: Chloroflexus_aurantiacus_J-10-fl
0.200 0.002 19396
0.200 0.002 23091
0.200 0.002 23752
0.200 0.002 24694
sum: 1.465
---
sig: Aciduliprofundum_boonei_T469
0.014 0.002 23395
0.091 0.002 22928
0.167 0.002 22146
0.200 0.002 14250
sum: 0.471
---
sig: Akkermansia_muciniphila_ATCC_BAA-835
0.048 0.002 18378
0.050 0.002 22251
0.111 0.002 20588
0.200 0.002 19387
sum: 0.603
---
sig: Archaeoglobus_fulgidus_DSM_4304
0.022 0.004 21717
0.033 0.002 18328
0.037 0.004 12315
0.037 0.004 24104
sum: 0.269
---
sig: Bacteroides_thetaiotaomicron_VPI-5482
0.071 0.002 13507
0.100 0.002 17806
0.200 0.002 16448
0.200 0.002 21891
sum: 0.775
---
sig: Bacteroides_vulgatus_ATCC_8482
0.200 0.002 16448
0.200 0.002 16780
0.200 0.002 21891
0.200 0.002 23091
sum: 1.428
---
sig: Bordetella_bronchiseptica_strain_RB50
0.167 0.002 14990
0.200 0.002 20246
0.200 0.002 21044
0.200 0.002 21375
sum: 1.365
---
sig: Burkholderia1_xenovorans_LB400_chromosome_1,_complete_sequence
0.062 0.002 17952
0.091 0.002 19577
0.125 0.002 21544
0.200 0.002 19840
sum: 0.823
---
sig: Caldisaccharolyticus_DSM_8903
0.200 0.002 19599
0.200 0.002 21102
0.200 0.002 21997
0.200 0.002 23106
sum: 4.101
---

level1.txt

# running sourmash subcommand: search_mxt
reading gxtfile for level 1
read 5902 nodes
reading mxt file
loading ../data/15genome.fa.1.sig
loading ../data/15genome.fa.10.sig
loading ../data/15genome.fa.11.sig
loading ../data/15genome.fa.12.sig
loading ../data/15genome.fa.13.sig
loading ../data/15genome.fa.14.sig
loading ../data/15genome.fa.15.sig
loading ../data/15genome.fa.2.sig
loading ../data/15genome.fa.3.sig
loading ../data/15genome.fa.4.sig
loading ../data/15genome.fa.5.sig
loading ../data/15genome.fa.6.sig
loading ../data/15genome.fa.7.sig
loading ../data/15genome.fa.8.sig
loading ../data/15genome.fa.9.sig
sig: Acidobacterium_capsulatum_ATCC_51196
0.022 0.006 6572
0.022 0.006 11225
0.024 0.006 6352
0.043 0.002 11081
sum: 0.182
---
sig: Caldibescii_DSM_6725
0.200 0.002 10359
0.200 0.002 10641
0.200 0.002 10776
0.200 0.002 11256
sum: 2.317
---
sig: Chlorobiumlimicola_DSM_245
0.200 0.002 8495
0.200 0.002 11345
0.200 0.002 11356
0.200 0.002 11432
sum: 1.575
---
sig: Chlorobiumphaeobacteroides_DSM_266
0.071 0.002 6560
0.071 0.002 9557
0.111 0.002 11587
0.200 0.002 6394
sum: 0.598
---
sig: Chlorobiumphaeovibrioides_DSM_265
0.026 0.006 8980
0.045 0.002 11609
0.059 0.002 9749
0.111 0.002 8494
sum: 0.385
---
sig: Chlorobiumtepidum_TLS
0.042 0.002 9031
0.050 0.002 10282
0.053 0.008 6742
0.200 0.002 6523
sum: 0.594
---
sig: Chloroflexus_aurantiacus_J-10-fl
0.018 0.002 10946
0.026 0.002 6217
0.031 0.002 8007
0.067 0.002 7676
sum: 0.233
---
sig: Aciduliprofundum_boonei_T469
0.167 0.002 7470
0.200 0.002 8749
sum: 0.367
---
sig: Akkermansia_muciniphila_ATCC_BAA-835
0.024 0.002 11599
0.037 0.002 6712
0.037 0.002 9394
0.200 0.002 7443
sum: 0.364
---
sig: Archaeoglobus_fulgidus_DSM_4304
0.020 0.002 6431
0.020 0.002 7426
0.020 0.002 10992
0.037 0.004 7835
sum: 0.124
---
sig: Bacteroides_thetaiotaomicron_VPI-5482
0.026 0.004 7868
0.071 0.002 11834
0.200 0.002 8952
0.200 0.002 10693
sum: 0.598
---
sig: Bacteroides_vulgatus_ATCC_8482
0.031 0.002 9886
0.040 0.004 11933
0.200 0.002 8952
0.200 0.002 10693
sum: 0.642
---
sig: Bordetella_bronchiseptica_strain_RB50
0.038 0.002 6715
0.038 0.002 7643
0.038 0.002 8184
0.200 0.002 7229
sum: 0.569
---
sig: Burkholderia1_xenovorans_LB400_chromosome_1,_complete_sequence
0.062 0.002 8125
0.125 0.002 8647
0.125 0.002 11655
0.200 0.002 6455
sum: 0.687
---
sig: Caldisaccharolyticus_DSM_8903
0.200 0.002 10359
0.200 0.002 10641
0.200 0.002 10808
0.200 0.002 11256
sum: 2.329
---

level2.txt

# running sourmash subcommand: search_mxt
reading gxtfile for level 2
read 2893 nodes
reading mxt file
loading ../data/15genome.fa.1.sig
loading ../data/15genome.fa.10.sig
loading ../data/15genome.fa.11.sig
loading ../data/15genome.fa.12.sig
loading ../data/15genome.fa.13.sig
loading ../data/15genome.fa.14.sig
loading ../data/15genome.fa.15.sig
loading ../data/15genome.fa.2.sig
loading ../data/15genome.fa.3.sig
loading ../data/15genome.fa.4.sig
loading ../data/15genome.fa.5.sig
loading ../data/15genome.fa.6.sig
loading ../data/15genome.fa.7.sig
loading ../data/15genome.fa.8.sig
loading ../data/15genome.fa.9.sig
sig: Acidobacterium_capsulatum_ATCC_51196
0.004 0.002 5982
0.022 0.006 4472
0.043 0.002 5804
sum: 0.070
---
sig: Caldibescii_DSM_6725
0.111 0.002 5133
0.200 0.002 4367
0.200 0.002 5228
0.200 0.002 5235
sum: 0.854
---
sig: Chlorobiumlimicola_DSM_245
0.023 0.004 3816
sum: 0.023
---
sig: Chlorobiumphaeobacteroides_DSM_266
0.017 0.004 5434
sum: 0.017
---
sig: Chlorobiumphaeovibrioides_DSM_265
0.019 0.004 5091
0.019 0.004 5444
0.026 0.006 3242
0.026 0.006 4175
sum: 0.155
---
sig: Chlorobiumtepidum_TLS
0.023 0.012 5461
0.053 0.008 4028
sum: 0.075
---
sig: Chloroflexus_aurantiacus_J-10-fl
0.018 0.002 4151
0.018 0.002 5346
0.018 0.002 5392
0.067 0.002 5078
sum: 0.179
---
sig: Aciduliprofundum_boonei_T469
0.200 0.002 5335
sum: 0.200
---
sig: Akkermansia_muciniphila_ATCC_BAA-835
0.020 0.002 3374
0.024 0.002 4244
0.024 0.002 5597
sum: 0.069
---
sig: Archaeoglobus_fulgidus_DSM_4304
0.009 0.006 5985
0.020 0.002 5523
sum: 0.029
---
sig: Bacteroides_thetaiotaomicron_VPI-5482
0.014 0.004 4446
0.023 0.006 4148
0.200 0.002 3809
sum: 0.237
---
sig: Bacteroides_vulgatus_ATCC_8482
0.024 0.002 5285
0.025 0.004 4598
0.025 0.004 5255
0.200 0.002 3809
sum: 0.323
---
sig: Bordetella_bronchiseptica_strain_RB50
0.023 0.002 3778
0.026 0.002 4582
0.026 0.002 5049
0.038 0.002 4247
sum: 0.235
---
sig: Burkholderia1_xenovorans_LB400_chromosome_1,_complete_sequence
0.035 0.004 4971
0.062 0.002 3558
0.125 0.002 3285
0.125 0.002 4944
sum: 0.385
---
sig: Caldisaccharolyticus_DSM_8903
0.067 0.002 5620
0.200 0.002 3737
0.200 0.002 4367
0.200 0.002 5298
sum: 0.948
---

level3.txt

# running sourmash subcommand: search_mxt
reading gxtfile for level 3
read 1561 nodes
reading mxt file
loading ../data/15genome.fa.1.sig
loading ../data/15genome.fa.10.sig
loading ../data/15genome.fa.11.sig
loading ../data/15genome.fa.12.sig
loading ../data/15genome.fa.13.sig
loading ../data/15genome.fa.14.sig
loading ../data/15genome.fa.15.sig
loading ../data/15genome.fa.2.sig
loading ../data/15genome.fa.3.sig
loading ../data/15genome.fa.4.sig
loading ../data/15genome.fa.5.sig
loading ../data/15genome.fa.6.sig
loading ../data/15genome.fa.7.sig
loading ../data/15genome.fa.8.sig
loading ../data/15genome.fa.9.sig
sig: Acidobacterium_capsulatum_ATCC_51196
0.004 0.002 2221
0.004 0.002 2931
sum: 0.008
---
sig: Caldibescii_DSM_6725
0.027 0.002 2423
0.038 0.006 2083
0.038 0.006 2118
0.200 0.002 2304
sum: 0.321
---
sig: Chlorobiumlimicola_DSM_245
0.023 0.004 1733
sum: 0.023
---
sig: Chlorobiumphaeobacteroides_DSM_266
sum: 0.000
---
sig: Chlorobiumphaeovibrioides_DSM_265
0.026 0.006 1980
0.026 0.006 2682
0.026 0.006 2774
0.026 0.006 3168
sum: 0.171
---
sig: Chlorobiumtepidum_TLS
0.053 0.008 2261
0.053 0.008 3178
sum: 0.105
---
sig: Chloroflexus_aurantiacus_J-10-fl
0.012 0.002 2077
0.013 0.002 2451
0.018 0.002 2129
0.067 0.002 2563
sum: 0.119
---
sig: Aciduliprofundum_boonei_T469
0.200 0.002 2908
sum: 0.200
---
sig: Akkermansia_muciniphila_ATCC_BAA-835
0.020 0.002 2335
0.020 0.002 2648
0.024 0.002 2439
sum: 0.065
---
sig: Archaeoglobus_fulgidus_DSM_4304
0.020 0.002 2267
sum: 0.020
---
sig: Bacteroides_thetaiotaomicron_VPI-5482
sum: 0.000
---
sig: Bacteroides_vulgatus_ATCC_8482
0.024 0.002 2433
0.025 0.004 1743
sum: 0.049
---
sig: Bordetella_bronchiseptica_strain_RB50
0.018 0.002 2410
0.018 0.002 3135
0.023 0.002 1902
0.026 0.002 2615
sum: 0.083
---
sig: Burkholderia1_xenovorans_LB400_chromosome_1,_complete_sequence
0.035 0.004 2575
0.125 0.002 1777
0.125 0.002 2662
0.125 0.002 2699
sum: 0.433
---
sig: Caldisaccharolyticus_DSM_8903
0.059 0.004 2664
0.067 0.002 2436
0.200 0.002 1916
0.200 0.002 2510
sum: 0.670
---

level4.txt

# running sourmash subcommand: search_mxt
reading gxtfile for level 4
read 849 nodes
reading mxt file
loading ../data/15genome.fa.1.sig
loading ../data/15genome.fa.10.sig
loading ../data/15genome.fa.11.sig
loading ../data/15genome.fa.12.sig
loading ../data/15genome.fa.13.sig
loading ../data/15genome.fa.14.sig
loading ../data/15genome.fa.15.sig
loading ../data/15genome.fa.2.sig
loading ../data/15genome.fa.3.sig
loading ../data/15genome.fa.4.sig
loading ../data/15genome.fa.5.sig
loading ../data/15genome.fa.6.sig
loading ../data/15genome.fa.7.sig
loading ../data/15genome.fa.8.sig
loading ../data/15genome.fa.9.sig
sig: Acidobacterium_capsulatum_ATCC_51196
0.004 0.002 1455
sum: 0.004
---
sig: Caldibescii_DSM_6725
0.012 0.002 1351
0.038 0.006 1393
sum: 0.051
---
sig: Chlorobiumlimicola_DSM_245
sum: 0.000
---
sig: Chlorobiumphaeobacteroides_DSM_266
sum: 0.000
---
sig: Chlorobiumphaeovibrioides_DSM_265
0.019 0.004 881
0.026 0.006 1299
sum: 0.045
---
sig: Chlorobiumtepidum_TLS
0.053 0.008 1496
sum: 0.053
---
sig: Chloroflexus_aurantiacus_J-10-fl
0.009 0.002 952
sum: 0.009
---
sig: Aciduliprofundum_boonei_T469
sum: 0.000
---
sig: Akkermansia_muciniphila_ATCC_BAA-835
0.020 0.002 1621
sum: 0.020
---
sig: Archaeoglobus_fulgidus_DSM_4304
0.020 0.002 839
0.020 0.002 1526
sum: 0.041
---
sig: Bacteroides_thetaiotaomicron_VPI-5482
sum: 0.000
---
sig: Bacteroides_vulgatus_ATCC_8482
sum: 0.000
---
sig: Bordetella_bronchiseptica_strain_RB50
0.018 0.002 1025
0.018 0.002 1511
sum: 0.035
---
sig: Burkholderia1_xenovorans_LB400_chromosome_1,_complete_sequence
0.023 0.002 883
0.125 0.002 889
0.125 0.002 1231
sum: 0.273
---
sig: Caldisaccharolyticus_DSM_8903
0.016 0.002 1522
0.059 0.004 1204
0.059 0.004 1614
0.067 0.002 1453
sum: 0.217
---

level5.txt

# running sourmash subcommand: search_mxt
reading gxtfile for level 5
read 449 nodes
reading mxt file
loading ../data/15genome.fa.1.sig
loading ../data/15genome.fa.10.sig
loading ../data/15genome.fa.11.sig
loading ../data/15genome.fa.12.sig
loading ../data/15genome.fa.13.sig
loading ../data/15genome.fa.14.sig
loading ../data/15genome.fa.15.sig
loading ../data/15genome.fa.2.sig
loading ../data/15genome.fa.3.sig
loading ../data/15genome.fa.4.sig
loading ../data/15genome.fa.5.sig
loading ../data/15genome.fa.6.sig
loading ../data/15genome.fa.7.sig
loading ../data/15genome.fa.8.sig
loading ../data/15genome.fa.9.sig
sig: Acidobacterium_capsulatum_ATCC_51196
sum: 0.000
---
sig: Caldibescii_DSM_6725
sum: 0.000
---
sig: Chlorobiumlimicola_DSM_245
sum: 0.000
---
sig: Chlorobiumphaeobacteroides_DSM_266
sum: 0.000
---
sig: Chlorobiumphaeovibrioides_DSM_265
sum: 0.000
---
sig: Chlorobiumtepidum_TLS
0.053 0.008 700
sum: 0.053
---
sig: Chloroflexus_aurantiacus_J-10-fl
sum: 0.000
---
sig: Aciduliprofundum_boonei_T469
sum: 0.000
---
sig: Akkermansia_muciniphila_ATCC_BAA-835
0.020 0.002 712
sum: 0.020
---
sig: Archaeoglobus_fulgidus_DSM_4304
0.020 0.002 419
sum: 0.020
---
sig: Bacteroides_thetaiotaomicron_VPI-5482
sum: 0.000
---
sig: Bacteroides_vulgatus_ATCC_8482
sum: 0.000
---
sig: Bordetella_bronchiseptica_strain_RB50
0.018 0.002 561
sum: 0.018
---
sig: Burkholderia1_xenovorans_LB400_chromosome_1,_complete_sequence
sum: 0.000
---
sig: Caldisaccharolyticus_DSM_8903
0.059 0.004 429
0.067 0.002 589
sum: 0.125
---