Fail at jsm.py train

[GoogleCodeExporter]

What steps will reproduce the problem?
1.jsm.py train joint_snv_mix_two mm10_mouse_ref.fa 129tumor.bam 129normal.bam 
2.
3.

What is the expected output? What do you see instead?

[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Traceback (most recent call last):
  File "/users/jwu/bin/jsm.py", line 128, in <module>
    args.func(args)
  File "run.pyx", line 105, in joint_snv_mix.run.train (joint_snv_mix/run.c:2452)
  File "run.pyx", line 177, in joint_snv_mix.run.ModelFactory.get_counter (joint_snv_mix/run.c:3293)
  File "bam.pyx", line 19, in joint_snv_mix.samtools.bam.BamFile.__cinit__ (joint_snv_mix/samtools/bam.c:804)
  File "bam.pyx", line 42, in joint_snv_mix.samtools.bam.BamFile._open_file (joint_snv_mix/samtools/bam.c:1065)
Exception: File 
/aveo/data/reference/dna/mouse/mm10/prepared_by_bwa/mm10_mouse_ref.fa does not 
have valid header - is it SAM/BAM format?



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

JointSNVMix 0.8b2 on Ubuntu

Please provide any additional information below.

Original issue reported on code.google.com by zhenhuaw...@gmail.com on 7 Mar 2013 at 10:11