readme.thrgibbs1
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readme.thrgibbs1 [2014/11/27 12:50] – shogo | readme.thrgibbs1 [2018/04/12 20:25] – [Options] shogo | ||
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OPTION fixed_var all 1 2 3 | OPTION fixed_var all 1 2 3 | ||
</ | </ | ||
- | Store all samples for solutions in " | + | Store all samples for solutions in " |
< | < | ||
OPTION fixed_var mean | OPTION fixed_var mean | ||
</ | </ | ||
- | Only posterior means and SD for solutions are calculated for all effects in " | + | Only posterior means and SD for solutions are calculated for all effects in " |
< | < | ||
OPTION fixed_var mean 1 2 3 | OPTION fixed_var mean 1 2 3 | ||
- | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | + | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " |
</ | </ | ||
< | < | ||
OPTION solution all | OPTION solution all | ||
</ | </ | ||
+ | Caution: this option will create a huge output solution file when you run many rounds and/or use a large model. | ||
Store all samples for solutions in " | Store all samples for solutions in " | ||
< | < | ||
OPTION solution all 1 2 3 | OPTION solution all 1 2 3 | ||
</ | </ | ||
+ | Caution: this option will create a huge output solution file when you run many rounds and/or use a large model. | ||
Store all samples for solutions in " | Store all samples for solutions in " | ||
< | < | ||
OPTION solution mean | OPTION solution mean | ||
</ | </ | ||
- | Only posterior means and SD for solutions are calculated for all effects in " | + | Only posterior means and SD for solutions are calculated for all effects in " |
< | < | ||
OPTION solution mean 1 2 3 | OPTION solution mean 1 2 3 | ||
</ | </ | ||
- | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " | + | Only posterior means and SD for solutions are calculated for effects 1, 2, and 3 in " |
< | < | ||
OPTION cont 10000 | OPTION cont 10000 | ||
</ | </ | ||
- | " | + | " |
+ | When using " | ||
< | < | ||
OPTION prior 5 2 -1 5 | OPTION prior 5 2 -1 5 | ||
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OPTION residual 1 | OPTION residual 1 | ||
</ | </ | ||
- | Set the residual variance = 1. | + | Set the residual variance = 1 (no need for binary traits). |
+ | < | ||
+ | OPTION pos_def x.x | ||
+ | </ | ||
+ | Specify checking pos-def for fixed effects where x.x is a tolerance (default=1d-08). | ||
< | < | ||
OPTION censored 1 0 | OPTION censored 1 0 | ||
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</ | </ | ||
Specify the SNP file name to use genotype data. | Specify the SNP file name to use genotype data. | ||
+ | |||
+ | ==== Save intermediate results for "cold start" ==== | ||
+ | |||
+ | OPTION save_halfway_samples n | ||
+ | |||
+ | This option can help the 'cold start' (to continue the sampling when the program accidentally stops before completing the run). An integer value //n// is needed. In every //n// rounds, the program saves intermediate samples to 2 files ('' | ||
+ | |||
+ | To restart, add '' | ||
+ | |||
+ | === Tips === | ||
+ | * Small //n// will make the program slow because of frequent file writing. The //n// should be a multiple of the interval (the 3rd number you will input in the beginning of the program). | ||
+ | * If the program stops during burn-in, the restart will fail because '' | ||
+ | * The cold start may add tiny numerical errors to the samples. Samples from the cold start wouldn' | ||
+ | * If, unfortunately, | ||
+ | |||
+ | === Example === | ||
+ | Put the following option in your parameter file. | ||
+ | |||
+ | OPTION save_halfway_samples 100 | ||
+ | |||
+ | Run '' | ||
+ | |||
+ | '**** saving halfway samples in every | ||
+ | |||
+ | In this case, we assume the number of total samples is 3000, the burn-in is 0, and the interval is 10. | ||
+ | |||
+ | | ||
+ | 3000 0 | ||
+ | Give n to store every n-th sample? (1 means store all samples) | ||
+ | 10 | ||
+ | |||
+ | Make sure the intermediate results are saved to files. | ||
+ | |||
+ | 100 rounds | ||
+ | G | ||
+ | 2758. | ||
+ | 1900. | ||
+ | 2019. | ||
+ | G | ||
+ | 225.5 -91.35 | ||
+ | | ||
+ | | ||
+ | R | ||
+ | 1755. | ||
+ | 868.7 | ||
+ | 817.0 | ||
+ | * Last seeds = 1877469549 | ||
+ | * Number of samples kept = 100 | ||
+ | solutions stored in binary file: " | ||
+ | solutions stored in file: " | ||
+ | |||
+ | Stop the program. In this case, program stops in the round 880. | ||
+ | |||
+ | | ||
+ | forrtl: error (69): process interrupted (SIGINT) | ||
+ | Image PC Routine | ||
+ | thrgibbs1f90 | ||
+ | thrgibbs1f90 | ||
+ | |||
+ | Make sure there are the following 5 files. | ||
+ | |||
+ | binary_final_solutions | ||
+ | |||
+ | Browse the file '' | ||
+ | |||
+ | Saved on 2017-03-10 10:53:22 | ||
+ | | ||
+ | State in the current run: | ||
+ | last round = 800 | ||
+ | sampled in this run | ||
+ | total number of samples = 3000 | ||
+ | number of burn-in | ||
+ | interval | ||
+ | | ||
+ | Suggestion for the input in next run: | ||
+ | total number of samples = 2200 | ||
+ | number of burn-in | ||
+ | interval | ||
+ | | ||
+ | When you restart the program, do not forget to put the following option | ||
+ | in your parameter file. | ||
+ | | ||
+ | |||
+ | Put the option '' | ||
+ | |||
+ | OPTION cont 1 | ||
+ | |||
+ | Run '' | ||
+ | |||
+ | '*** continuous sampling selected *** previous # samples = 1 | ||
+ | |||
+ | **NOTE: Although the message may say the previous number of sample is 1, you can ignore it. The program recognizes it is the cold start mode and works correctly.** | ||
+ | |||
+ | Input the three numbers that are shown in '' | ||
+ | |||
+ | | ||
+ | 2200 0 | ||
+ | Give n to store every n-th sample? (1 means store all samples) | ||
+ | 10 | ||
+ | |||
+ | The program will start from the round 801 as expected. | ||
+ | |||
+ | | ||
+ | G | ||
+ | | ||
+ | | ||
+ | | ||
+ | G | ||
+ | | ||
+ | | ||
+ | | ||
+ | R | ||
+ | | ||
+ | | ||
+ | | ||
+ | |||
+ | Just wait the analysis. You can interrupt the program again. The final results will be basically the same to ones from a non-stop analysis. | ||
+ | |||
+ |
readme.thrgibbs1.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1