gfedonin / epistat Goto Github PK

Hi @gFedonin,

During the installation of the software, it was found that the following data was missing

WARNING: the following files are missing in your kit:
examples/intergene/mtb_gwas/Amikacin/Amikacin.epistat.prm
examples/intergene/mtb_gwas/Amikacin/Amikacin.lower.pvalue.fdr.prm
examples/intergene/mtb_gwas/Amikacin/Amikacin.upper.pvalue.fdr.prm
examples/intergene/mtb_gwas/Amikacin/Amikacin.xparr
examples/intragene/alleles/mtb/phen/9drugs.all.mk_coevolmtx.prm
examples/intragene/alleles/mtb/phen/9drugs.lower.pvalue.unord_pairs.sites2.fdr.prm
examples/intragene/alleles/mtb/phen/9drugs.mk_coevolmtx.prm
examples/intragene/alleles/mtb/phen/9drugs.pairs2.upper.FDR5.mk_summary.cfg
examples/intragene/alleles/mtb/phen/9drugs.sites2.lower.FDR5.mk_summary.cfg
examples/intragene/alleles/mtb/phen/9drugs.upper.pvalue.unord_pairs.pairs2.fdr.prm
examples/intragene/alleles/mtb/phen/9drugs.xparr
examples/intragene/alleles/mtb/phen/epistat.phen.prm
examples/intragene/alleles/mtb/phen/estimate_fdr.txt
examples/intragene/alleles/mtb/phen/min_RR_SR.site2pheno
examples/intragene/alleles/mtb/phen/run_epistat.prm
Please inform the author.

Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'Epistat' version 'v0.10.1'

Can you provide the above data again！
Thank you for your help!

Hi @gFedonin,

I am trying to run the EpiStat pipeline on my own data. After generating the permuted samples, .xpar files, and calculating the statistics for each sample, the pipeline gets to the stage of creating the null model and fails with the following error:

Building zero model distribution and calculating statistics!
EpistatNullModel::init_(): Start reading data files:
First pass:
....................  ETA:   0:00Out of memory!

EpistatNullModel DESTROYED

I tried varying the number of permutations (with -p) between 10,000 and 100, but all fail.

Is there some way around this? Am I doing something wrong, or do I just need to run the pipeline on a very high RAM machine? (I am trialling it on my desktop, which only has 32GB of RAM).

Thank you for your help!