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Simulate genomic data on demand
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Decide how to handle mininum and maximum number of cases needed by GTCA #49

Open mmeier93 opened 3 years ago

mmeier93 commented 3 years ago

Based on various tests run with different values of --gwas_cases, it seems GTCA requires for you to have a minimum of 10 cases.

Indeed:

# Run GCTA
  gcta64     --bfile chr12-simulated_hapgen-updated     --simu-cc 8 32     --simu-causal-loci chr12-causal.snplist     --out chr12-gwas-statistics

Command exit status:
  1

Command output:
  *******************************************************************
  * Genome-wide Complex Trait Analysis (GCTA)
  * version 1.93.2 beta Linux
  * (C) 2010-present, Jian Yang, The University of Queensland
  * Please report bugs to Jian Yang <jian.yang.qt@gmail.com>
  *******************************************************************
  Analysis started at 09:30:43 UTC on Fri Jan 08 2021.
  Hostname: ffe8248f84de

  Accepted options:
  --bfile chr12-simulated_hapgen-updated
  --simu-cc 8 32
  Error: --simu-cc, Invalid number of cases. Minimun number 10.
  An error occurs, please check the options or data

Command wrapper:
  *******************************************************************
  * Genome-wide Complex Trait Analysis (GCTA)
  * version 1.93.2 beta Linux
  * (C) 2010-present, Jian Yang, The University of Queensland
  * Please report bugs to Jian Yang <jian.yang.qt@gmail.com>
  *******************************************************************
  Analysis started at 09:30:43 UTC on Fri Jan 08 2021.
  Hostname: ffe8248f84de

  Accepted options:
  --bfile chr12-simulated_hapgen-updated
  --simu-cc 8 32
  Error: --simu-cc, Invalid number of cases. Minimun number 10.
  An error occurs, please check the options or data

The same kind of error applies when the number of controls falls under 10:

# Run GCTA
  gcta64     --bfile chr13-simulated_hapgen-updated     --simu-cc 40 0     --simu-causal-loci chr13-causal.snplist     --out chr13-gwas-statistics

Command exit status:
  1

Command output:
  *******************************************************************
  * Genome-wide Complex Trait Analysis (GCTA)
  * version 1.93.2 beta Linux
  * (C) 2010-present, Jian Yang, The University of Queensland
  * Please report bugs to Jian Yang <jian.yang.qt@gmail.com>
  *******************************************************************
  Analysis started at 09:35:17 UTC on Fri Jan 08 2021.
  Hostname: 7231c35b47a0

  Accepted options:
  --bfile chr13-simulated_hapgen-updated
  --simu-cc 40 0
  Error: --simu-cc, Invalid number of controls. Minimum number 10.
  An error occurs, please check the options or data

Command wrapper:
  *******************************************************************
  * Genome-wide Complex Trait Analysis (GCTA)
  * version 1.93.2 beta Linux
  * (C) 2010-present, Jian Yang, The University of Queensland
  * Please report bugs to Jian Yang <jian.yang.qt@gmail.com>
  *******************************************************************
  Analysis started at 09:35:17 UTC on Fri Jan 08 2021.
  Hostname: 7231c35b47a0

  Accepted options:
  --bfile chr13-simulated_hapgen-updated
  --simu-cc 40 0
  Error: --simu-cc, Invalid number of controls. Minimum number 10.
  An error occurs, please check the options or data

Objective: decide if an extra check to prevent this scenario is needed. If so, could implement some Groovy logic following the calculation of num_cases and num_controls.