Fails locally - Githubissues

richel@sonic:~/GitHubs/razzo_project$ ./scripts/3_run_razzo.sh ./scripts/3_run_razzo.sh: line 11: module: command not found ./scripts/3_run_razzo.sh: line 12: module: command not found ./scripts/3_run_razzo.sh: line 13: module: command not found ./data/0.2-0.15-1-0.1/1/parameters.RDa Registered S3 method overwritten by 'geiger': method from unique.multiPhylo ape [1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 1/3: -754.40206955876" [1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior" [1] "Log evidence for model 2/3: -721.904285029982" [1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 3/3: -1573.97071174917" site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd 1 JC69 strict birth_death -754.4021 13.2597809 2 JC69 strict yule -721.9043 11.4243613 3 GTR strict birth_death -1573.9707 0.4278837 weight 1 7.698241e-15 2 1.000000e+00 3 0.000000e+00 [1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior" [1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 1/3: -734.219702838099" [1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior" [1] "Log evidence for model 2/3: -727.963282954922" [1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 3/3: -1581.47550237193" site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd 1 JC69 strict birth_death -734.2197 14.816277 2 JC69 strict yule -727.9633 11.890358 3 GTR strict birth_death -1581.4755 0.531501 weight 1 0.001914428 2 0.998085572 3 0.000000000 [1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior" [1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 1/3: -734.219702838099" [1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior" [1] "Log evidence for model 2/3: -727.963282954922" [1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 3/3: -1581.47550237193" site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd 1 JC69 strict birth_death -734.2197 14.816277 2 JC69 strict yule -727.9633 11.890358 3 GTR strict birth_death -1581.4755 0.531501 weight 1 0.001914428 2 0.998085572 3 0.000000000 [1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior" [1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" tree inference_model inference_model_weight site_model clock_model 1 true generative 7.698241e-15 JC69 strict 2 true candidate 1.000000e+00 JC69 strict 3 twin generative 1.914428e-03 JC69 strict 4 twin candidate 9.980856e-01 JC69 strict 5 twin generative 1.914428e-03 JC69 strict 6 twin candidate 9.980856e-01 JC69 strict tree_prior error_1 error_2 error_3 error_4 1 birth_death 0.1519073 0.1650348 0.1685397 0.1624784 2 yule 0.1519073 0.1810251 0.1772348 0.1768255 3 birth_death 0.1619638 0.1772607 0.1763823 0.1730027 4 yule 0.1619638 0.1905475 0.1899067 0.1890990 5 birth_death 0.1619638 0.1772607 0.1763823 0.1730027 6 yule 0.1619638 0.1905475 0.1899067 0.1890990 ./data/0.2-0.15-1-0.1/2/parameters.RDa Registered S3 method overwritten by 'geiger': method from unique.multiPhylo ape [1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 1/3: -125.127414460308" [1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior" [1] "Log evidence for model 2/3: -124.988271649075" [1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 3/3: -124.440201190081" site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd 1 JC69 strict birth_death -125.1274 0.4217221 2 JC69 strict yule -124.9883 0.4380050 3 GTR strict birth_death -124.4402 0.4278201 weight 1 0.2416944 2 0.2777766 3 0.4805290 [1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior" [1] "Selected model 2/2 with GTR site model, strict clock model and birth_death tree prior" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 1/3: -125.076090007881" [1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior" [1] "Log evidence for model 2/3: -124.931537283633" [1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 3/3: -124.986869735681" site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd 1 JC69 strict birth_death -125.0761 0.4641394 2 JC69 strict yule -124.9315 0.4798728 3 GTR strict birth_death -124.9869 0.4233559 weight 1 0.3078018 2 0.3556719 3 0.3365263 [1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior" [1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 1/3: -125.076090007881" [1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior" ^[[B[1] "Log evidence for model 2/3: -124.931537283633" [1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior" [1] "Log evidence for model 3/3: -124.986869735681" site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd 1 JC69 strict birth_death -125.0761 0.4641394 2 JC69 strict yule -124.9315 0.4798728 3 GTR strict birth_death -124.9869 0.4233559 weight 1 0.3078018 2 0.3556719 3 0.3365263 [1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior" [1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" [1] "from_col_idx: 7" [1] "ncol(df): 10" [1] "length(nltts): 4" tree inference_model inference_model_weight site_model clock_model 1 true generative 0.2416944 JC69 strict 2 true candidate 0.4805290 GTR strict 3 twin generative 0.3078018 JC69 strict 4 twin candidate 0.3556719 JC69 strict 5 twin generative 0.3078018 JC69 strict 6 twin candidate 0.3556719 JC69 strict tree_prior error_1 error_2 error_3 error_4 1 birth_death 0.1413237 0.11798135 0.11148182 0.0895663 2 birth_death 0.1413237 0.09146386 0.10661641 0.1035050 3 birth_death 0.1255922 0.10909046 0.12307749 0.1166971 4 yule 0.1255922 0.12145778 0.05122381 0.1039105 5 birth_death 0.1255922 0.10909046 0.12307749 0.1166971 6 yule 0.1255922 0.12145778 0.05122381 0.1039105 ./scripts/3_run_razzo.sh: line 19: ilename"): command not found ./scripts/3_run_razzo.sh: line 20: syntax error near unexpected token `done' ./scripts/3_run_razzo.sh: line 20: `done'

Looks great, except for the tables:

[1] "/home/richel/GitHubs/razzo_project/data/0.2-0.15-1-0.1/1/parameters.RDa"
[2] "/home/richel/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/parameters.RDa"
./scripts/3_run_razzo.sh: line 11: module: command not found
./scripts/3_run_razzo.sh: line 12: module: command not found
./scripts/3_run_razzo.sh: line 13: module: command not found
./scripts/3_run_razzo.sh: line 14: module: command not found
./data/0.2-0.15-1-0.1/1/parameters.RDa
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
[1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 1/3: -754.40206955876"
[1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior"
[1] "Log evidence for model 2/3: -721.904285029982"
[1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 3/3: -1573.97071174917"
  site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd
1            JC69           strict     birth_death    -754.4021      13.2597809
2            JC69           strict            yule    -721.9043      11.4243613
3             GTR           strict     birth_death   -1573.9707       0.4278837
        weight
1 7.698241e-15
2 1.000000e+00
3 0.000000e+00
[1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 1/3: -734.219702838099"
[1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior"
[1] "Log evidence for model 2/3: -727.963282954922"
[1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 3/3: -1581.47550237193"
  site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd
1            JC69           strict     birth_death    -734.2197       14.816277
2            JC69           strict            yule    -727.9633       11.890358
3             GTR           strict     birth_death   -1581.4755        0.531501
       weight
1 0.001914428
2 0.998085572
3 0.000000000
[1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 1/3: -734.219702838099"
[1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior"
[1] "Log evidence for model 2/3: -727.963282954922"
[1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 3/3: -1581.47550237193"
  site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd
1            JC69           strict     birth_death    -734.2197       14.816277
2            JC69           strict            yule    -727.9633       11.890358
3             GTR           strict     birth_death   -1581.4755        0.531501
       weight
1 0.001914428
2 0.998085572
3 0.000000000
[1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
  tree inference_model inference_model_weight site_model clock_model
1 true      generative           7.698241e-15       JC69      strict
2 true       candidate           1.000000e+00       JC69      strict
3 twin      generative           1.914428e-03       JC69      strict
4 twin       candidate           9.980856e-01       JC69      strict
5 twin      generative           1.914428e-03       JC69      strict
6 twin       candidate           9.980856e-01       JC69      strict
   tree_prior   error_1   error_2   error_3   error_4
1 birth_death 0.1519073 0.1650348 0.1685397 0.1624784
2        yule 0.1519073 0.1810251 0.1772348 0.1768255
3 birth_death 0.1619638 0.1772607 0.1763823 0.1730027
4        yule 0.1619638 0.1905475 0.1899067 0.1890990
5 birth_death 0.1619638 0.1772607 0.1763823 0.1730027
6        yule 0.1619638 0.1905475 0.1899067 0.1890990
./data/0.2-0.15-1-0.1/2/parameters.RDa
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
[1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 1/3: -125.127414460308"
[1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior"
[1] "Log evidence for model 2/3: -124.988271649075"
[1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 3/3: -124.440201190081"
  site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd
1            JC69           strict     birth_death    -125.1274       0.4217221
2            JC69           strict            yule    -124.9883       0.4380050
3             GTR           strict     birth_death    -124.4402       0.4278201
     weight
1 0.2416944
2 0.2777766
3 0.4805290
[1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Selected model 2/2 with GTR site model, strict clock model and birth_death tree prior"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 1/3: -125.076090007881"
[1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior"
[1] "Log evidence for model 2/3: -124.931537283633"
[1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 3/3: -124.986869735681"
  site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd
1            JC69           strict     birth_death    -125.0761       0.4641394
2            JC69           strict            yule    -124.9315       0.4798728
3             GTR           strict     birth_death    -124.9869       0.4233559
     weight
1 0.3078018
2 0.3556719
3 0.3365263
[1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "Estimating evidence for model 1/3 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 1/3: -125.076090007881"
[1] "Estimating evidence for model 2/3 with JC69 site model, strict clock model and yule tree prior"
[1] "Log evidence for model 2/3: -124.931537283633"
[1] "Estimating evidence for model 3/3 with GTR site model, strict clock model and birth_death tree prior"
[1] "Log evidence for model 3/3: -124.986869735681"
  site_model_name clock_model_name tree_prior_name marg_log_lik marg_log_lik_sd
1            JC69           strict     birth_death    -125.0761       0.4641394
2            JC69           strict            yule    -124.9315       0.4798728
3             GTR           strict     birth_death    -124.9869       0.4233559
     weight
1 0.3078018
2 0.3556719
3 0.3365263
[1] "Selected model 1/2 with JC69 site model, strict clock model and birth_death tree prior"
[1] "Selected model 2/2 with JC69 site model, strict clock model and yule tree prior"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
[1] "from_col_idx: 7"
[1] "ncol(df): 10"
[1] "length(nltts): 4"
  tree inference_model inference_model_weight site_model clock_model
1 true      generative              0.2416944       JC69      strict
2 true       candidate              0.4805290        GTR      strict
3 twin      generative              0.3078018       JC69      strict
4 twin       candidate              0.3556719       JC69      strict
5 twin      generative              0.3078018       JC69      strict
6 twin       candidate              0.3556719       JC69      strict
   tree_prior   error_1    error_2    error_3   error_4
1 birth_death 0.1413237 0.11798135 0.11148182 0.0895663
2 birth_death 0.1413237 0.09146386 0.10661641 0.1035050
3 birth_death 0.1255922 0.10909046 0.12307749 0.1166971
4        yule 0.1255922 0.12145778 0.05122381 0.1039105
5 birth_death 0.1255922 0.10909046 0.12307749 0.1166971
6        yule 0.1255922 0.12145778 0.05122381 0.1039105
richel@sonic:~/GitHubs/razzo_project$

richelbilderbeek / razzo_project

Fails locally #2