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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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Error in gzfile(file, "wb") : cannot open the connection #356

Closed SYSUMSD closed 3 years ago

SYSUMSD commented 3 years ago

I am using this package to analysis heritability of diseases by GLMM. My dataset compose of 23,000 individuals and 1.5 million markers. I have run the example data correctly. This is the code used:

Rscript step1_fitNULLGLMM.R --plinkFile=/home/msd/SAIGE-master/extdata/input/nfam_100_nindep_0_step1_includeMoreRareVariants_poly --phenoFile=/home/msd/SAIGE-master/extdata/input/pheno_1000samples.txt_withdosages_withBothTraitTypes.txt --phenoCol=y_binary --covarColList=x1,x2 --sampleIDColinphenoFile=IID --traitType=binary --outputPrefix=/home/msd/SAIGE-TEST/example_binary --nThreads=4 --LOCO=FALSE

But when I used this code to analysis my dataset:

Rscript step1_fitNULLGLMM.R --plinkFile=/home/msd/ShortcutTo96/biobank/biobank_sample_genetics/filter_genome_indi_1/whole_chromosome_1_ld_pruned --phenoFile=/home/msd/ShortcutTo96/biobank/biobank_sample_genetics/filter_genome_indi_1/GLMM/phen_diabete_1.txt --phenoCol=diabete_status --covarColList=age,gender --sampleIDColinphenoFile=IID --traitType=binary --outputPrefix==/home/msd/SAIGE-TEST/example_diabete --nThreads=80 --LOCO=FALSE

I got a error:

Error in gzfile(file, "wb") : cannot open the connection
Calls: fitNULLGLMM -> save -> gzfile
In addition: Warning messages:
1: In file.create(varRatioFile, showWarnings = TRUE) :
  cannot create file '=/home/msd/SAIGE-TEST/example_diabete.varianceRatio.txt', reason 'No such file or directory'
2: In file.create(modelOut, showWarnings = TRUE) :
  cannot create file '=/home/msd/SAIGE-TEST/example_diabete.rda', reason 'No such file or directory'
3: In gzfile(file, "wb") :
  cannot open compressed file '=/home/msd/SAIGE-TEST/example_diabete.rda', probable reason 'No such file or directory'
Execution halted

It looks like I cannot write the result to disk. But I can write the example result to this dir:"/home/msd/SAIGE-TEST/"

What's wrong with my code? Is the project too big to run correctly? It looks like don't too bigger than the saige-gene paper's UKbiobank analysis.

SYSUMSD commented 3 years ago

Ok...I have made a syntax mistake....