[mamba-help] Problem with mamba output-no error msg

[Ulrich, A. <ann...@im...>]

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