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Roth-Lab / JointSNVMix

Automatically exported from code.google.com/p/joint-snv-mix
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joint_snv_mix crashed during training #9

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Simply ran:

jsm.py train snv_mix_two human_g1k_v37.fasta 04_Cleaned.bam 05_Cleaned.bam 
JointSNVMix-0.7.5/config/joint_priors.cfg  
JointSNVMix-0.7.5/config/joint_params.cfg output.param

Traceback (after several hours):

Sub-sampled 0 positions from ref GL000248.1
Total sub-sample size is 860974
Traceback (most recent call last):
  File "/usr/local/bin/jsm.py", line 224, in <module>
    args.func(args)
  File "/usr/local/lib/python2.7/dist-packages/joint_snv_mix/runners/train.py", line 34, in snv_mix_two_train
    params = get_indep_params(args)
  File "/usr/local/lib/python2.7/dist-packages/joint_snv_mix/runners/train.py", line 93, in get_indep_params
    priors.read_from_file(args.priors_file_name)
  File "snv_mix.pyx", line 257, in joint_snv_mix.trainers.snv_mix.PairedSnvMixPriors.read_from_file (joint_snv_mix/trainers/snv_mix.c:4840)
  File "/usr/lib/python2.7/ConfigParser.py", line 599, in get
    raise NoSectionError(section)
ConfigParser.NoSectionError: No section: 'pi_N'

Original issue reported on code.google.com by dan.s...@gmail.com on 1 Feb 2012 at 5:03

GoogleCodeExporter commented 9 years ago 
Hi,
I think you are running the wrong command. If you want JointSNVMix run

jsm.py train joint_snv_mix_two human_g1k_v37.fasta 04_Cleaned.bam 
05_Cleaned.bam JointSNVMix-0.7.5/config/joint_priors.cfg  
JointSNVMix-0.7.5/config/joint_params.cfg output.param

Notice joint_snv_mix_two inplace of snv_mix_two. 

The latter command runs the independent SNVMix model on each sample and joins 
the results post-hoc, it also requires different a config file "indep.cfg".

Please let me know if that fixes the problem and I can close this.

Cheers,
Andy

Original comment by AndrewJL...@gmail.com on 1 Feb 2012 at 5:22

GoogleCodeExporter commented 9 years ago 
D'oh, thanks Andy.  PEBKAC indeed.

Original comment by dan.s...@gmail.com on 2 Feb 2012 at 8:52

GoogleCodeExporter commented 9 years ago

Original comment by AndrewJL...@gmail.com on 2 Feb 2012 at 3:54