Fail at jsm.py train

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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 [email protected] on 7 Mar 2013 at 10:11