[mamba-help] Problem with mamba output-no error msg
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From: Ulrich, A. <ann...@im...> - 2017-02-06 17:36:39
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Dear Manuel, I have been trying to analyse a small set of rare variants in a cohort of Parkinson`s disease patients but my output files contain only the header and I get no error message just a log file which I cannot make sense of. My plinkseq project contains plink binary files, no VCFs. I will copy my script here: module load mamba/1.0.0 mamba --project PD_proj --locdb /project/silk/users/au615/PD_all/hg19/locdb --seqdb /project/silk/users/au615/PD_all/hg19/seqdb.hg19 --mask all.group reg=chr12:123262000..123300000 --phenotype PD --perm 1 --a 1.5 --t .7 --module SEMGEM --fileout /project/silk/users/au615/PD_all/testSEMGEM And the content of the logfile: 2017-02-06 17:18:11,101 - INFO - Argument N: None 2017-02-06 17:18:11,101 - INFO - Argument Q: False 2017-02-06 17:18:11,101 - INFO - Argument R: False 2017-02-06 17:18:11,101 - INFO - Argument Sigma: None 2017-02-06 17:18:11,101 - INFO - Argument T: False 2017-02-06 17:18:11,101 - INFO - Argument Vp: None 2017-02-06 17:18:11,102 - INFO - Argument a: '1.5' 2017-02-06 17:18:11,102 - INFO - Argument amv: False 2017-02-06 17:18:11,102 - INFO - Argument burn: 1000 2017-02-06 17:18:11,102 - INFO - Argument case: 2 2017-02-06 17:18:11,102 - INFO - Argument covariates: '' 2017-02-06 17:18:11,102 - INFO - Argument delta: None 2017-02-06 17:18:11,102 - INFO - Argument fileout: '/project/silk/users/au615/PD_all/testSEMGEM' 2017-02-06 17:18:11,102 - INFO - Argument filterfile: 'NA' 2017-02-06 17:18:11,102 - INFO - Argument gene: None 2017-02-06 17:18:11,102 - INFO - Argument grep: False 2017-02-06 17:18:11,102 - INFO - Argument gtexdb: None 2017-02-06 17:18:11,103 - INFO - Argument gtexrpkm: 'None' 2017-02-06 17:18:11,103 - INFO - Argument gwas: False 2017-02-06 17:18:11,103 - INFO - Argument gwasin: 'MAMBA.gwas' 2017-02-06 17:18:11,103 - INFO - Argument indep: False 2017-02-06 17:18:11,103 - INFO - Argument locdb: '/project/silk/users/au615/PD_all/hg19/locdb' 2017-02-06 17:18:11,103 - INFO - Argument loci: 1 2017-02-06 17:18:11,103 - INFO - Argument locset: 'refseq' 2017-02-06 17:18:11,103 - INFO - Argument mafiles: None 2017-02-06 17:18:11,103 - INFO - Argument mask: 'all.group' 2017-02-06 17:18:11,103 - INFO - Argument minrpkm: -10000 2017-02-06 17:18:11,103 - INFO - Argument module: 'SEMGEM' 2017-02-06 17:18:11,103 - INFO - Argument monogenic: False 2017-02-06 17:18:11,104 - INFO - Argument monogenicin: 'MAMBA.monogenic' 2017-02-06 17:18:11,104 - INFO - Argument ncpu: 1 2017-02-06 17:18:11,104 - INFO - Argument niter: 4000 2017-02-06 17:18:11,104 - INFO - Argument nt: 0 2017-02-06 17:18:11,104 - INFO - Argument nvars: None 2017-02-06 17:18:11,104 - INFO - Argument outputdir: '.' 2017-02-06 17:18:11,104 - INFO - Argument perms: '1' 2017-02-06 17:18:11,104 - INFO - Argument phenfile: None 2017-02-06 17:18:11,104 - INFO - Argument phenotype: 'PD' 2017-02-06 17:18:11,104 - INFO - Argument pipeline: ['SEMGEM'] 2017-02-06 17:18:11,104 - INFO - Argument plot: False 2017-02-06 17:18:11,105 - INFO - Argument project: 'PD_proj' 2017-02-06 17:18:11,105 - INFO - Argument protdb: None 2017-02-06 17:18:11,105 - INFO - Argument pvalthr: 0.001 2017-02-06 17:18:11,105 - INFO - Argument refdb: None 2017-02-06 17:18:11,105 - INFO - Argument rpkmplots: False 2017-02-06 17:18:11,105 - INFO - Argument rr: 4 2017-02-06 17:18:11,105 - INFO - Argument sample: False 2017-02-06 17:18:11,105 - INFO - Argument seed: False 2017-02-06 17:18:11,105 - INFO - Argument seqdb: '/project/silk/users/au615/PD_all/hg19/seqdb.hg19' 2017-02-06 17:18:11,105 - INFO - Argument strata: False 2017-02-06 17:18:11,105 - INFO - Argument t: '.7' 2017-02-06 17:18:11,105 - INFO - Argument tissue: False 2017-02-06 17:18:11,106 - INFO - Argument two_sided: False 2017-02-06 17:18:11,106 - INFO - Argument vcfs: None 2017-02-06 17:18:11,106 - INFO - Argument verbosity: 'INFO' 2017-02-06 17:18:11,106 - INFO - Argument version: False 2017-02-06 17:18:11,106 - INFO - Running module SEMGEM I hope you can spot the problem easily, I will keep on trying in the meantime, thank you very much for your help. Kind regards, Anna |