exit: -9 (Computing ancestral state alignement

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Tyler Ruddenfort

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Nov 25, 2020, 10:25:47 AM11/25/20
to bali-phy-users
Hi Dr. Redelings,

I was trying to us bp-analyze in my 8 runs each has roughly 19000 iterations. Unfortunately, when I use bp-analyze to summarize all 8 runs, it suddenly stops at 'Computing ancestral state alignment with exit code of -9.

I hope you can explain to me what is happening with my analysis. I tried to reduce my runs to 7 runs only and bp-analyze seems to work perfectly fine but when I include my last run, suddenly the error appears.

Also, in the command log, something appears;

exit: -9
  err: Node 'node_13': present in 9800/15744 = 62.2459% of samples.

I hope you can help me fix this error message.

I'm really sorry as I do not know how else to describe this since I am new to using BAli-Phy and I don't know anything about programming.

Apologies for the inconvenience.

Thanks,
Tyler Ruddenfort



Benjamin Redelings

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Nov 25, 2020, 10:52:14 AM11/25/20
to bali-ph...@googlegroups.com

Hi Tyler,

Thanks for the bug report.

Can you send me the whole command log as an attachment?  So, bp-analyze runs some utility programs to produce the summary, and it looks like one of them crashed.  If I can see a bit more of the log, it will be more clear what program crashed, and possibly why.

-BenRI

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Tyler Ruddenfort

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Nov 25, 2020, 12:26:45 PM11/25/20
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Hello Ben,

Seems like I cannot attach a file so here is the contents of the report. 

Thanks

Best,
Tyler




-----------------------------------------------------------
'statreport' '5cgtase_old/C1.log' '6cgtase_old/C1.log' '7cgtase_old/C1.log' '8cgtase_old/C1.log' '9cgtase_old/C1.log' '10cgtase_old/C1.log' '11cgtase_pld/C1.log' '12cgtase_old/C1.log' '--skip=4000' > 'Results/Report'
'trees-consensus' '--map-tree=Results/MAP.PP.tree' '--greedy-consensus=Results/greedy.PP.tree' '--report=Results/consensus' '5cgtase_old/C1.trees' '6cgtase_old/C1.trees' '7cgtase_old/C1.trees' '8cgtase_old/C1.trees' '9cgtase_old/C1.trees' '10cgtase_old/C1.trees' '11cgtase_pld/C1.trees' '12cgtase_old/C1.trees' '--support-levels=Results/c-levels.plot' '--skip=4000' '--consensus=0.5:Results/c50.PP.tree,0.66:Results/c66.PP.tree,0.8:Results/c80.PP.tree,0.9:Results/c90.PP.tree,0.95:Results/c95.PP.tree,0.99:Results/c99.PP.tree,1.0:Results/c100.PP.tree'
'tree-tool' 'Results/greedy.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/greedy.tree'
'tree-tool' 'Results/MAP.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/MAP.tree'
'tree-tool' 'Results/c50.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c50.tree'
'tree-tool' 'Results/c66.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c66.tree'
'tree-tool' 'Results/c80.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c80.tree'
'tree-tool' 'Results/c90.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c90.tree'
'tree-tool' 'Results/c95.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c95.tree'
'tree-tool' 'Results/c99.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c99.tree'
'tree-tool' 'Results/c100.PP.tree' '--strip-internal-names' '--name-all-nodes' > 'Results/c100.tree'
'draw-tree' 'c50.tree' '--layout=equal-daylight'
'draw-tree' 'c50.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'c66.tree' '--layout=equal-daylight'
'draw-tree' 'c66.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'c80.tree' '--layout=equal-daylight'
'draw-tree' 'c80.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'c90.tree' '--layout=equal-daylight'
'draw-tree' 'c90.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'c95.tree' '--layout=equal-daylight'
'draw-tree' 'c95.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'c99.tree' '--layout=equal-daylight'
'draw-tree' 'c99.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'c100.tree' '--layout=equal-daylight'
'draw-tree' 'c100.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'greedy.tree' '--layout=equal-daylight'
'draw-tree' 'greedy.tree' '--layout=equal-daylight' '--output=svg'
'draw-tree' 'MAP.tree' '--layout=equal-daylight'
'draw-tree' 'MAP.tree' '--layout=equal-daylight' '--output=svg'
'pickout' '--no-header' '--large' 'pi' < 'Results/consensus' > 'Results/partitions'
'trees-bootstrap' '--pred=Results/partitions.pred' '--LOD-table=Results/LOD-table' '--pseudocount=1' '5cgtase_old/C1.trees' '6cgtase_old/C1.trees' '7cgtase_old/C1.trees' '8cgtase_old/C1.trees' '9cgtase_old/C1.trees' '10cgtase_old/C1.trees' '11cgtase_pld/C1.trees' '12cgtase_old/C1.trees' '--skip=4000' > 'Results/partitions.bs'
'/usr/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence-PP.pdf' < '/home/michael/Applications/bali-phy-3.5.0/lib/bali-phy/libexec/compare-runs.R'
'/usr/bin/R' '--slave' '--vanilla' '--args' 'Results/LOD-table' 'Results/convergence1-PP.svg' 'Results/convergence2-PP.svg' < '/home/michael/Applications/bali-phy-3.5.0/lib/bali-phy/libexec/compare-runs2.R'
'trees-to-SRQ' 'Results/partitions.pred' '--max-points=1000' '--skip=4000' '5cgtase_old/C1.trees' '6cgtase_old/C1.trees' '7cgtase_old/C1.trees' '8cgtase_old/C1.trees' '9cgtase_old/C1.trees' '10cgtase_old/C1.trees' '11cgtase_pld/C1.trees' '12cgtase_old/C1.trees' > 'Results/partitions.SRQ'
'trees-to-SRQ' 'Results/c50.tree' '--max-points=1000' '--skip=4000' '5cgtase_old/C1.trees' '6cgtase_old/C1.trees' '7cgtase_old/C1.trees' '8cgtase_old/C1.trees' '9cgtase_old/C1.trees' '10cgtase_old/C1.trees' '11cgtase_pld/C1.trees' '12cgtase_old/C1.trees' > 'Results/c50.SRQ'
'trees-distances' 'matrix' '--max=400' '--jitter=0.3' '--skip=4000' '5cgtase_old/C1.trees' '6cgtase_old/C1.trees' '7cgtase_old/C1.trees' > 'Results/tree-1-2-3.M'
'/usr/bin/R' '--slave' '--vanilla' '--args' '400' '400' '400' 'Results/tree-1-2-3.M' 'Results/tree-1-2-3.svg' < '/home/michael/Applications/bali-phy-3.5.0/lib/bali-phy/libexec/tree-plot3.R'
  out: [1] 400 400 400

'/usr/bin/R' '--slave' '--vanilla' '--args' '400' '400' '400' 'Results/tree-1-2-3.M' < '/home/michael/Applications/bali-phy-3.5.0/lib/bali-phy/libexec/tree-plot3-3D.R'
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-2.785977 0.686346 3.175353 3 313
-4.054959 5.272481 -1.925314 3 314
-2.892064 -5.023589 -0.472324 3 315
-3.035027 2.841418 -4.793556 3 316
-3.150941 -4.437280 0.471436 3 317
-3.175698 -3.922038 -0.761888 3 318
13.813337 6.997467 -4.168013 3 319
11.606832 6.934461 -4.774013 3 320
7.117688 0.824044 0.683440 3 321
14.603130 7.852888 -6.095094 3 322
11.303321 1.723291 1.785650 3 323
-4.276780 1.091040 -4.249393 3 324
-3.054912 1.522882 2.342976 3 325
-2.715879 0.245832 3.620688 3 326
-3.194330 -4.977558 -0.223969 3 327
-2.951739 1.252332 2.583719 3 328
13.719591 0.741705 3.100774 3 329
14.081647 0.226512 2.245921 3 330
6.457002 6.716027 -3.377483 3 331
-4.409223 -0.976277 -5.178163 3 332
-2.732123 0.288452 3.058460 3 333
8.862461 2.019997 2.586691 3 334
10.152636 0.591770 3.772530 3 335
12.530727 0.317460 -9.371442 3 336
12.531057 -5.619607 -4.164947 3 337
8.973596 1.330603 1.287412 3 338
13.048977 2.481949 -7.327602 3 339
-3.369129 -4.056836 -2.166516 3 340
-1.497052 1.755368 1.498213 3 341
-2.439286 -0.486687 -7.639919 3 342
-3.212918 -3.146989 1.652161 3 343
-1.459454 2.212229 0.703849 3 344
-4.018989 -0.158173 -7.198277 3 345
-5.535494 -1.035786 -5.148871 3 346
6.953770 1.395179 1.619936 3 347
-2.838685 0.346736 1.992350 3 348
-3.569117 4.123086 -0.746147 3 349
-3.729490 4.013294 -2.807292 3 350
-3.990526 -1.262025 -4.253600 3 351
-3.003195 1.400374 1.922195 3 352
-3.408242 -3.527156 -2.142367 3 353
-2.668174 -0.034856 3.155915 3 354
-2.679402 1.108466 1.326582 3 355
-3.716685 4.838205 -1.138173 3 356
-2.772557 0.772288 2.019452 3 357
-2.762754 0.091233 2.771446 3 358
-2.276462 -3.189412 -3.014182 3 359
-3.309031 -4.230484 -0.352545 3 360
-3.872571 4.184740 -1.810458 3 361
-2.813282 0.480048 2.135606 3 362
-2.997659 1.578551 2.793542 3 363
-3.749714 3.941776 -1.143779 3 364
-2.622817 0.533472 1.882950 3 365
-3.712744 4.248116 -1.403813 3 366
-2.125225 5.429531 -2.427145 3 367
-2.704220 0.296211 3.011847 3 368
-3.351514 -2.247571 -0.325893 3 369
-2.940059 1.031396 2.803201 3 370
-3.294494 6.607928 -2.821979 3 371
-3.183813 -4.853293 -0.870673 3 372
-2.612395 0.940147 2.958539 3 373
-1.735383 2.304357 1.131667 3 374
-3.034795 -4.554913 0.005387 3 375
-1.516962 1.604006 2.425004 3 376
-2.420154 0.222335 3.327428 3 377
-3.601438 4.016592 -3.157397 3 378
-2.170200 5.240352 -3.010493 3 379
-4.581681 -0.003525 -5.865510 3 380
-4.562514 0.485102 -4.522611 3 381
-3.320436 -4.565889 -1.428079 3 382
-1.952671 -2.746954 -3.465257 3 383
-6.083091 6.414904 -1.270224 3 384
-2.922921 0.489293 2.681845 3 385
-3.304776 -2.705298 -0.302755 3 386
-3.233687 -4.314664 -0.467984 3 387
-2.983188 -4.638292 -1.208928 3 388
-2.416594 0.267057 3.183487 3 389
-3.264658 -2.776372 0.214466 3 390
-2.958399 1.370270 1.469220 3 391
-3.291068 -4.872194 -1.379552 3 392
-3.985102 -5.464541 0.309167 3 393
-3.203356 -3.756874 -0.411330 3 394
-3.936668 0.625658 3.155557 3 395
-2.151177 -2.719853 -2.783877 3 396
-3.254079 -4.585447 -0.309778 3 397
-2.581051 -0.305201 2.723441 3 398
-2.898184 -4.740876 -0.123981 3 399

'alignment-cat' 'Results/Work/P1.initial-unordered.fasta' '--reorder-by-tree=Results/c50.tree' > 'Results/P1.initial.fasta'
'alignment-max' > 'Results/Work/P1.max-unordered.fasta'
'alignment-cat' 'Results/Work/P1.max-unordered.fasta' '--reorder-by-tree=Results/c50.tree' > 'Results/P1.max.fasta'
'summarize-ancestors' 'Results/P1.max.fasta' '-n' 'Results/c50.tree' '-g' 'Results/c50.tree' '-A' '5cgtase_old/C1.P1.fastas' '-T' '5cgtase_old/C1.trees' '-A' '6cgtase_old/C1.P1.fastas' '-T' '6cgtase_old/C1.trees' '-A' '7cgtase_old/C1.P1.fastas' '-T' '7cgtase_old/C1.trees' '-A' '8cgtase_old/C1.P1.fastas' '-T' '8cgtase_old/C1.trees' '-A' '9cgtase_old/C1.P1.fastas' '-T' '9cgtase_old/C1.trees' '-A' '10cgtase_old/C1.P1.fastas' '-T' '10cgtase_old/C1.trees' '-A' '11cgtase_pld/C1.P1.fastas' '-T' '11cgtase_pld/C1.trees' '-A' '12cgtase_old/C1.P1.fastas' '-T' '12cgtase_old/C1.trees' > 'Results/P1.ancestors.fasta'
  err: Node 'node_13': present in 9800/15744 = 62.2459% of samples.
Node 'node_10': present in 15742/15744 = 99.9873% of samples.
Node 'node_12': present in 15744/15744 = 100% of samples.
Node 'node_3': present in 15742/15744 = 99.9873% of samples.
Node 'node_4': present in 15740/15744 = 99.9746% of samples.
Node 'node_6': present in 15476/15744 = 98.2978% of samples.
Node 'node_2': present in 15287/15744 = 97.0973% of samples.
Node 'node_9': present in 15743/15744 = 99.9936% of samples.
Node 'node_11': present in 15736/15744 = 99.9492% of samples.
Node 'node_8': present in 15735/15744 = 99.9428% of samples.
Node 'node_5': present in 15617/15744 = 99.1933% of samples.
Node 'node_7': present in 15741/15744 = 99.9809% of samples.
Node 'node_1': present in 15743/15744 = 99.9936% of samples.
Node 'node_22': present in 9800/15744 = 62.2459% of samples.
Node 'node_21': present in 15742/15744 = 99.9873% of samples.
Node 'node_15': present in 0/15744 = 0% of samples.
Node 'node_16': present in 15734/15744 = 99.9365% of samples.
Node 'node_17': present in 14227/15744 = 90.3646% of samples.
Node 'node_20': present in 15729/15744 = 99.9047% of samples.
Node 'node_19': present in 15112/15744 = 95.9858% of samples.
Node 'node_18': present in 0/15744 = 0% of samples.
Node 'node_14': present in 15732/15744 = 99.9238% of samples.
Node 'node_30': present in 15739/15744 = 99.9682% of samples.
Node 'node_29': present in 15738/15744 = 99.9619% of samples.
Node 'node_23': present in 15734/15744 = 99.9365% of samples.
Node 'node_24': present in 14611/15744 = 92.8036% of samples.
Node 'node_25': present in 13436/15744 = 85.3404% of samples.
Node 'node_28': present in 15729/15744 = 99.9047% of samples.
Node 'node_27': present in 15183/15744 = 96.4367% of samples.
Node 'node_26': present in 15736/15744 = 99.9492% of samples.
Node 'node_31': present in 15735/15744 = 99.9428% of samples.
Node 'node_32': present in 11683/15744 = 74.206% of samples.
Node 'node_33': present in 12839/15744 = 81.5485% of samples.
Node 'node_35': present in 15735/15744 = 99.9428% of samples.
Node 'node_34': present in 15684/15744 = 99.6189% of samples.
Node 'node_36': present in 15672/15744 = 99.5427% of samples.
Node 'node_37': present in 9539/15744 = 60.5882% of samples.
Node 'node_38': present in 15725/15744 = 99.8793% of samples.
Node 'node_39': present in 15673/15744 = 99.549% of samples.
Node 'node_40': present in 9445/15744 = 59.9911% of samples.
Node 'node_41': present in 15695/15744 = 99.6888% of samples.
Node 'node_42': present in 12495/15744 = 79.3636% of samples.
Node 'node_43': present in 15619/15744 = 99.206% of samples.
Node 'node_44': present in 12296/15744 = 78.0996% of samples.
Node 'node_45': present in 15649/15744 = 99.3966% of samples.
Node 'node_46': present in 15544/15744 = 98.7297% of samples.
Node 'node_47': present in 15674/15744 = 99.5554% of samples.
Node 'node_48': present in 15668/15744 = 99.5173% of samples.
Group 'node_13<=node_22': present in 9800/15744 = 62.2459% of samples.
Group 'node_13<=Z35484.1': present in 15744/15744 = 100% of samples.
Group 'node_13<=KJ526074.1': present in 15744/15744 = 100% of samples.
Group 'node_10<=node_46': present in 15742/15744 = 99.9873% of samples.
Group 'node_10<=X59044.1': present in 15744/15744 = 100% of samples.
Group 'node_10<=U83799.1': present in 15744/15744 = 100% of samples.
Group 'node_12<=node_21': present in 15744/15744 = 100% of samples.
Group 'node_12<=X78145.1': present in 15744/15744 = 100% of samples.
Group 'node_12<=KM200046.1': present in 15744/15744 = 100% of samples.
Group 'node_3<=node_15': present in 15742/15744 = 99.9873% of samples.
Group 'node_3<=AY770576.1': present in 15744/15744 = 100% of samples.
Group 'node_3<=AY770575.1': present in 15744/15744 = 100% of samples.
Group 'node_4<=node_16': present in 15740/15744 = 99.9746% of samples.
Group 'node_4<=DQ192528.1': present in 15744/15744 = 100% of samples.
Group 'node_4<=AB072372.1': present in 15744/15744 = 100% of samples.
Group 'node_6<=node_17': present in 15476/15744 = 98.2978% of samples.
Group 'node_6<=KC284749.1': present in 15744/15744 = 100% of samples.
Group 'node_6<=EF363797.1': present in 15744/15744 = 100% of samples.
Group 'node_2<=node_17': present in 15287/15744 = 97.0973% of samples.
Group 'node_2<=AY251462.1': present in 15744/15744 = 100% of samples.
Group 'node_2<=AX356717.1': present in 15744/15744 = 100% of samples.
Group 'node_9<=node_28': present in 15743/15744 = 99.9936% of samples.
Group 'node_9<=X15752.1': present in 15744/15744 = 100% of samples.
Group 'node_9<=FJ232953.1': present in 15744/15744 = 100% of samples.
Group 'node_11<=node_20': present in 15736/15744 = 99.9492% of samples.
Group 'node_11<=X68326.1': present in 15744/15744 = 100% of samples.
Group 'node_11<=X66106.1': present in 15744/15744 = 100% of samples.
Group 'node_8<=node_19': present in 15735/15744 = 99.9428% of samples.
Group 'node_8<=M19880.1': present in 15744/15744 = 100% of samples.
Group 'node_8<=AY478421.1': present in 15744/15744 = 100% of samples.
Group 'node_5<=node_19': present in 15617/15744 = 99.1933% of samples.
Group 'node_5<=DQ631916.1': present in 15744/15744 = 100% of samples.
Group 'node_5<=AF302787.2': present in 15744/15744 = 100% of samples.
Group 'node_7<=node_18': present in 15741/15744 = 99.9809% of samples.
Group 'node_7<=KF384448.1': present in 15744/15744 = 100% of samples.
Group 'node_7<=KF010775.1': present in 15744/15744 = 100% of samples.
Group 'node_1<=A18991.1': present in 15744/15744 = 100% of samples.
Group 'node_1<=node_14': present in 15743/15744 = 99.9936% of samples.
Group 'node_1<=AB201304.1': present in 15744/15744 = 100% of samples.
Group 'node_22<=node_30': present in 15741/15744 = 99.9809% of samples.
Group 'node_22<=node_13': present in 9800/15744 = 62.2459% of samples.
Group 'node_22<=KJ526075.1': present in 15744/15744 = 100% of samples.
Group 'node_21<=node_29': present in 15742/15744 = 99.9873% of samples.
Group 'node_21<=node_12': present in 15744/15744 = 100% of samples.
Group 'node_21<=M33302.1': present in 15744/15744 = 100% of samples.
Group 'node_15<=node_23': present in 15737/15744 = 99.9555% of samples.
Group 'node_15<=node_3': present in 15742/15744 = 99.9873% of samples.
Group 'node_15<=RQRY01000000': present in 15744/15744 = 100% of samples.
Group 'node_15<=KF270899.1': present in 15744/15744 = 100% of samples.
Group 'node_15<=HQ876173.1': present in 15744/15744 = 100% of samples.
Group 'node_16<=node_24': present in 15734/15744 = 99.9365% of samples.
Group 'node_16<=node_4': present in 15740/15744 = 99.9746% of samples.
Group 'node_16<=AB025721.1': present in 15744/15744 = 100% of samples.
Group 'node_17<=node_25': present in 14231/15744 = 90.39% of samples.
Group 'node_17<=node_6': present in 15476/15744 = 98.2978% of samples.
Group 'node_17<=node_2': present in 15287/15744 = 97.0973% of samples.
Group 'node_20<=node_28': present in 15729/15744 = 99.9047% of samples.
Group 'node_20<=node_11': present in 15736/15744 = 99.9492% of samples.
Group 'node_20<=AM748796.1': present in 15744/15744 = 100% of samples.
Group 'node_19<=node_27': present in 15225/15744 = 96.7035% of samples.
Group 'node_19<=node_8': present in 15735/15744 = 99.9428% of samples.
Group 'node_19<=node_5': present in 15617/15744 = 99.1933% of samples.
Group 'node_18<=node_26': present in 15736/15744 = 99.9492% of samples.
Group 'node_18<=node_7': present in 15741/15744 = 99.9809% of samples.
Group 'node_18<=X59045.1': present in 15744/15744 = 100% of samples.
Group 'node_18<=M12777.1': present in 15744/15744 = 100% of samples.
Group 'node_18<=AF047363.1': present in 15744/15744 = 100% of samples.
Group 'node_14<=node_1': present in 15743/15744 = 99.9936% of samples.
Group 'node_14<=node_33': present in 15732/15744 = 99.9238% of samples.
Group 'node_14<=AB082929.2': present in 15744/15744 = 100% of samples.
Group 'node_30<=node_47': present in 15739/15744 = 99.9682% of samples.
Group 'node_30<=node_22': present in 15741/15744 = 99.9809% of samples.
Group 'node_30<=M57692.1': present in 15744/15744 = 100% of samples.
Group 'node_29<=node_38': present in 15738/15744 = 99.9619% of samples.
Group 'node_29<=node_21': present in 15742/15744 = 99.9873% of samples.
Group 'node_29<=M28053.1': present in 15744/15744 = 100% of samples.
Group 'node_23<=node_31': present in 15735/15744 = 99.9428% of samples.
Group 'node_23<=node_15': present in 15737/15744 = 99.9555% of samples.
Group 'node_23<=D13068.1': present in 15744/15744 = 100% of samples.
Group 'node_24<=node_32': present in 14611/15744 = 92.8036% of samples.
Group 'node_24<=node_16': present in 15734/15744 = 99.9365% of samples.
Group 'node_24<=M15264.1': present in 15744/15744 = 100% of samples.
Group 'node_25<=node_33': present in 13448/15744 = 85.4167% of samples.
Group 'node_25<=node_17': present in 14231/15744 = 90.39% of samples.
Group 'node_25<=AX453023.1': present in 15744/15744 = 100% of samples.
Group 'node_28<=node_35': present in 15735/15744 = 99.9428% of samples.
Group 'node_28<=node_20': present in 15729/15744 = 99.9047% of samples.
Group 'node_28<=node_9': present in 15743/15744 = 99.9936% of samples.
Group 'node_27<=node_34': present in 15684/15744 = 99.6189% of samples.
Group 'node_27<=node_19': present in 15225/15744 = 96.7035% of samples.
Group 'node_27<=M17366.1': present in 15744/15744 = 100% of samples.
Group 'node_26<=node_45': present in 15736/15744 = 99.9492% of samples.
Group 'node_26<=node_18': present in 15736/15744 = 99.9492% of samples.
Group 'node_26<=EU305539.1': present in 15744/15744 = 100% of samples.
Group 'node_31<=node_36': present in 15735/15744 = 99.9428% of samples.
Group 'node_31<=node_23': present in 15735/15744 = 99.9428% of samples.
Group 'node_31<=AF011388.1': present in 15744/15744 = 100% of samples.
Group 'node_32<=node_40': present in 12804/15744 = 81.3262% of samples.
Group 'node_32<=node_24': present in 14611/15744 = 92.8036% of samples.
Group 'node_32<=AB015670.1': present in 15744/15744 = 100% of samples.
Group 'node_33<=node_14': present in 15732/15744 = 99.9238% of samples.
Group 'node_33<=node_37': present in 12839/15744 = 81.5485% of samples.
Group 'node_33<=node_25': present in 13448/15744 = 85.4167% of samples.
Group 'node_35<=node_41': present in 15736/15744 = 99.9492% of samples.
Group 'node_35<=node_28': present in 15735/15744 = 99.9428% of samples.
Group 'node_35<=AM933612.1': present in 15744/15744 = 100% of samples.
Group 'node_34<=node_38': present in 15727/15744 = 99.892% of samples.
Group 'node_34<=node_27': present in 15684/15744 = 99.6189% of samples.
Group 'node_34<=JX101460.1': present in 15744/15744 = 100% of samples.
Group 'node_36<=node_39': present in 15673/15744 = 99.549% of samples.
Group 'node_36<=node_31': present in 15735/15744 = 99.9428% of samples.
Group 'node_36<=D90243.1': present in 15744/15744 = 100% of samples.
Group 'node_37<=node_33': present in 12839/15744 = 81.5485% of samples.
Group 'node_37<=node_40': present in 9541/15744 = 60.6009% of samples.
Group 'node_37<=AJ850087.1': present in 15744/15744 = 100% of samples.
Group 'node_38<=node_41': present in 15727/15744 = 99.892% of samples.
Group 'node_38<=node_34': present in 15727/15744 = 99.892% of samples.
Group 'node_38<=node_29': present in 15738/15744 = 99.9619% of samples.
Group 'node_39<=node_42': present in 15736/15744 = 99.9492% of samples.
Group 'node_39<=node_36': present in 15673/15744 = 99.549% of samples.
Group 'node_39<=JF280087.1': present in 15744/15744 = 100% of samples.
Group 'node_40<=node_37': present in 9541/15744 = 60.6009% of samples.
Group 'node_40<=node_44': present in 15612/15744 = 99.1616% of samples.
Group 'node_40<=node_32': present in 12804/15744 = 81.3262% of samples.
Group 'node_41<=node_43': present in 15695/15744 = 99.6888% of samples.
Group 'node_41<=node_38': present in 15727/15744 = 99.892% of samples.
Group 'node_41<=node_35': present in 15736/15744 = 99.9492% of samples.
Group 'node_42<=node_44': present in 12495/15744 = 79.3636% of samples.
Group 'node_42<=node_39': present in 15736/15744 = 99.9492% of samples.
Group 'node_42<=AJ876899.1': present in 15744/15744 = 100% of samples.
Group 'node_43<=node_45': present in 15650/15744 = 99.4029% of samples.
Group 'node_43<=node_41': present in 15695/15744 = 99.6888% of samples.
Group 'node_43<=EU644086.2': present in 15744/15744 = 100% of samples.
Group 'node_44<=node_40': present in 15612/15744 = 99.1616% of samples.
Group 'node_44<=node_46': present in 15544/15744 = 98.7297% of samples.
Group 'node_44<=node_42': present in 12495/15744 = 79.3636% of samples.
Group 'node_45<=node_47': present in 15725/15744 = 99.8793% of samples.
Group 'node_45<=node_43': present in 15650/15744 = 99.4029% of samples.
Group 'node_45<=node_26': present in 15736/15744 = 99.9492% of samples.
Group 'node_46<=node_44': present in 15544/15744 = 98.7297% of samples.
Group 'node_46<=node_48': present in 15706/15744 = 99.7586% of samples.
Group 'node_46<=node_10': present in 15742/15744 = 99.9873% of samples.
Group 'node_47<=node_48': present in 15674/15744 = 99.5554% of samples.
Group 'node_47<=node_45': present in 15725/15744 = 99.8793% of samples.
Group 'node_47<=node_30': present in 15739/15744 = 99.9682% of samples.
Group 'node_48<=node_46': present in 15706/15744 = 99.7586% of samples.
Group 'node_48<=node_47': present in 15674/15744 = 99.5554% of samples.
Group 'node_48<=KJ806554.1': present in 15744/15744 = 100% of samples.

 exit: -9
  err: Node 'node_13': present in 9800/15744 = 62.2459% of samples.
Node 'node_10': present in 15742/15744 = 99.9873% of samples.
Node 'node_12': present in 15744/15744 = 100% of samples.
Node 'node_3': present in 15742/15744 = 99.9873% of samples.
Node 'node_4': present in 15740/15744 = 99.9746% of samples.
Node 'node_6': present in 15476/15744 = 98.2978% of samples.
Node 'node_2': present in 15287/15744 = 97.0973% of samples.
Node 'node_9': present in 15743/15744 = 99.9936% of samples.
Node 'node_11': present in 15736/15744 = 99.9492% of samples.
Node 'node_8': present in 15735/15744 = 99.9428% of samples.
Node 'node_5': present in 15617/15744 = 99.1933% of samples.
Node 'node_7': present in 15741/15744 = 99.9809% of samples.
Node 'node_1': present in 15743/15744 = 99.9936% of samples.
Node 'node_22': present in 9800/15744 = 62.2459% of samples.
Node 'node_21': present in 15742/15744 = 99.9873% of samples.
Node 'node_15': present in 0/15744 = 0% of samples.
Node 'node_16': present in 15734/15744 = 99.9365% of samples.
Node 'node_17': present in 14227/15744 = 90.3646% of samples.
Node 'node_20': present in 15729/15744 = 99.9047% of samples.
Node 'node_19': present in 15112/15744 = 95.9858% of samples.
Node 'node_18': present in 0/15744 = 0% of samples.
Node 'node_14': present in 15732/15744 = 99.9238% of samples.
Node 'node_30': present in 15739/15744 = 99.9682% of samples.
Node 'node_29': present in 15738/15744 = 99.9619% of samples.
Node 'node_23': present in 15734/15744 = 99.9365% of samples.
Node 'node_24': present in 14611/15744 = 92.8036% of samples.
Node 'node_25': present in 13436/15744 = 85.3404% of samples.
Node 'node_28': present in 15729/15744 = 99.9047% of samples.
Node 'node_27': present in 15183/15744 = 96.4367% of samples.
Node 'node_26': present in 15736/15744 = 99.9492% of samples.
Node 'node_31': present in 15735/15744 = 99.9428% of samples.
Node 'node_32': present in 11683/15744 = 74.206% of samples.
Node 'node_33': present in 12839/15744 = 81.5485% of samples.
Node 'node_35': present in 15735/15744 = 99.9428% of samples.
Node 'node_34': present in 15684/15744 = 99.6189% of samples.
Node 'node_36': present in 15672/15744 = 99.5427% of samples.
Node 'node_37': present in 9539/15744 = 60.5882% of samples.
Node 'node_38': present in 15725/15744 = 99.8793% of samples.
Node 'node_39': present in 15673/15744 = 99.549% of samples.
Node 'node_40': present in 9445/15744 = 59.9911% of samples.
Node 'node_41': present in 15695/15744 = 99.6888% of samples.
Node 'node_42': present in 12495/15744 = 79.3636% of samples.
Node 'node_43': present in 15619/15744 = 99.206% of samples.
Node 'node_44': present in 12296/15744 = 78.0996% of samples.
Node 'node_45': present in 15649/15744 = 99.3966% of samples.
Node 'node_46': present in 15544/15744 = 98.7297% of samples.
Node 'node_47': present in 15674/15744 = 99.5554% of samples.
Node 'node_48': present in 15668/15744 = 99.5173% of samples.
Group 'node_13<=node_22': present in 9800/15744 = 62.2459% of samples.
Group 'node_13<=Z35484.1': present in 15744/15744 = 100% of samples.
Group 'node_13<=KJ526074.1': present in 15744/15744 = 100% of samples.
Group 'node_10<=node_46': present in 15742/15744 = 99.9873% of samples.
Group 'node_10<=X59044.1': present in 15744/15744 = 100% of samples.
Group 'node_10<=U83799.1': present in 15744/15744 = 100% of samples.
Group 'node_12<=node_21': present in 15744/15744 = 100% of samples.
Group 'node_12<=X78145.1': present in 15744/15744 = 100% of samples.
Group 'node_12<=KM200046.1': present in 15744/15744 = 100% of samples.
Group 'node_3<=node_15': present in 15742/15744 = 99.9873% of samples.
Group 'node_3<=AY770576.1': present in 15744/15744 = 100% of samples.
Group 'node_3<=AY770575.1': present in 15744/15744 = 100% of samples.
Group 'node_4<=node_16': present in 15740/15744 = 99.9746% of samples.
Group 'node_4<=DQ192528.1': present in 15744/15744 = 100% of samples.
Group 'node_4<=AB072372.1': present in 15744/15744 = 100% of samples.
Group 'node_6<=node_17': present in 15476/15744 = 98.2978% of samples.
Group 'node_6<=KC284749.1': present in 15744/15744 = 100% of samples.
Group 'node_6<=EF363797.1': present in 15744/15744 = 100% of samples.
Group 'node_2<=node_17': present in 15287/15744 = 97.0973% of samples.
Group 'node_2<=AY251462.1': present in 15744/15744 = 100% of samples.
Group 'node_2<=AX356717.1': present in 15744/15744 = 100% of samples.
Group 'node_9<=node_28': present in 15743/15744 = 99.9936% of samples.
Group 'node_9<=X15752.1': present in 15744/15744 = 100% of samples.
Group 'node_9<=FJ232953.1': present in 15744/15744 = 100% of samples.
Group 'node_11<=node_20': present in 15736/15744 = 99.9492% of samples.
Group 'node_11<=X68326.1': present in 15744/15744 = 100% of samples.
Group 'node_11<=X66106.1': present in 15744/15744 = 100% of samples.
Group 'node_8<=node_19': present in 15735/15744 = 99.9428% of samples.
Group 'node_8<=M19880.1': present in 15744/15744 = 100% of samples.
Group 'node_8<=AY478421.1': present in 15744/15744 = 100% of samples.
Group 'node_5<=node_19': present in 15617/15744 = 99.1933% of samples.
Group 'node_5<=DQ631916.1': present in 15744/15744 = 100% of samples.
Group 'node_5<=AF302787.2': present in 15744/15744 = 100% of samples.
Group 'node_7<=node_18': present in 15741/15744 = 99.9809% of samples.
Group 'node_7<=KF384448.1': present in 15744/15744 = 100% of samples.
Group 'node_7<=KF010775.1': present in 15744/15744 = 100% of samples.
Group 'node_1<=A18991.1': present in 15744/15744 = 100% of samples.
Group 'node_1<=node_14': present in 15743/15744 = 99.9936% of samples.
Group 'node_1<=AB201304.1': present in 15744/15744 = 100% of samples.
Group 'node_22<=node_30': present in 15741/15744 = 99.9809% of samples.
Group 'node_22<=node_13': present in 9800/15744 = 62.2459% of samples.
Group 'node_22<=KJ526075.1': present in 15744/15744 = 100% of samples.
Group 'node_21<=node_29': present in 15742/15744 = 99.9873% of samples.
Group 'node_21<=node_12': present in 15744/15744 = 100% of samples.
Group 'node_21<=M33302.1': present in 15744/15744 = 100% of samples.
Group 'node_15<=node_23': present in 15737/15744 = 99.9555% of samples.
Group 'node_15<=node_3': present in 15742/15744 = 99.9873% of samples.
Group 'node_15<=RQRY01000000': present in 15744/15744 = 100% of samples.
Group 'node_15<=KF270899.1': present in 15744/15744 = 100% of samples.
Group 'node_15<=HQ876173.1': present in 15744/15744 = 100% of samples.
Group 'node_16<=node_24': present in 15734/15744 = 99.9365% of samples.
Group 'node_16<=node_4': present in 15740/15744 = 99.9746% of samples.
Group 'node_16<=AB025721.1': present in 15744/15744 = 100% of samples.
Group 'node_17<=node_25': present in 14231/15744 = 90.39% of samples.
Group 'node_17<=node_6': present in 15476/15744 = 98.2978% of samples.
Group 'node_17<=node_2': present in 15287/15744 = 97.0973% of samples.
Group 'node_20<=node_28': present in 15729/15744 = 99.9047% of samples.
Group 'node_20<=node_11': present in 15736/15744 = 99.9492% of samples.
Group 'node_20<=AM748796.1': present in 15744/15744 = 100% of samples.
Group 'node_19<=node_27': present in 15225/15744 = 96.7035% of samples.
Group 'node_19<=node_8': present in 15735/15744 = 99.9428% of samples.
Group 'node_19<=node_5': present in 15617/15744 = 99.1933% of samples.
Group 'node_18<=node_26': present in 15736/15744 = 99.9492% of samples.
Group 'node_18<=node_7': present in 15741/15744 = 99.9809% of samples.
Group 'node_18<=X59045.1': present in 15744/15744 = 100% of samples.
Group 'node_18<=M12777.1': present in 15744/15744 = 100% of samples.
Group 'node_18<=AF047363.1': present in 15744/15744 = 100% of samples.
Group 'node_14<=node_1': present in 15743/15744 = 99.9936% of samples.
Group 'node_14<=node_33': present in 15732/15744 = 99.9238% of samples.
Group 'node_14<=AB082929.2': present in 15744/15744 = 100% of samples.
Group 'node_30<=node_47': present in 15739/15744 = 99.9682% of samples.
Group 'node_30<=node_22': present in 15741/15744 = 99.9809% of samples.
Group 'node_30<=M57692.1': present in 15744/15744 = 100% of samples.
Group 'node_29<=node_38': present in 15738/15744 = 99.9619% of samples.
Group 'node_29<=node_21': present in 15742/15744 = 99.9873% of samples.
Group 'node_29<=M28053.1': present in 15744/15744 = 100% of samples.
Group 'node_23<=node_31': present in 15735/15744 = 99.9428% of samples.
Group 'node_23<=node_15': present in 15737/15744 = 99.9555% of samples.
Group 'node_23<=D13068.1': present in 15744/15744 = 100% of samples.
Group 'node_24<=node_32': present in 14611/15744 = 92.8036% of samples.
Group 'node_24<=node_16': present in 15734/15744 = 99.9365% of samples.
Group 'node_24<=M15264.1': present in 15744/15744 = 100% of samples.
Group 'node_25<=node_33': present in 13448/15744 = 85.4167% of samples.
Group 'node_25<=node_17': present in 14231/15744 = 90.39% of samples.
Group 'node_25<=AX453023.1': present in 15744/15744 = 100% of samples.
Group 'node_28<=node_35': present in 15735/15744 = 99.9428% of samples.
Group 'node_28<=node_20': present in 15729/15744 = 99.9047% of samples.
Group 'node_28<=node_9': present in 15743/15744 = 99.9936% of samples.
Group 'node_27<=node_34': present in 15684/15744 = 99.6189% of samples.
Group 'node_27<=node_19': present in 15225/15744 = 96.7035% of samples.
Group 'node_27<=M17366.1': present in 15744/15744 = 100% of samples.
Group 'node_26<=node_45': present in 15736/15744 = 99.9492% of samples.
Group 'node_26<=node_18': present in 15736/15744 = 99.9492% of samples.
Group 'node_26<=EU305539.1': present in 15744/15744 = 100% of samples.
Group 'node_31<=node_36': present in 15735/15744 = 99.9428% of samples.
Group 'node_31<=node_23': present in 15735/15744 = 99.9428% of samples.
Group 'node_31<=AF011388.1': present in 15744/15744 = 100% of samples.
Group 'node_32<=node_40': present in 12804/15744 = 81.3262% of samples.
Group 'node_32<=node_24': present in 14611/15744 = 92.8036% of samples.
Group 'node_32<=AB015670.1': present in 15744/15744 = 100% of samples.
Group 'node_33<=node_14': present in 15732/15744 = 99.9238% of samples.
Group 'node_33<=node_37': present in 12839/15744 = 81.5485% of samples.
Group 'node_33<=node_25': present in 13448/15744 = 85.4167% of samples.
Group 'node_35<=node_41': present in 15736/15744 = 99.9492% of samples.
Group 'node_35<=node_28': present in 15735/15744 = 99.9428% of samples.
Group 'node_35<=AM933612.1': present in 15744/15744 = 100% of samples.
Group 'node_34<=node_38': present in 15727/15744 = 99.892% of samples.
Group 'node_34<=node_27': present in 15684/15744 = 99.6189% of samples.
Group 'node_34<=JX101460.1': present in 15744/15744 = 100% of samples.
Group 'node_36<=node_39': present in 15673/15744 = 99.549% of samples.
Group 'node_36<=node_31': present in 15735/15744 = 99.9428% of samples.
Group 'node_36<=D90243.1': present in 15744/15744 = 100% of samples.
Group 'node_37<=node_33': present in 12839/15744 = 81.5485% of samples.
Group 'node_37<=node_40': present in 9541/15744 = 60.6009% of samples.
Group 'node_37<=AJ850087.1': present in 15744/15744 = 100% of samples.
Group 'node_38<=node_41': present in 15727/15744 = 99.892% of samples.
Group 'node_38<=node_34': present in 15727/15744 = 99.892% of samples.
Group 'node_38<=node_29': present in 15738/15744 = 99.9619% of samples.
Group 'node_39<=node_42': present in 15736/15744 = 99.9492% of samples.
Group 'node_39<=node_36': present in 15673/15744 = 99.549% of samples.
Group 'node_39<=JF280087.1': present in 15744/15744 = 100% of samples.
Group 'node_40<=node_37': present in 9541/15744 = 60.6009% of samples.
Group 'node_40<=node_44': present in 15612/15744 = 99.1616% of samples.
Group 'node_40<=node_32': present in 12804/15744 = 81.3262% of samples.
Group 'node_41<=node_43': present in 15695/15744 = 99.6888% of samples.
Group 'node_41<=node_38': present in 15727/15744 = 99.892% of samples.
Group 'node_41<=node_35': present in 15736/15744 = 99.9492% of samples.
Group 'node_42<=node_44': present in 12495/15744 = 79.3636% of samples.
Group 'node_42<=node_39': present in 15736/15744 = 99.9492% of samples.
Group 'node_42<=AJ876899.1': present in 15744/15744 = 100% of samples.
Group 'node_43<=node_45': present in 15650/15744 = 99.4029% of samples.
Group 'node_43<=node_41': present in 15695/15744 = 99.6888% of samples.
Group 'node_43<=EU644086.2': present in 15744/15744 = 100% of samples.
Group 'node_44<=node_40': present in 15612/15744 = 99.1616% of samples.
Group 'node_44<=node_46': present in 15544/15744 = 98.7297% of samples.
Group 'node_44<=node_42': present in 12495/15744 = 79.3636% of samples.
Group 'node_45<=node_47': present in 15725/15744 = 99.8793% of samples.
Group 'node_45<=node_43': present in 15650/15744 = 99.4029% of samples.
Group 'node_45<=node_26': present in 15736/15744 = 99.9492% of samples.
Group 'node_46<=node_44': present in 15544/15744 = 98.7297% of samples.
Group 'node_46<=node_48': present in 15706/15744 = 99.7586% of samples.
Group 'node_46<=node_10': present in 15742/15744 = 99.9873% of samples.
Group 'node_47<=node_48': present in 15674/15744 = 99.5554% of samples.
Group 'node_47<=node_45': present in 15725/15744 = 99.8793% of samples.
Group 'node_47<=node_30': present in 15739/15744 = 99.9682% of samples.
Group 'node_48<=node_46': present in 15706/15744 = 99.7586% of samples.
Group 'node_48<=node_47': present in 15674/15744 = 99.5554% of samples.
Group 'node_48<=KJ806554.1': present in 15744/15744 = 100% of samples.


Tyler Ruddenfort

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Dec 1, 2020, 3:58:55 AM12/1/20
to bali-phy-users
Hi Ben,

Just wanted to let you know that I still can't troubleshoot this on my end. Is there any news regarding this bug?
Thank you very much.

Best,
Tyler

Benjamin Redelings

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Dec 1, 2020, 11:44:29 PM12/1/20
to bali-ph...@googlegroups.com

Hi Tyler,

It looks like if you run the following command (in the right directory) then it should start working, but crash:

'summarize-ancestors' 'Results/P1.max.fasta' '-n' 'Results/c50.tree' '-g' 'Results/c50.tree' '-A' '5cgtase_old/C1.P1.fastas' '-T' '5cgtase_old/C1.trees' '-A' '6cgtase_old/C1.P1.fastas' '-T' '6cgtase_old/C1.trees' '-A' '7cgtase_old/C1.P1.fastas' '-T' '7cgtase_old/C1.trees' '-A' '8cgtase_old/C1.P1.fastas' '-T' '8cgtase_old/C1.trees' '-A' '9cgtase_old/C1.P1.fastas' '-T' '9cgtase_old/C1.trees' '-A' '10cgtase_old/C1.P1.fastas' '-T' '10cgtase_old/C1.trees' '-A' '11cgtase_pld/C1.P1.fastas' '-T' '11cgtase_pld/C1.trees' '-A' '12cgtase_old/C1.P1.fastas' '-T' '12cgtase_old/C1.trees' > 'Results/P1.ancestors.fasta'

In order for me to reproduce the crash, I need to be able to run the command with the same data files you have.  Would it be possible for you to send me an archive containing all the *cgtase_old directories?  If so, how big would this be?

I'm wondering if you get a crash running bp-analyze on just the 12cgtase_old directory alone.  If so, then you could just send me that one.

-BenRI

Tyler Ruddenfort

unread,
Dec 3, 2020, 12:05:16 PM12/3/20
to bali-phy-users
Hi Ben,

Sorry for the late response, I uploaded the files via GDrive and you can access them through the link I sent you via email. The entire folder is about 5.5GB. I tried running just the 12cgtase_old but it didn't give me any errors.

Best,
Tyler

Benjamin Redelings

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Jan 19, 2021, 9:35:05 PMJan 19
to bali-ph...@googlegroups.com

Hi Tyler,

Thank you for the files.

It looks like creating the ancestral sequence alignment was both (i) slow and (ii) used too much memory when summarizing a lot of chains.  I've made a fix for this and published it here:

    https://github.com/bredelings/BAli-Phy/releases/tag/3.5.99

Can you try it out and see if it fixes your problem?

-BenRI

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