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matsengrp / linearham

A Bayesian Phylo-HMM for B cell receptor sequence analysis
http://matsengrp.github.io/linearham
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crash in asr/ess script #88

Closed psathyrella closed 2 years ago

psathyrella commented 2 years ago

I'm getting this error, and can't figure out anything about what's causing it:

Error in checkForRemoteErrors(val) :
  2 nodes produced errors; first error: missing value where TRUE/FALSE needed
Calls: unlist ... <Anonymous> -> dynamicClusterApply -> checkForRemoteErrors
Execution halted

when i run this command (input files attached):

Rscript --slave --vanilla scripts/run_bootstrap_asr_ess.R lh_revbayes_run.trees cluster_seqs.fasta 0.1 0.05 1 0 linearham_run.trees linearham_run.log linearham_run.ess

edit: should have said -- this is running with super smaller N iterations and whatnot, which I'm sure is dumb, but otoh i don't see anything obviously wrong with these input files, so maybe a more informative error would be worthwhile.

edit 2: I think this is the other error it mentions:

Error in checkForRemoteErrors(val) : 
  2 nodes produced errors; first error: no applicable method for 'unroot' applied to an object of class "NULL"
Calls: unlist ... <Anonymous> -> dynamicClusterApply -> checkForRemoteErrors
psathyrella commented 2 years ago

edit: ok gh is refusing to attach files, here are contents:

lh_revbayes_run.trees:

 Iteration  RBLogLikelihood Prior   alpha   er[1]   er[2]   er[3]   er[4]   er[5]   er[6]   pi[1]   pi[2]   pi[3]   pi[4]   tree    sr[1]   sr[2]   sr[3]   sr[4]   LHLogLikelihood LogWeight   NaiveSequence   VGene   V5pDel  V3pDel  VFwkInsertion   VDInsertion DGene   D5pDel  D3pDel  DJInsertion JGene   J5pDel  J3pDel  JFwkInsertion
0   -1007.66    88.4922 0.0549294   0.0589244   0.373014    0.0895696   0.0566064   0.249337    0.172549    0.305679    0.300634    0.220527    0.173161    (((((033021-P4-D8-HC-igh:0.000468,033021-P3-B6-HC-igh:0.002451):0.003174,((041321-P1-A9-HC-igh:0.012926,033021-P2-C10-HC-igh:0.006553):0.000691,(033021-P4-E5-HC-igh:0.013727,033021-P4-B11-HC-R-igh:0.010030):0.002855):0.004252):0.005975,(040921-P5-E10-HC-igh:0.003284,(((033021-P1-F6-HC-R-igh:0.023830,((040921-P3-C5-HC-igh:0.045718,040921-P3-E8-HC-igh:0.044025):0.008100,((040921-P1-A3-HC-igh:0.010744,(((040921-P2-B4-HC-igh:0.002973,040921-P3-D4-HC-igh:0.013510):0.008742,040921-P3-E10-HC-igh:0.000554):0.017159,040921-P3-F4-HC-igh:0.001918):0.054709):0.000333,040921-P3-G2-HC-igh:0.052801):0.008304):0.008218):0.001699,041321-P3-A6-HC-R-igh:0.000932):0.008641,040921-P5-D4-HC-igh:0.011451):0.003581):0.002709):0.006267,040921-P6-B6-HC-igh:0.002175):0.003466,040921-P3-G11-HC-igh:0.089490,naive:0.009423):0.0;  6.08954e-12 3.68067e-06 0.00887719  3.99112 -550.168    457.492 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
10  -913.388    91.5608 0.00853924  0.0685431   0.451114    0.187889    0.0884874   0.139153    0.0648129   0.278513    0.317416    0.232333    0.171737    (naive:0.001162,040921-P6-B6-HC-igh:0.011511,(((((033021-P2-C10-HC-igh:0.000225,((033021-P3-B6-HC-igh:0.002674,033021-P4-D8-HC-igh:0.000198):0.008256,(033021-P1-F6-HC-R-igh:0.000372,(041321-P1-A9-HC-igh:0.016921,(033021-P4-B11-HC-R-igh:0.011968,033021-P4-E5-HC-igh:0.001918):0.015347):0.014250):0.000037):0.002125):0.007593,(040921-P1-A3-HC-igh:0.028609,(((040921-P3-G11-HC-igh:0.031076,((040921-P3-F4-HC-igh:0.021270,040921-P3-D4-HC-igh:0.008190):0.014256,(040921-P3-G2-HC-igh:0.034792,(040921-P3-E10-HC-igh:0.007218,040921-P2-B4-HC-igh:0.012614):0.005030):0.001438):0.015736):0.002251,040921-P3-E8-HC-igh:0.044025):0.028301,040921-P3-C5-HC-igh:0.067960):0.033555):0.004663):0.010026,040921-P5-E10-HC-igh:0.003814):0.003438,040921-P5-D4-HC-igh:0.000561):0.001908,041321-P3-A6-HC-R-igh:0.001945):0.000404):0.0;  6.08954e-12 3.68067e-06 0.00887719  3.99112 -457.189    456.199 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
20  -855.883    105.368 0.295914    0.137352    0.274282    0.173169    0.0697001   0.248463    0.0970331   0.235707    0.302431    0.248427    0.213435    ((((((041321-P1-A9-HC-igh:0.005722,((033021-P4-B11-HC-R-igh:0.010059,033021-P4-E5-HC-igh:0.003475):0.014996,033021-P2-C10-HC-igh:0.000659):0.000188):0.007634,033021-P1-F6-HC-R-igh:0.001955):0.002705,(033021-P4-D8-HC-igh:0.002842,(033021-P3-B6-HC-igh:0.002892,((((((040921-P3-E10-HC-igh:0.003211,(040921-P3-D4-HC-igh:0.012693,040921-P3-F4-HC-igh:0.007503):0.001475):0.000142,040921-P2-B4-HC-igh:0.010012):0.001424,040921-P3-G11-HC-igh:0.007022):0.000329,040921-P3-G2-HC-igh:0.002363):0.064489,040921-P3-E8-HC-igh:0.057282):0.019066,(040921-P1-A3-HC-igh:0.009834,040921-P3-C5-HC-igh:0.048471):0.012561):0.007189):0.000817):0.000451):0.004698,(040921-P5-D4-HC-igh:0.000232,040921-P6-B6-HC-igh:0.003754):0.000044):0.000940,041321-P3-A6-HC-R-igh:0.001078):0.003448,naive:0.000823,040921-P5-E10-HC-igh:0.002220):0.0;  0.00496968  0.10132 0.588876    3.30483 -402.274    453.609 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
30  -862.533    110.345 0.530448    0.145583    0.290717    0.183546    0.0738767   0.20343 0.102847    0.276496    0.232663    0.289538    0.201303    (((040921-P5-D4-HC-igh:0.002219,041321-P3-A6-HC-R-igh:0.001244):0.000005,(((041321-P1-A9-HC-igh:0.011078,((033021-P1-F6-HC-R-igh:0.005451,((040921-P3-C5-HC-igh:0.022929,040921-P1-A3-HC-igh:0.008431):0.003023,((((040921-P3-G2-HC-igh:0.001963,040921-P3-E10-HC-igh:0.003118):0.002899,040921-P2-B4-HC-igh:0.000409):0.000052,((040921-P3-F4-HC-igh:0.019872,040921-P3-D4-HC-igh:0.021494):0.003334,040921-P3-G11-HC-igh:0.010271):0.004346):0.045313,040921-P3-E8-HC-igh:0.048504):0.005060):0.002951):0.005845,((033021-P4-E5-HC-igh:0.003861,033021-P4-B11-HC-R-igh:0.002393):0.014996,033021-P2-C10-HC-igh:0.003729):0.000313):0.000290):0.003775,(033021-P4-D8-HC-igh:0.000146,033021-P3-B6-HC-igh:0.002664):0.001863):0.002337,040921-P6-B6-HC-igh:0.006782):0.002314):0.007523,naive:0.000692,040921-P5-E10-HC-igh:0.001087):0.0;  0.0391606   0.271329    0.841218    2.84829 -413.232    449.301 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
40  -859.89 105.359 0.458735    0.0814071   0.248658    0.169252    0.0642903   0.311228    0.125164    0.279645    0.237738    0.295854    0.186764    ((041321-P3-A6-HC-R-igh:0.001306,040921-P6-B6-HC-igh:0.001647):0.009809,((((040921-P3-C5-HC-igh:0.039886,040921-P1-A3-HC-igh:0.012663):0.010284,(033021-P3-B6-HC-igh:0.006775,((((040921-P3-G11-HC-igh:0.009666,((040921-P3-G2-HC-igh:0.009262,((040921-P3-F4-HC-igh:0.005703,040921-P3-D4-HC-igh:0.018979):0.007349,040921-P2-B4-HC-igh:0.000265):0.007520):0.002888,040921-P3-E10-HC-igh:0.007814):0.001697):0.045313,040921-P3-E8-HC-igh:0.024599):0.030745,((((033021-P4-E5-HC-igh:0.003861,033021-P4-B11-HC-R-igh:0.001494):0.010502,041321-P1-A9-HC-igh:0.011315):0.000825,033021-P2-C10-HC-igh:0.003557):0.002649,033021-P1-F6-HC-R-igh:0.004264):0.002714):0.012989,033021-P4-D8-HC-igh:0.004692):0.000585):0.001106):0.002629,040921-P5-E10-HC-igh:0.000170):0.001678,040921-P5-D4-HC-igh:0.008782):0.002637,naive:0.004538):0.0;  0.0260189   0.224126    0.787755    2.9621  -410.862    449.028 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
50  -860.775    101.112 0.165902    0.0904398   0.212868    0.160984    0.0229069   0.406929    0.105872    0.266495    0.222732    0.27718 0.233594    (naive:0.004733,(040921-P5-D4-HC-igh:0.001204,((((033021-P4-D8-HC-igh:0.003792,033021-P3-B6-HC-igh:0.003571):0.001559,((033021-P1-F6-HC-R-igh:0.006668,((033021-P4-B11-HC-R-igh:0.002847,033021-P4-E5-HC-igh:0.012212):0.026996,041321-P1-A9-HC-igh:0.015275):0.000949):0.000892,((((040921-P3-D4-HC-igh:0.012593,040921-P3-F4-HC-igh:0.007072):0.005524,(040921-P3-G11-HC-igh:0.018247,((040921-P3-E10-HC-igh:0.006670,040921-P2-B4-HC-igh:0.013218):0.003502,040921-P3-G2-HC-igh:0.001027):0.001868):0.000876):0.076699,040921-P3-E8-HC-igh:0.026272):0.007716,033021-P2-C10-HC-igh:0.001828):0.001151):0.008962):0.004039,(040921-P3-C5-HC-igh:0.047964,040921-P1-A3-HC-igh:0.023258):0.006105):0.004006,(040921-P6-B6-HC-igh:0.003902,040921-P5-E10-HC-igh:0.006604):0.001192):0.000585):0.001244,041321-P3-A6-HC-R-igh:0.007737):0.0;  0.000128418 0.0167021   0.289106    3.69406 -409.577    451.198 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
60  -859.872    113.576 0.19994 0.131358    0.308663    0.0921671   0.0335493   0.314695    0.119568    0.252601    0.234888    0.278122    0.234389    (naive:0.000241,(041321-P3-A6-HC-R-igh:0.002212,(040921-P5-E10-HC-igh:0.006016,(040921-P6-B6-HC-igh:0.002111,040921-P5-D4-HC-igh:0.000142):0.005343):0.000985):0.000961,(((033021-P1-F6-HC-R-igh:0.003152,(((040921-P3-E8-HC-igh:0.045275,((040921-P3-D4-HC-igh:0.012329,040921-P3-F4-HC-igh:0.005171):0.003908,(((040921-P3-G11-HC-igh:0.009535,040921-P2-B4-HC-igh:0.005946):0.002521,040921-P3-G2-HC-igh:0.003613):0.001391,040921-P3-E10-HC-igh:0.004297):0.001728):0.033416):0.003971,(041321-P1-A9-HC-igh:0.008147,(033021-P4-B11-HC-R-igh:0.004403,033021-P4-E5-HC-igh:0.005631):0.004362):0.003655):0.001028,033021-P2-C10-HC-igh:0.004053):0.004402):0.000269,(033021-P3-B6-HC-igh:0.003044,033021-P4-D8-HC-igh:0.007868):0.002259):0.001765,(040921-P3-C5-HC-igh:0.025020,040921-P1-A3-HC-igh:0.008750):0.010617):0.006035):0.0;  0.000530094 0.0337407   0.383501    3.58223 -409.04 450.832 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
70  -856.903    109.28  0.0122334   0.152014    0.212775    0.139253    0.0693723   0.359015    0.0675702   0.247666    0.243164    0.291987    0.217184    (041321-P3-A6-HC-R-igh:0.001359,((040921-P6-B6-HC-igh:0.001257,((((033021-P3-B6-HC-igh:0.005330,033021-P4-D8-HC-igh:0.004199):0.002423,(040921-P3-C5-HC-igh:0.024297,040921-P1-A3-HC-igh:0.011288):0.009411):0.002050,(((((((((040921-P2-B4-HC-igh:0.005572,040921-P3-G11-HC-igh:0.003055):0.004933,040921-P3-G2-HC-igh:0.002355):0.005374,040921-P3-E10-HC-igh:0.005721):0.004439,040921-P3-F4-HC-igh:0.005256):0.001899,040921-P3-D4-HC-igh:0.010501):0.021395,040921-P3-E8-HC-igh:0.045275):0.040091,033021-P2-C10-HC-igh:0.000620):0.000158,((033021-P4-B11-HC-R-igh:0.000046,033021-P4-E5-HC-igh:0.009733):0.020814,041321-P1-A9-HC-igh:0.021401):0.008436):0.001421,033021-P1-F6-HC-R-igh:0.001108):0.006075):0.003075,040921-P5-E10-HC-igh:0.000858):0.000367):0.003920,040921-P5-D4-HC-igh:0.002113):0.001761,naive:0.001029):0.0;  0.000530094 0.0337407   0.383501    3.58223 -405.26 451.643 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
80  -852.251    108.587 0.116251    0.163809    0.181035    0.1182  0.0590238   0.419377    0.0585547   0.255438    0.219412    0.30115 0.224   ((((033021-P1-F6-HC-R-igh:0.002663,((033021-P4-E5-HC-igh:0.002865,033021-P4-B11-HC-R-igh:0.000716):0.010524,041321-P1-A9-HC-igh:0.008053):0.009647):0.000113,033021-P2-C10-HC-igh:0.001735):0.009658,(((040921-P3-C5-HC-igh:0.042345,040921-P1-A3-HC-igh:0.010735):0.006094,033021-P4-D8-HC-igh:0.001903):0.001687,((((040921-P3-F4-HC-igh:0.019238,((040921-P3-E10-HC-igh:0.000396,040921-P3-G11-HC-igh:0.008671):0.000402,(040921-P3-G2-HC-igh:0.004255,040921-P2-B4-HC-igh:0.006061):0.000594):0.005412):0.001844,040921-P3-D4-HC-igh:0.010501):0.048236,040921-P3-E8-HC-igh:0.045275):0.015669,033021-P3-B6-HC-igh:0.005415):0.001935):0.004068):0.005680,naive:0.003970,(((040921-P5-D4-HC-igh:0.001219,040921-P6-B6-HC-igh:0.000211):0.001424,040921-P5-E10-HC-igh:0.001182):0.001259,041321-P3-A6-HC-R-igh:0.003967):0.000674):0.0;  3.6469e-06  0.00283274  0.139794    3.85737 -402.219    450.032 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
90  -849.87 105.032 0.177986    0.0960529   0.293448    0.114384    0.0453157   0.30055 0.150249    0.256852    0.215091    0.302817    0.225239    (((040921-P5-E10-HC-igh:0.000730,040921-P6-B6-HC-igh:0.000465):0.006583,040921-P5-D4-HC-igh:0.001129):0.001347,((((040921-P3-C5-HC-igh:0.042345,040921-P1-A3-HC-igh:0.011738):0.009141,(((033021-P2-C10-HC-igh:0.002009,(041321-P1-A9-HC-igh:0.008150,(033021-P4-B11-HC-R-igh:0.005063,033021-P4-E5-HC-igh:0.008301):0.008731):0.004430):0.005062,(033021-P1-F6-HC-R-igh:0.000818,((040921-P3-D4-HC-igh:0.008891,((040921-P3-G2-HC-igh:0.001013,(040921-P3-E10-HC-igh:0.000124,(040921-P2-B4-HC-igh:0.003779,040921-P3-G11-HC-igh:0.005007):0.000038):0.000267):0.005033,040921-P3-F4-HC-igh:0.011764):0.004972):0.089147,040921-P3-E8-HC-igh:0.045275):0.011299):0.001372):0.000949,033021-P4-D8-HC-igh:0.002970):0.002420):0.004591,033021-P3-B6-HC-igh:0.004419):0.001962,041321-P3-A6-HC-R-igh:0.005171):0.007906,naive:0.006825):0.0;  0.000226075 0.0221183   0.323823    3.65383 -399.602    450.268 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0   
100 -852.086    104.081 0.338437    0.147888    0.346529    0.147259    0.0540175   0.220759    0.0835466   0.247871    0.227387    0.298078    0.226664    ((040921-P5-D4-HC-igh:0.008518,(040921-P5-E10-HC-igh:0.000773,(((033021-P3-B6-HC-igh:0.001075,033021-P4-D8-HC-igh:0.003497):0.003097,((040921-P3-C5-HC-igh:0.037295,040921-P1-A3-HC-igh:0.014312):0.012065,((033021-P2-C10-HC-igh:0.002015,((033021-P4-E5-HC-igh:0.002545,033021-P4-B11-HC-R-igh:0.000358):0.015892,041321-P1-A9-HC-igh:0.020588):0.008209):0.002070,((040921-P3-E8-HC-igh:0.057267,(040921-P3-D4-HC-igh:0.003695,((((040921-P3-G2-HC-igh:0.009355,040921-P3-G11-HC-igh:0.019162):0.003536,040921-P2-B4-HC-igh:0.000728):0.001375,040921-P3-E10-HC-igh:0.000748):0.005035,040921-P3-F4-HC-igh:0.006921):0.005047):0.046635):0.016820,033021-P1-F6-HC-R-igh:0.001326):0.006254):0.003655):0.004850):0.003758,041321-P3-A6-HC-R-igh:0.005460):0.000775):0.004875):0.000865,040921-P6-B6-HC-igh:0.005079,naive:0.003608):0.0;  0.0089244   0.134542    0.655051    3.20148 -402.097    449.989 CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC  IGHV1-2*02  0   1           IGHD1-1*p   0   0       IGHJp*p 0   0

cluster_seqs.fasta:

>naive
CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>041321-P1-A9-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGAACTGGGTGCGACAGGCCCCTGGACAGGGACTTGAGTGGATGGGATGGATCAACCCTATCAATGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAACCAGCGATTACAATTGGGACTTCCAGCAC
>033021-P2-C10-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAATGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P5-E10-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>033021-P4-B11-HC-R-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATTTGAATTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACTATGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAACCAGCGATTACAATTGGGACTTCCAGCAC
>033021-P1-F6-HC-R-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAATGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P3-G2-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGACTACTATTTAAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATTCGTCAACCCCAGAAATGGTGGCACAAACTATGCACGGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACATGTCCATCAGCACGGCCTACATGGAACTGAGCAGGCTAAAATCTGACGACACGGCCATATATTACTGTGCGAGAGGAAAAGACAGCGATTACAACTGGGACTTCCAGCAC
>033021-P4-D8-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P3-E8-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGACTATTATATGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATTTATCAACCCTACGAATGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCAAAATGACCAGAGACACGTCCATCAGCACAGTCTACATGGAGGTGAGCAGGCTGAGATCTGACGACTCGGCCGTTTATTACTGTGCGCGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P6-B6-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>041321-P3-A6-HC-R-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P1-A3-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGACTACTATATGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCAACCAGAGGTGCCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCAGCAGCACAGTCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>033021-P3-B6-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGTACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P3-D4-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGGCTACTATTTAAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATTCGTCAACCCCAGAAATGGTGGCACAAACTATGCACGGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACATGTCCATCAGCACGGCCTACATGGAGTTGAGCAGGCTAAAATCTGACGATACGGCCATATATTACTGTGCGAGAGGAAAAGACAGCGATTACAACTGGGACTTCCAGCAC
>040921-P5-D4-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAAACAGCGATTACAATTGGGACTTCCAGCAC
>040921-P3-E10-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGACTACTATTTAAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATTCGTCAACCCCAGAAATGGTGGCACAAACTATGCACGGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACATGTCCATCAGCACGGCCTACATGGAACTGAGCAGGCTAAAATCTGACGACACGGCCATATATTACTGTGCGAGAGGAAAAGACAGCGATTACAACTGGGACTTCCAGCAC
>040921-P3-F4-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGACTACTATTTAAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATTCGTCAACCCCAGACATGGTGGCACAAACTATGCACGGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACATGTCCATCAGTACGGCCTACATGGAGCTGAGCAGGCTAAAATCTGACGACACGGCCATATATTACTGTGCGAGAGGAAAAGACAGCGATTACAACTGGGACTTCCAGCAC
>040921-P3-G11-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGACTACTATTTAAACTGGGTGCGACAGGCCCCTGGACACGGGCTTGAGTGGATGGGATTCGTCAACCCCAGAAATGGTGGCACAAACTATGCACGGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACATGTCCGTCAGCACGGCCTACATGGAACTGAGCAGGCTAAAATCTGACGACACGGCCATATATTACTGTGCGAGAGGAAAAGACAGCGATTACAACTGGGACTTCCAGCAC
>033021-P4-E5-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCCGGATACACCTTCACCGGCTACTATTTGAATTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACTATGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAAAAACCAGCGATTACAATTGGGACTTCCAGCAC
>040921-P3-C5-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGGCTTCTGGATACACCTTCACCGACTACTATTTGAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTATCAGAGGTGCCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCACCGGCACAGCCTATATGGAGCTGAGAAGGCTGAATTCGGACGACACGGCCGTATATTACTGTGCGAGAGGAAAAAACAGCGATTATAATTGGGACTTCCAACAC
>040921-P2-B4-HC-igh
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGACTTCTGGATACACCTTCACCGACTACTATTTAAACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATTCGTCAACCCCAGAAATGGTGGCACAAACTATGCACGGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACATGTCCATCAGCACGGCCTACATGGAACTGAGCAGGCTAAAATCTGACGACACGGCCATATATTACTGTGCGAGAGGAAAAGACAGCGATTACAACTGGGACTTCCAGCAC
matsen commented 2 years ago

Thanks, Duncan! Do you happen to have a .trees file for a run that works?

psathyrella commented 2 years ago

[Uploading linearham_run.trees.txt…]()

matsen commented 2 years ago

Hm, can you check your link there? It seems to loop me back to the issue.

psathyrella commented 2 years ago

yeah, I didn't put a link, that's what github did when I attached a file -- for me it still says "uploading...". I guess a step up from yesterday when it couldn't attach anything? Anyway here's the correct file: lh_revbayes_run.trees.txt

matsen commented 2 years ago

Thanks. Can you try loading the problematic file into R? It doesn't obviously work when I copy-paste your log above into a file:

> df = read.table("lh_revbayes_run.trees.txt", sep="\t")
> df = read.table("lh_revbayes_run.trees.copypaste.txt", sep="\t")
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  :
  line 2 did not have 35 elements
>
psathyrella commented 2 years ago

I cannot, i didn't keep the file around; i guess copy pasting changed the formatting. I'll reopen if it happens again but atm I can't remember/figure out exactly what I was running.