Joint snv mix train error

[GoogleCodeExporter]

What steps will reproduce the problem?
1. after installation, when running 
"/BiO2/EwhaColonLung/Python-2.7.2/bin/jsm.py train joint_snv_mix_two", error as 
follow:
Traceback (most recent call last):
  File "/BiO2/EwhaColonLung/Python-2.7.2/bin/jsm.py", line 224, in <module>
    args.func(args)
  File "/BiO2/EwhaColonLung/Python-2.7.2/lib/python2.7/site-packages/joint_snv_mix/runners/train.py", line 61, in joint_snv_mix_two_train
    train(model, sample, args)
  File "/BiO2/EwhaColonLung/Python-2.7.2/lib/python2.7/site-packages/joint_snv_mix/runners/train.py", line 110, in train
    model.fit(sample, args.convergence_threshold, args.max_iters)
  File "joint_snv_mix.pyx", line 388, in joint_snv_mix.trainers.joint_snv_mix.JointSnvMixModel.fit (joint_snv_mix/trainers/joint_snv_mix.c:7567)
  File "joint_snv_mix.pyx", line 450, in joint_snv_mix.trainers.joint_snv_mix.JointSnvMixModelTrainer.train (joint_snv_mix/trainers/joint_snv_mix.c:8106)
  File "joint_snv_mix.pyx", line 486, in joint_snv_mix.trainers.joint_snv_mix.JointSnvMixModelTrainer._check_convergence (joint_snv_mix/trainers/joint_snv_mix.c:8413)
Exception: Lower bound decreased exiting.

What is the expected output? What do you see instead?
 prameter.txt

What version of the product are you using? On what operating system?

JointSNVMix-0.7.4 python 2.7

operating system 
Linux gteam.kobic.re.kr 2.6.18-194.11.3.el5 #1 SMP Mon Aug 30 16:19:16 EDT 2010 
x86_64 x86_64 x86_64 GNU/Linux
Please provide any additional information below.

Original issue reported on code.google.com by psj...@gmail.com on 10 Jan 2012 at 4:05

[GoogleCodeExporter]

Could you post the output of the program up to that point? This behaviour maybe 
due to a real bug or numerical precision problems. 

The program is currently set to throw an error if the lower bound decreases. I 
could alter that so that a warning is printed instead, but I need to confirm it 
is just a precision problem.

Andrew

Original comment by AndrewJL...@gmail.com on 11 Jan 2012 at 1:18

• Changed state: Accepted

[GoogleCodeExporter]

I tested 9 samples using joint-snv-mix-two train model for making parameter 
files. 
8 samples worked well.. One of them does not work. 
I attach the output file of train error message. 

seongjin

Original comment by psj...@gmail.com on 11 Jan 2012 at 5:54

Attachments:

• trainError

[GoogleCodeExporter]

The output looks normal. Do you know what the average and max depth of coverage 
are for that sample? One problem may be sites with extremely high depth.

If you need to process the files urgently before I get this fixed, you can use 
the parameters from the end of that file to run the classify command.

Alternatively, if any of the cases you have analysed are a similar type of 
cancer, you could also use the parameter file from them. The parameters from 
other cases will probably be similar, as long as the same platform was used for 
sequencing.

Original comment by AndrewJL...@gmail.com on 12 Jan 2012 at 2:40

[GoogleCodeExporter]

I get the same error. Is there a fix available yet?

Using SNVmix 0.7.5 on Mac OS 10.7 (Lion)

Only have limited output before the error (attached)

I can try to get coverage stats if wanted.

Original comment by dgoode.s...@gmail.com on 30 Mar 2012 at 5:30

Attachments:

• jsm_train_error.txt

[GoogleCodeExporter]

Sorry about the inactivity on this issue. I have recently had a simple idea on 
how to fix this though. 

It may be possible to avoid the issue by setting the --convergence_threshold 
flag when training to a value above the default of 0.000001 to something like 
0.01. This will hopefully cause the EM algorithm to stop before the numerical 
issues kick in and the lower bound decreases.

In principle the estimates of the parameters will be a little worse, but I 
think the difference in classification performance would be negligible.

Original comment by AndrewJL...@gmail.com on 13 Jun 2012 at 8:08

[GoogleCodeExporter]

The same issue. 
I providing two logs: error and output. 

Original comment by mik...@gmail.com on 3 Jul 2012 at 1:03

Attachments:

• file_11777.txt.err
• file_11777.txt.out