AllTheBacteria’s 0.2 Database Release Creation Report

Published

Thursday, the 1^th of August, 2024

Databases created for release 0.2

The list of database files:

  - Created allthebacteria-r0.2-k21.zip 

  - Created allthebacteria-r0.2-k31.zip 

  - Created allthebacteria-r0.2-k51.zip

Summary of database

Looking only at the first k-value defined in 21, 31, 51.

Summary example for the new databases

The manifest for /group/ctbrowngrp4/2024-ccbaumler-allthebacteria/allthebacteria-r0.2/allthebacteria-r0.2-sigs/allthebacteria-r0.2-k21.zip:


[K** loading from '/group/ctbrowngrp4/2024-ccbaumler-allthebacteria/allthebacteria-r0.2/allthebacteria-r0.2-metadata/allthebacteria-r0.2-mf.csv'
path filetype: StandaloneManifestIndex
location: /group/ctbrowngrp4/2024-ccbaumler-allthebacteria/allthebacteria-r0.2/allthebacteria-r0.2-metadata/allthebacteria-r0.2-mf.csv
is database? yes
has manifest? yes
num signatures: 5793795

[K** examining manifest...
total hashes: 23318584698
summary of sketches:
   1931265 sketches with DNA, k=31, scaled=1000, abund 7753638099 total hashes
   1931265 sketches with DNA, k=51, scaled=1000, abund 7778434121 total hashes
   1931265 sketches with DNA, k=21, scaled=1000, abund 7786512478 total hashes

Replicate these results:

sourmash sig summarize database.zip

Workflow details for databases release 0.2

For the 1931265 sequences in the create databases, there are 1546 missing signatures from the expected 1932812.

Expand for details

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SAMN30443542
SAMN30443543
SAMN30443549
SAMN30443551
SAMN30443956
SAMN30443957
SAMN30443960
SAMN30443961
SAMN30443968
SAMN30443977
SAMN30444005
SAMN30444006
SAMN30444743
SAMN30444746
SAMN30444747
SAMN30444761
SAMN30444767
SAMN30444772
SAMN30444773
SAMN30444774
SAMN30444775
SAMN30444776
SAMN30444810
SAMN30444811
SAMN30444815
SAMN30444818
SAMN30444819
SAMN30444820
SAMN30444824
SAMN30444825
SAMN30444874
SAMN30444877
SAMN30444878
SAMN30444880
SAMN30444882
SAMN30444883
SAMN30444884
SAMN30444886
SAMN30444887
SAMN30444888
SAMN30444890
SAMN30444891
SAMN30444892
SAMN30444895
SAMN30444910
SAMN30445191
SAMN30445192
SAMN30445194
SAMN30446270
SAMN30446271
SAMN30446273
SAMN30446274
SAMN30446329
SAMN30446333
SAMN30446334
SAMN30446335
SAMN30446336
SAMN30446342
SAMN30446376
SAMN30446380
SAMN30446381
SAMN30446383
SAMN30446387
SAMN30446389
SAMN30446390
SAMN30446391
SAMN30446393
SAMN30446395
SAMN30446398
SAMN30446399
SAMN30446401
SAMN30446453
SAMN30446455
SAMN30447951
SAMN30447953
SAMN30447960
SAMN30447963
SAMN30448063
SAMN30448067
SAMN30448079
SAMN30448080
SAMN30448082
SAMN30448083
SAMN30448084
SAMN30448085
SAMN30448086
SAMN30448088
SAMN30448091
SAMN30448092
SAMN30448644
SAMN30448646
SAMN30448679
SAMN30448681
SAMN30448683
SAMN30448685
SAMN30448687
SAMN30448689
SAMN30465587
SAMN30465996
SAMN30465997
SAMN30465998
SAMN30466001
SAMN30466005
SAMN30466007
SAMN30466008
SAMN30466010
SAMN30466011
SAMN30466014
SAMN30466017
SAMN30466021
SAMN30466023
SAMN30466028
SAMN30466030
SAMN30466033
SAMN30467052
SAMN30467332
SAMN30467334
SAMN30467339
SAMN30467340
SAMN30467508
SAMN30467509
SAMN30467515
SAMN30467516
SAMN30467517
SAMN30467521
SAMN30467531
SAMN30467579
SAMN30467580
SAMN30467581
SAMN30467582
SAMN30467586
SAMN30467588
SAMN30467590
SAMN30467591
SAMN30467600
SAMN30467604
SAMN30467608
SAMN30467610
SAMN30467612
SAMN30467613
SAMN30467628
SAMN30467630
SAMN30467634
SAMN30467635
SAMN30467636
SAMN30467637
SAMN30467639
SAMN30467642
SAMN30467643
SAMN30467648
SAMN30467649
SAMN30467650
SAMN30467654
SAMN30467658
SAMN30467660
SAMN30467662
SAMN30467663
SAMN30467665
SAMN30468147
SAMN30468149
SAMN30468184
SAMN30468187
SAMN30468207
SAMN30468208
SAMN30468236
SAMN30468237
SAMN30468241
SAMN30468242
SAMN30468246
SAMN30468247
SAMN30468254
SAMN30468255
SAMN30468261
SAMN30468569
SAMN30468570
SAMN30468571
SAMN30468575
SAMN30468578
SAMN30468584
SAMN30468585
SAMN30468586
SAMN30468587
SAMN30468605
SAMN30468608
SAMN30468609
SAMN30468610
SAMN30468613
SAMN30468614
SAMN30468618
SAMN30468619
SAMN30468620
SAMN30468622
SAMN30468623
SAMN30468626
SAMN30468628
SAMN30468635
SAMN30468679
SAMN30468680
SAMN30468690
SAMN30468722
SAMN30468723
SAMN30468764
SAMN30468765
SAMN30468767
SAMN30468771
SAMN30468772
SAMN30468773
SAMN30468776
SAMN30468989
SAMN30468991
SAMN30468993
SAMN30468995
SAMN30468996
SAMN30468999
SAMN30469002
SAMN30469003
SAMN30469005
SAMN30469007
SAMN30469009
SAMN30469011
SAMN30469012
SAMN30469013
SAMN30469016
SAMN30469405
SAMN30469412
SAMN30469415
SAMN30469416
SAMN30469419
SAMN30469420
SAMN30469425
SAMN30469426
SAMN30469428
SAMN30469431
SAMN30469434
SAMN30469443
SAMN30469445
SAMN30469448
SAMN30469449
SAMN30469450
SAMN30469455
SAMN30469458
SAMN30469460
SAMN30469462
SAMN30469464
SAMN30469466
SAMN30469467
SAMN30469471
SAMN30469485
SAMN30469489
SAMN30469491
SAMN30469493
SAMN30469503
SAMN30469504
SAMN30469505
SAMN30469508
SAMN30469511
SAMN30469512
SAMN30469515
SAMN30469516
SAMN30469519
SAMN30469522
SAMN30469525
SAMN30469527
SAMN30469528
SAMN30469531
SAMN30469532
SAMN30469533
SAMN30469536
SAMN30469540
SAMN30469543
SAMN30469546
SAMN30469548
SAMN30469549
SAMN30469550
SAMN30469552
SAMN30469553
SAMN30469572
SAMN30469576
SAMN30469577
SAMN30469578
SAMN30469580
SAMN30469581
SAMN30470042
SAMN30470043
SAMN30471259
SAMN30471261
SAMN30473540
SAMN30473541
SAMN30473543
SAMN30473544
SAMN30473545
SAMN30473547
SAMN30473552
SAMN30473554
SAMN30473559
SAMN30473560
SAMN30473561
SAMN30473562
SAMN30473564
SAMN30473566
SAMN30473567
SAMN30473568
SAMN30473572
SAMN30473574
SAMN30473575
SAMN30473577
SAMN30473578
SAMN30473580
SAMN30473581
SAMN30473582
SAMN30473590
SAMN30473592
SAMN30473593
SAMN30473594
SAMN30473612
SAMN30473616
SAMN30473618
SAMN30473619
SAMN30473621
SAMN30473625
SAMN30473628
SAMN30473629
SAMN30473632
SAMN30473633
SAMN30473635
SAMN30473636
SAMN30473637
SAMN30473638
SAMN30473642
SAMN30473643
SAMN30473644
SAMN30473646
SAMN30473650
SAMN30473651
SAMN30473655
SAMN30473657
SAMN30473662
SAMN30473664
SAMN30478060
SAMN30478062
SAMN30478065
SAMN30478066
SAMN30478224
SAMN30478225
SAMN30478226
SAMN30478227
SAMN30478229
SAMN30478239
SAMN30478253
SAMN30478254
SAMN30478256
SAMN30478258
SAMN30478264
SAMN30478288
SAMN30478336
SAMN30478337
SAMN30478343
SAMN30478345
SAMN30478381
SAMN30478383
SAMN30478387
SAMN30478388
SAMN30478389
SAMN30478390
SAMN30478417
SAMN30478419
SAMN30478548
SAMN30478549
SAMN30478553
SAMN30478555
SAMN30478557
SAMN30478591
SAMN30478592
SAMN30478593
SAMN30479081
SAMN30479082
SAMN30479086
SAMN30480151
SAMN30480152
SAMN30480153
SAMN30480155
SAMN30480156
SAMN30480171
SAMN30480551
SAMN30480552
SAMN30480553
SAMN30480555
SAMN30481974
SAMN30481975
SAMN30481988
SAMN30481989
SAMN30481990
SAMN30481991
SAMN30481994
SAMN30485154
SAMN30487348
SAMN30487354
SAMN30487358
SAMN30487359
SAMN30487362
SAMN30487363
SAMN30487391
SAMN30487400
SAMN30487401
SAMN30487402
SAMN30487404
SAMN30487405
SAMN30487406
SAMN30487410
SAMN30487411
SAMN30487413
SAMN30487414
SAMN30487451
SAMN30488425
SAMN30488443
SAMN30489266
SAMN30489267
SAMN30489268
SAMN30489269
SAMN30489271
SAMN30489274
SAMN30489276
SAMN30489277
SAMN30489278
SAMN30489279
SAMN30489284
SAMN30489285
SAMN30489291
SAMN30489293
SAMN30489294
SAMN30489295
SAMN30489300
SAMN30489301
SAMN30489303
SAMN30489305
SAMN30496886
SAMN30496954
SAMN30496955
SAMN30496956
SAMN30497147
SAMN30497148
SAMN30497149
SAMN30497218
SAMN30497219
SAMN30497220
SAMN30497251
SAMN30497252
SAMN30497254
SAMN30497375
SAMN30497376
SAMN30497377
SAMN30497380
SAMN30497431
SAMN30497434
SAMN30497436
SAMN30497825
SAMN30497826
SAMN30497827
SAMN30497903
SAMN30497905
SAMN30497911
SAMN30497916
SAMN30498069
SAMN30498071
SAMN30498076
SAMN30498079
SAMN30498080
SAMN30498084
SAMN30498087
SAMN30498120
SAMN30498121
SAMN30498126
SAMN30498128
SAMN30498147
SAMN30498153
SAMN30498154
SAMN30498156
SAMN30498342
SAMN30498345
SAMN30498348
SAMN30498349
SAMN30498352
SAMN30498353
SAMN30498402
SAMN30498433
SAMN30498436
SAMN30498437
SAMN30498439
SAMN30498440
SAMN30498442
SAMN30498443
SAMN30498449
SAMN30498450
SAMN30498451
SAMN30498452
SAMN30498457
SAMN30498461
SAMN30498465
SAMN30498466
SAMN30498477
SAMN30498478
SAMN30498480
SAMN30498481
SAMN30498486
SAMN30498487
SAMN30498489
SAMN30498490
SAMN30498491
SAMN30498492
SAMN30498493
SAMN30498495
SAMN30498501
SAMN30498502
SAMN30498503
SAMN30499728
SAMN30499729
SAMN30499733
SAMN30499737
SAMN30499746
SAMN30499748

Failures: Sequences failed to download or sketch

The script find_missing_files.sh was used to identify the missing sequences amoung the tar.xz archives. This script found 1547 missing sequences.

Expand for details

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Key 1: salmonella_enterica__121.asm.tar.xz/1
    Value 1/1547: salmonella_enterica__121/SAMN30489285.fa
    Value 2/1547: salmonella_enterica__121/SAMN30444895.fa
    Value 3/1547: salmonella_enterica__121/SAMN30471261.fa
    Value 4/1547: salmonella_enterica__121/SAMN30348942.fa
    Value 5/1547: salmonella_enterica__121/SAMN30444774.fa
    Value 6/1547: salmonella_enterica__121/SAMN30469449.fa
    Value 7/1547: salmonella_enterica__121/SAMN30469548.fa
    Value 8/1547: salmonella_enterica__121/SAMN30410534.fa
    Value 9/1547: salmonella_enterica__121/SAMN30324049.fa
    Value 10/1547: salmonella_enterica__121/SAMN30308497.fa
    Value 11/1547: salmonella_enterica__121/SAMN30444892.fa
    Value 12/1547: salmonella_enterica__121/SAMN30469420.fa
    Value 13/1547: salmonella_enterica__121/SAMN30468255.fa
    Value 14/1547: salmonella_enterica__121/SAMN30394976.fa
    Value 15/1547: salmonella_enterica__121/SAMN30444880.fa
    Value 16/1547: salmonella_enterica__121/SAMN30415381.fa
    Value 17/1547: salmonella_enterica__121/SAMN30444887.fa
    Value 18/1547: salmonella_enterica__121/SAMN30467663.fa
    Value 19/1547: salmonella_enterica__121/SAMN30444776.fa
    Value 20/1547: salmonella_enterica__121/SAMN30346068.fa
    Value 21/1547: salmonella_enterica__121/SAMN30323530.fa
    Value 22/1547: salmonella_enterica__121/SAMN30385713.fa
    Value 23/1547: salmonella_enterica__121/SAMN30346857.fa
    Value 24/1547: salmonella_enterica__121/SAMN30370696.fa
    Value 25/1547: salmonella_enterica__121/SAMN30395183.fa
    Value 26/1547: salmonella_enterica__121/SAMN30415461.fa
    Value 27/1547: salmonella_enterica__121/SAMN30395050.fa
    Value 28/1547: salmonella_enterica__121/SAMN30468586.fa
    Value 29/1547: salmonella_enterica__121/SAMN30383454.fa
    Value 30/1547: salmonella_enterica__121/SAMN30348649.fa
    Value 31/1547: salmonella_enterica__121/SAMN30467334.fa
    Value 32/1547: salmonella_enterica__121/SAMN30438459.fa
    Value 33/1547: salmonella_enterica__121/SAMN30345538.fa
    Value 34/1547: salmonella_enterica__121/SAMN30285971.fa
    Value 35/1547: salmonella_enterica__121/SAMN30498153.fa
    Value 36/1547: salmonella_enterica__121/SAMN30282704.fa
    Value 37/1547: salmonella_enterica__121/SAMN30313376.fa
    Value 38/1547: salmonella_enterica__121/SAMN30467517.fa
    Value 39/1547: salmonella_enterica__121/SAMN30415395.fa
    Value 40/1547: salmonella_enterica__121/SAMN30408276.fa
    Value 41/1547: salmonella_enterica__121/SAMN30380025.fa
    Value 42/1547: salmonella_enterica__121/SAMN30346426.fa
    Value 43/1547: salmonella_enterica__121/SAMN30349195.fa
    Value 44/1547: salmonella_enterica__121/SAMN30285889.fa
    Value 45/1547: salmonella_enterica__121/SAMN30346429.fa
    Value 46/1547: salmonella_enterica__121/SAMN30499748.fa
    Value 47/1547: salmonella_enterica__121/SAMN30283165.fa
    Value 48/1547: salmonella_enterica__121/SAMN30349194.fa
    Value 49/1547: salmonella_enterica__121/SAMN30346396.fa
    Value 50/1547: salmonella_enterica__121/SAMN30497147.fa
    Value 51/1547: salmonella_enterica__121/SAMN30313342.fa
    Value 52/1547: salmonella_enterica__121/SAMN30344337.fa
    Value 53/1547: salmonella_enterica__121/SAMN30496956.fa
    Value 54/1547: salmonella_enterica__121/SAMN30285885.fa
    Value 55/1547: salmonella_enterica__121/SAMN30344340.fa
    Value 56/1547: salmonella_enterica__121/SAMN30497218.fa
    Value 57/1547: salmonella_enterica__121/SAMN30283159.fa
    Value 58/1547: salmonella_enterica__121/SAMN30379969.fa
    Value 59/1547: salmonella_enterica__121/SAMN30282927.fa
    Value 60/1547: salmonella_enterica__121/SAMN30380024.fa
    Value 61/1547: salmonella_enterica__121/SAMN30281451.fa
    Value 62/1547: salmonella_enterica__121/SAMN30346568.fa
    Value 63/1547: salmonella_enterica__121/SAMN30344284.fa
    Value 64/1547: salmonella_enterica__121/SAMN30468241.fa
    Value 65/1547: salmonella_enterica__121/SAMN30469576.fa
    Value 66/1547: salmonella_enterica__121/SAMN30274394.fa
    Value 67/1547: salmonella_enterica__121/SAMN30444815.fa
    Value 68/1547: salmonella_enterica__121/SAMN30469455.fa
    Value 69/1547: salmonella_enterica__121/SAMN30469428.fa
    Value 70/1547: salmonella_enterica__121/SAMN30308492.fa
    Value 71/1547: salmonella_enterica__121/SAMN30312068.fa
    Value 72/1547: salmonella_enterica__121/SAMN30370712.fa
    Value 73/1547: salmonella_enterica__121/SAMN30371186.fa
    Value 74/1547: salmonella_enterica__121/SAMN30312027.fa
    Value 75/1547: salmonella_enterica__121/SAMN30388419.fa
    Value 76/1547: salmonella_enterica__121/SAMN30388417.fa
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    Value 1377/1547: salmonella_enterica__121/SAMN30346058.fa
    Value 1378/1547: salmonella_enterica__121/SAMN30351417.fa
    Value 1379/1547: salmonella_enterica__121/SAMN30314315.fa
    Value 1380/1547: salmonella_enterica__121/SAMN30416863.fa
    Value 1381/1547: salmonella_enterica__121/SAMN30416862.fa
    Value 1382/1547: salmonella_enterica__121/SAMN30324839.fa
    Value 1383/1547: salmonella_enterica__121/SAMN30283375.fa
    Value 1384/1547: salmonella_enterica__121/SAMN30348637.fa
    Value 1385/1547: salmonella_enterica__121/SAMN30469412.fa
    Value 1386/1547: salmonella_enterica__121/SAMN30468613.fa
    Value 1387/1547: salmonella_enterica__121/SAMN30415399.fa
    Value 1388/1547: salmonella_enterica__121/SAMN30396260.fa
    Value 1389/1547: salmonella_enterica__121/SAMN30321945.fa
    Value 1390/1547: salmonella_enterica__121/SAMN30395156.fa
    Value 1391/1547: salmonella_enterica__121/SAMN30284536.fa
    Value 1392/1547: salmonella_enterica__121/SAMN30379455.fa
    Value 1393/1547: salmonella_enterica__121/SAMN30436939.fa
    Value 1394/1547: salmonella_enterica__121/SAMN30395024.fa
    Value 1395/1547: salmonella_enterica__121/SAMN30386644.fa
    Value 1396/1547: salmonella_enterica__121/SAMN30443961.fa
    Value 1397/1547: salmonella_enterica__121/SAMN30433333.fa
    Value 1398/1547: salmonella_enterica__121/SAMN30396356.fa
    Value 1399/1547: salmonella_enterica__121/SAMN30489295.fa
    Value 1400/1547: salmonella_enterica__121/SAMN30444877.fa
    Value 1401/1547: salmonella_enterica__121/SAMN30283341.fa
    Value 1402/1547: salmonella_enterica__121/SAMN30282367.fa
    Value 1403/1547: salmonella_enterica__121/SAMN30396318.fa
    Value 1404/1547: salmonella_enterica__121/SAMN30395016.fa
    Value 1405/1547: salmonella_enterica__121/SAMN30303261.fa
    Value 1406/1547: salmonella_enterica__121/SAMN30431525.fa
    Value 1407/1547: salmonella_enterica__121/SAMN30344333.fa
    Value 1408/1547: salmonella_enterica__121/SAMN30349595.fa
    Value 1409/1547: salmonella_enterica__121/SAMN30498126.fa
    Value 1410/1547: salmonella_enterica__121/SAMN30487362.fa
    Value 1411/1547: salmonella_enterica__121/SAMN30469416.fa
    Value 1412/1547: salmonella_enterica__121/SAMN30281453.fa
    Value 1413/1547: salmonella_enterica__121/SAMN30396460.fa
    Value 1414/1547: salmonella_enterica__121/SAMN30473650.fa
    Value 1415/1547: salmonella_enterica__121/SAMN30348999.fa
    Value 1416/1547: salmonella_enterica__121/SAMN30345543.fa
    Value 1417/1547: salmonella_enterica__121/SAMN30481988.fa
    Value 1418/1547: salmonella_enterica__121/SAMN30415483.fa
    Value 1419/1547: salmonella_enterica__121/SAMN30467649.fa
    Value 1420/1547: salmonella_enterica__121/SAMN30446387.fa
    Value 1421/1547: salmonella_enterica__121/SAMN30282384.fa
    Value 1422/1547: salmonella_enterica__121/SAMN30377979.fa
    Value 1423/1547: salmonella_enterica__121/SAMN30322027.fa
    Value 1424/1547: salmonella_enterica__121/SAMN30438643.fa
    Value 1425/1547: salmonella_enterica__121/SAMN30443537.fa
    Value 1426/1547: salmonella_enterica__121/SAMN30438586.fa
    Value 1427/1547: salmonella_enterica__121/SAMN30313364.fa
    Value 1428/1547: salmonella_enterica__121/SAMN30313343.fa
    Value 1429/1547: salmonella_enterica__121/SAMN30348975.fa
    Value 1430/1547: salmonella_enterica__121/SAMN30473581.fa
    Value 1431/1547: salmonella_enterica__121/SAMN30283345.fa
    Value 1432/1547: salmonella_enterica__121/SAMN30383462.fa
    Value 1433/1547: salmonella_enterica__121/SAMN30447960.fa
    Value 1434/1547: salmonella_enterica__121/SAMN30386609.fa
    Value 1435/1547: salmonella_enterica__121/SAMN30379957.fa
    Value 1436/1547: salmonella_enterica__121/SAMN30496954.fa
    Value 1437/1547: salmonella_enterica__121/SAMN30467654.fa
    Value 1438/1547: salmonella_enterica__121/SAMN30443528.fa
    Value 1439/1547: salmonella_enterica__121/SAMN30349189.fa
    Value 1440/1547: salmonella_enterica__121/SAMN30498402.fa
    Value 1441/1547: salmonella_enterica__121/SAMN30408275.fa
    Value 1442/1547: salmonella_enterica__121/SAMN30346073.fa
    Value 1443/1547: salmonella_enterica__121/SAMN30325335.fa
    Value 1444/1547: salmonella_enterica__121/SAMN30346397.fa
    Value 1445/1547: salmonella_enterica__121/SAMN30313369.fa
    Value 1446/1547: salmonella_enterica__121/SAMN30388494.fa
    Value 1447/1547: salmonella_enterica__121/SAMN30369679.fa
    Value 1448/1547: salmonella_enterica__121/SAMN30412436.fa
    Value 1449/1547: salmonella_enterica__121/SAMN30499746.fa
    Value 1450/1547: salmonella_enterica__121/SAMN30344438.fa
    Value 1451/1547: salmonella_enterica__121/SAMN30348976.fa
    Value 1452/1547: salmonella_enterica__121/SAMN30323040.fa
    Value 1453/1547: salmonella_enterica__121/SAMN30473593.fa
    Value 1454/1547: salmonella_enterica__121/SAMN30469458.fa
    Value 1455/1547: salmonella_enterica__121/SAMN30437959.fa
    Value 1456/1547: salmonella_enterica__121/SAMN30415403.fa
    Value 1457/1547: salmonella_enterica__121/SAMN30395208.fa
    Value 1458/1547: salmonella_enterica__121/SAMN30473567.fa
    Value 1459/1547: salmonella_enterica__121/SAMN30473580.fa
    Value 1460/1547: salmonella_enterica__121/SAMN30348257.fa
    Value 1461/1547: salmonella_enterica__121/SAMN30498084.fa
    Value 1462/1547: salmonella_enterica__121/SAMN30282295.fa
    Value 1463/1547: salmonella_enterica__121/SAMN30438573.fa
    Value 1464/1547: salmonella_enterica__121/SAMN30448644.fa
    Value 1465/1547: salmonella_enterica__121/SAMN30415400.fa
    Value 1466/1547: salmonella_enterica__121/SAMN30349589.fa
    Value 1467/1547: salmonella_enterica__121/SAMN30281840.fa
    Value 1468/1547: salmonella_enterica__121/SAMN30346648.fa
    Value 1469/1547: salmonella_enterica__121/SAMN30346647.fa
    Value 1470/1547: salmonella_enterica__121/SAMN30444772.fa
    Value 1471/1547: salmonella_enterica__121/SAMN30415452.fa
    Value 1472/1547: salmonella_enterica__121/SAMN30415386.fa
    Value 1473/1547: salmonella_enterica__121/SAMN30415439.fa
    Value 1474/1547: salmonella_enterica__121/SAMN30415515.fa
    Value 1475/1547: salmonella_enterica__121/SAMN30415462.fa
    Value 1476/1547: salmonella_enterica__121/SAMN30481989.fa
    Value 1477/1547: salmonella_enterica__121/SAMN30396127.fa
    Value 1478/1547: salmonella_enterica__121/SAMN30498348.fa
    Value 1479/1547: salmonella_enterica__121/SAMN30346861.fa
    Value 1480/1547: salmonella_enterica__121/SAMN30468610.fa
    Value 1481/1547: salmonella_enterica__121/SAMN30467600.fa
    Value 1482/1547: salmonella_enterica__121/SAMN30473629.fa
    Value 1483/1547: salmonella_enterica__121/SAMN30410471.fa
    Value 1484/1547: salmonella_enterica__121/SAMN30438187.fa
    Value 1485/1547: salmonella_enterica__121/SAMN30313373.fa
    Value 1486/1547: salmonella_enterica__121/SAMN30370023.fa
    Value 1487/1547: salmonella_enterica__121/SAMN30325422.fa
    Value 1488/1547: salmonella_enterica__121/SAMN30469580.fa
    Value 1489/1547: salmonella_enterica__121/SAMN30398036.fa
    Value 1490/1547: salmonella_enterica__121/SAMN30497220.fa
    Value 1491/1547: salmonella_enterica__121/SAMN30346437.fa
    Value 1492/1547: salmonella_enterica__121/SAMN30480551.fa
    Value 1493/1547: salmonella_enterica__121/SAMN30443957.fa
    Value 1494/1547: salmonella_enterica__121/SAMN30369734.fa
    Value 1495/1547: salmonella_enterica__121/SAMN30369417.fa
    Value 1496/1547: salmonella_enterica__121/SAMN30469450.fa
    Value 1497/1547: salmonella_enterica__121/SAMN30325469.fa
    Value 1498/1547: salmonella_enterica__121/SAMN30281449.fa
    Value 1499/1547: salmonella_enterica__121/SAMN30349757.fa
    Value 1500/1547: salmonella_enterica__121/SAMN30346435.fa
    Value 1501/1547: salmonella_enterica__121/SAMN30444746.fa
    Value 1502/1547: salmonella_enterica__121/SAMN30388412.fa
    Value 1503/1547: salmonella_enterica__121/SAMN30313344.fa
    Value 1504/1547: salmonella_enterica__121/SAMN30396793.fa
    Value 1505/1547: salmonella_enterica__121/SAMN30325336.fa
    Value 1506/1547: salmonella_enterica__121/SAMN30281456.fa
    Value 1507/1547: salmonella_enterica__121/SAMN30467509.fa
    Value 1508/1547: salmonella_enterica__121/SAMN30497826.fa
    Value 1509/1547: salmonella_enterica__121/SAMN30443525.fa
    Value 1510/1547: salmonella_enterica__121/SAMN30468626.fa
    Value 1511/1547: salmonella_enterica__121/SAMN30369681.fa
    Value 1512/1547: salmonella_enterica__121/SAMN30468772.fa
    Value 1513/1547: salmonella_enterica__121/SAMN30466021.fa
    Value 1514/1547: salmonella_enterica__121/SAMN30468635.fa
    Value 1515/1547: salmonella_enterica__121/SAMN30398041.fa
    Value 1516/1547: salmonella_enterica__121/SAMN30348978.fa
    Value 1517/1547: salmonella_enterica__121/SAMN30348255.fa
    Value 1518/1547: salmonella_enterica__121/SAMN30498071.fa
    Value 1519/1547: salmonella_enterica__121/SAMN30487348.fa
    Value 1520/1547: salmonella_enterica__121/SAMN30478388.fa
    Value 1521/1547: salmonella_enterica__121/SAMN30467052.fa
    Value 1522/1547: salmonella_enterica__121/SAMN30383452.fa
    Value 1523/1547: salmonella_enterica__121/SAMN30370699.fa
    Value 1524/1547: salmonella_enterica__121/SAMN30473664.fa
    Value 1525/1547: salmonella_enterica__121/SAMN30497219.fa
    Value 1526/1547: salmonella_enterica__121/SAMN30391999.fa
    Value 1527/1547: salmonella_enterica__121/SAMN30392314.fa
    Value 1528/1547: salmonella_enterica__121/SAMN30468690.fa
    Value 1529/1547: salmonella_enterica__121/SAMN30376328.fa
    Value 1530/1547: salmonella_enterica__121/SAMN30443549.fa
    Value 1531/1547: salmonella_enterica__121/SAMN30438715.fa
    Value 1532/1547: salmonella_enterica__121/SAMN30473566.fa
    Value 1533/1547: salmonella_enterica__121/SAMN30481975.fa
    Value 1534/1547: salmonella_enterica__121/SAMN30448082.fa
    Value 1535/1547: salmonella_enterica__121/SAMN30468149.fa
    Value 1536/1547: salmonella_enterica__121/SAMN30283582.fa
    Value 1537/1547: salmonella_enterica__121/SAMN30469405.fa
    Value 1538/1547: salmonella_enterica__121/SAMN30325222.fa
    Value 1539/1547: salmonella_enterica__121/SAMN30323100.fa
    Value 1540/1547: salmonella_enterica__121/SAMN30467612.fa
    Value 1541/1547: salmonella_enterica__121/SAMN30325365.fa
    Value 1542/1547: salmonella_enterica__121/SAMN30283606.fa
    Value 1543/1547: salmonella_enterica__121/SAMN30343464.fa
    Value 1544/1547: salmonella_enterica__121/SAMN30287024.fa
    Value 1545/1547: salmonella_enterica__121/SAMN30312074.fa
    Value 1546/1547: salmonella_enterica__121/SAMN30468628.fa
    Value 1547/1547: salmonella_enterica__121/SAMN30467515.fa

Within the workflow-cleanup directory, there is a the allthebacteria-r0.2-missing-files.csv file that may be used to manually check the archives for the missing sequences.

Expand for commands

Consider running:

cd /group/ctbrowngrp4/2024-ccbaumler-allthebacteria/allthebacteria-r0.2

~/database-releases/allthebacteria-workflow/scripts/extract_missing_files.py workflow-cleanup/allthebacteria-r0.2-missing-files.csv -d allthebacteria-r0.2-data/ -o missed-files

sourmash scripts manysketch missed-files/*/manysketch.csv -p k=21,k=31,k=51,scaled=1000,abund -o allthebacteria-r0.2-sigs/missed-files.zip}

sourmash sig cat allthebacteria-r0.2-sigs/missed-files.zip allthebacteria-r0.2-sigs/allthebacteria-r0.2-k21.zip -k 21 -o allthebacteria-r0.2-k21.zip
sourmash sig cat allthebacteria-r0.2-sigs/missed-files.zip allthebacteria-r0.2-sigs/allthebacteria-r0.2-k31.zip -k 31 -o allthebacteria-r0.2-k31.zip
sourmash sig cat allthebacteria-r0.2-sigs/missed-files.zip allthebacteria-r0.2-sigs/allthebacteria-r0.2-k51.zip -k 51 -o allthebacteria-r0.2-k51.zip