Error generating phenotype: running phenoalg

[cro280]

Hi guys, I'm very excited about the work that you are doing and all the potential that comes with HAPNEST.

I'm going through your tutorial now, but I am running into an error in the step for generating phenotype.

I run the commands

1. singularity exec --bind data/:/data/ containers/intervene-synthetic-data_latest.sif generate_geno 1 data/config.yaml
2. singularity exec --bind data/:/data/ containers/intervene-synthetic-data_latest.sif generate_pheno data/config.yaml

The only difference I made to the files supplied in the tutorial was to the config.yaml file where I changed the chromosome to-be generated to 19 instead of 1.

However, when I try to run the generate phenotype command I get this error:

vagrant@vagrant:~$ singularity exec --bind data/:/data/ containers/intervene-synthetic-data_latest.sif generate_pheno data/config.yaml
[ Info: Creating output directories
Running pipelines:
optimisation => false
phenotype => true
evaluation => false
preprocessing => false
genotype => false
[ Info: Using 1 thread/s for computations
[ Info: Generating synthetic phenotype data
[ Info: Processing chromosome 19
[ Info: No superpopulation specified
ERROR: LoadError: failed process: Process(phenoalg data/outputs/test/test_chr.parfile 123, ProcessSignaled(11)) [0]

Stacktrace:
[1] pipeline_error
@ ./process.jl:525 [inlined]
[2] run(::Cmd; wait::Bool)
@ Base ./process.jl:440
[3] run
@ ./process.jl:438 [inlined]
[4] synthetic_pheno(filepaths::Filepaths, options::Dict{Any, Any}, genetics_prefix::String, out_prefix::String, seed::Int64, chromosome::Int64)
@ Main /opt/intervene/scripts/algorithms/phenotype/phenotype_algorithm.jl:54
[5] create_synthetic_phenotype(options::Dict{Any, Any})
@ Main /opt/intervene/scripts/algorithms/phenotype/phenotype_algorithm.jl:79
[6] macro expansion
@ /opt/intervene/scripts/run_program.jl:39 [inlined]
[7] macro expansion
@ ./timing.jl:287 [inlined]
[8] run_program(pipelines::Dict{String, Bool}, options::Dict{Any, Any})
@ Main /opt/intervene/scripts/run_program.jl:38
[9] main()
@ Main /opt/intervene/scripts/run_program.jl:113
[10] top-level scope
@ /opt/intervene/scripts/run_program.jl:117
in expression starting at /opt/intervene/scripts/run_program.jl:117

Any idea on what might be causing this and what I can try to do differently?

best,
Cato

[sophiewharrie]

Hi, apologies for the delay in responding to your question. The code appears to crash when it tries to run the phenoalg command - this is a standalone C program that can also be run outside of the main Julia pipeline (see here for documentation). I'm unable to replicate the error you describe but I would suggest trying out the following steps to help better understand the issue:

1. Check if the code generated the file data/outputs/test/test_chr.parfile before it crashed and check that the contents of the file matches the output below:

nPopulation 6
nTrait 1
a -0.4
b -1
c 0.5
nComponent 1
PropotionGeno 0.1,0.1,0.1,0.1,0.1,0.1
PropotionCovar 0,0,0,0,0,0
SampleList data/outputs/test/test_chr-19.sample
Polygenicity 0.005
Pleiotropy 1
TraitCorr 1
PopulationCorr 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
Prevalence 0.5,0.5,0.5,0.5,0.5,0.5
Reference data/inputs/processed/1KG+HGDP/Africa.Annot
GenoFile data/outputs/test/test_chr
Output data/outputs/test/test_chr
CompWeight 1,5,10

2. Start a shell inside of the container image:

singularity shell --bind data/:/data/,$PWD containers/intervene-synthetic-data_latest.sif

3. Run the command to generate phenotypes:

phenoalg data/outputs/test/test_chr.parfile 123

If this still doesn't work, hopefully you will at least get a more informative error message to understand what the problem may be