Hello, I've been trying to run fastGWA (GCTA) with Snakemake. I'm keeping getting the same error, for the same commands that work when I submit them with slurm without Snakemake, as a shell script.
Here is my command:
rule all:
input:
'results/fastGWA_Chr1'
rule fastgwa:
input:
bfile='Chr1.bed',
pheno='phenotypes',
grmid='grm_sparse.grm.id',
grmsp='grm_sparse.grm.sp'
output:
out='results/fastGWA_Chr1'
log: 'logs/fastgwa/fastGWA_Chr1.log'
benchmark: 'logs/fastgwa/fastGWA_Chr1.bench'
threads: 10
resources:
partition = "medium",
mem_gb=50,
time=60,
temp='${TMP_LOCAL}'
params:
bfile="Chr1",
grm="grm_sparse"
shell:
"""
(
/gcta64 \
--bfile {params.bfile} \
--grm-sparse {params.grm} \
--fastGWA-mlm \
--pheno {input.pheno} \
--maf 0.01 \
--thread-num {threads} \
--out {output.out}
)
"""
The error I keep getting is:
[Thu Sep 12 11:22:03 2024] rule fastgwa:
input: Chr1.bed, Chr1.bim, Chr1.fam, phenotypes, grm_sparse.grm.id, grm_sparse.grm.sp
output: results/fastGWA_Chr1
log: logs/fastgwa/fastGWA_Chr1.log
jobid: 1
benchmark: logs/fastgwa/fastGWA_Chr1.bench
reason: Missing output files: results/fastGWA_Chr1
threads: 10
resources: mem_mb=86066, mem_mib=82079, disk_mb=86066, disk_mib=82079, tmpdir=<TBD>, partition=medium, mem_gb=50, time=60, temp=${TMP_LOCAL}
When I look into log file from GCTA I get:
Error: missing the --out option
An error occurs, please check the options or data
2 answers
The error I'm keep getting is:
[Thu Sep 12 11:22:03 2024] rule fastgwa: input: Chr1.bed, Chr1.bim, Chr1.fam, phenotypes, grm_sparse.grm.id, grm_sparse.grm.sp output: results/fastGWA_Chr1 log: logs/fastgwa/fastGWA_Chr1.log jobid: 1 benchmark: logs/fastgwa/fastGWA_Chr1.bench reason: Missing output files: results/fastGWA_Chr1 threads: 10 resources: mem_mb=86066, mem_mib=82079, disk_mb=86066, disk_mib=82079, tmpdir=<TBD>, partition=medium, mem_gb=50, time=60, temp=${TMP_LOCAL}
This is not an error, it is snakemake informing you why rule fastgwa needs to be executed (see reason: Missing output files...)
Error: missing the --out option An error occurs, please check the options or data
This appears to be the actual error. Your shell directive looks a bit odd to me and in general also the formatting of your snakefile, at leats as posted here. Try with this:
shell:
r"""
gcta64 --bfile {params.bfile} --grm-sparse {params.grm} --fastGWA-mlm --pheno {input.pheno} --maf 0.01 --thread-num {threads} --out {output.out}
"""
You may have a space after a newline break \ and this trips bash. In fact I see a trailing space in line --pheno {input.pheno} \
Also, I'm not sure why/if you need to wrap in round brackets and use /gcta64 instead of gcta64 (without /).
For any vim users reading this, add this to your .vimrc:
highlight default ExtraWhitespace ctermbg=darkgreen guibg=#216000
match ExtraWhitespace '\s\+$'
No more invisible whitespace on the end of lines! No more of these nasty bugs!
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