Hi All,

I am trying a REL analyses on my workstation, Ubuntu, 16 reasonably fast cores and 24GM RAM.. Using the MPI version. The dataset is 115 sequences of length 250bases.  It has been running for 24 hours I don't know if it is hung- or just taking a long time. If someone could provide me with some intuition about how long I should expect to wait, I'd appreciate it!

Batchfile:
Code:

inputOptions = {};
inputOptions ["00"] = PATH_TO_CURRENT_BF + ".." + DIRECTORY_SEPARATOR + "data" + DIRECTORY_SEPARATOR + "data1.txt";
inputOptions ["01"] = "Universal";
inputOptions ["02"] = "y";
inputOptions ["03"] = "Codon Model";
inputOptions ["04"] = "MG94xREV";
inputOptions ["05"] = "Run All";
inputOptions ["06"] = "Independent Discrete";
inputOptions ["07"] = "Randomized";
inputOptions ["08"] = "3";
inputOptions ["09"] = "3";
inputOptions ["11"] = PATH_TO_CURRENT_BF + ".." + DIRECTORY_SEPARATOR + "Results" + DIRECTORY_SEPARATOR + "testingREL123.txt";;

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "dNdSRateAnalysis.bf", inputOptions); 

Screenout:
Code:

RUNNING MG94xREV MODEL COMPARISONS on /home/macmanes/hyphy1/TestSuite/REL/../data/data1.txt



########### 3x3 CLASSES ###########

+---------------------+---------------------+---------------+-------------------+-------------------+---------------+-----+-----------+
|       Model         |   Log Likelihood    | Synonymous CV |  NS Exp and CV    |  N/S Exp and CV   |    P-Value    | Prm |    AIC    |
+---------------------+---------------------+---------------+-------------------+-------------------+---------------+-----+-----------+
| Constant Rates      |         -3983.56857 |      N/A      |  1.07514, 0.00000 |  1.07514, 0.00000 |      N/A      |  231|    8429.14|
+---------------------+---------------------+---------------+-------------------+-------------------+---------------+-----+-----------+
| Prop. Var. Rates    |         -3719.80287 |    1.12333660 |  1.08118, 1.12334 |  1.08118, 0.00000 |      N/A      |  235|    7909.61|
+---------------------+---------------------+---------------+-------------------+-------------------+---------------+-----+-----------+
| Var. N.Syn. Rates   |         -3727.55268 |      N/A      |  1.19256, 1.31019 |  1.19256, 1.31019 |      N/A      |  235|    7925.11|
+---------------------+---------------------+---------------+-------------------+-------------------+---------------+-----+-----------+
| Dual Variable Rates |         -3680.58558 |    1.35916541 |  1.04872, 1.29836 |  2.99247, 1.74727 |      N/A      |  239|    7839.17|
+---------------------+---------------------+---------------+-------------------+-------------------+---------------+-----+-----------+ 

OK, so now I have another issue, related to the "Run Custom" suggestion: Using the HYPHYMP version, after "run custom" you are asked about "rate variation options", and you can select multiple options.. Typing in d gets you past this bank of selections and on to the 'distribution options'..  

When I try to implement this into the wrapper file and using the MPI version, it does not work, seems to not accept the 'd' command to complete this set of selections..

Batchfile:
Code:

inputOptions = {};
inputOptions ["00"] = PATH_TO_CURRENT_BF + ".." + DIRECTORY_SEPARATOR + "data" + DIRECTORY_SEPARATOR + "data1.txt";
inputOptions ["01"] = "Universal";
inputOptions ["02"] = "y";
inputOptions ["03"] = "Codon Model";
inputOptions ["04"] = "MG94xREV";
inputOptions ["05"] = "Run Custom";
inputOptions ["06"] = "Dual";
inputOptions ["07"] = "d";
inputOptions ["08"] = "Independent Discrete";
inputOptions ["09"] = "Randomized";
inputOptions ["10"] = "3";
inputOptions ["11"] = "3";
inputOptions ["12"] = PATH_TO_CURRENT_BF + ".." + DIRECTORY_SEPARATOR + "Results" + DIRECTORY_SEPARATOR + "testingREL751.txt";;

ExecuteAFile (HYPHY_BASE_DIRECTORY + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "dNdSRateAnalysis.bf", inputOptions); 

error:
Code:

Master node received an error:
Not a valid (or duplicate) option: 'd' passed to Choice List (with multiple selections) 'Rate Variation Models' using redirected stdin input
Call stack
2 : Choice List for Rate Variation Models with choice list:SKIP_NONE. Store result in modelTypes
1 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"dNdSRateAnalysis.bf" using basepath /home/macmanes/hyphy1/TestSuite/REL/. reading input from inputOptions

--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 7431 on node macmanes exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
 

I get basically the same error when not using the 'd' option.