Exception: Invalid reference passed.

[Henning Stehr]

Dear developers,

I am currently testing JointSNVMix (which looks very promising) on a pair of whole genome bam files. After about a day of calculation, it stopped with the output below. I am on a 64bit Linux machine with Python 2.6.6.

I have not yet tried to reproduce the error.

Thanks
Henning

Here is my command line:
python jsm.py classify joint_snv_mix_two --positions_file mypositions.pos hg19.fa control.bam tumor.bam joint_params.cfg out.jsnvmix2

Output:
chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr4_
Traceback (most recent call last):
  File "/project/genex/programs/bin/jsm.py", line 223, in <module>
    args.func(args)
  File "/project/genex/programs/lib/python/joint_snv_mix/runners/classify.py", line 72, in joint_snv_mix_two_classify
    classify(counter, classifier, args)
  File "/project/genex/programs/lib/python/joint_snv_mix/runners/classify.py", line 108, in classify
    classify_counter(counter, classifier, args.out_file_name)
  File "classifier.pyx", line 20, in joint_snv_mix.classifiers.classifier.classify_counter (joint_snv_mix/classifiers/classifier.c:927)
  File "positions_counter.pyx", line 28, in joint_snv_mix.counters.positions_counter.PositionsCounter.iter_ref (joint_snv_mix/counters/positions_counter.c:1435)
  File "joint_binary_quality_counter.pyx", line 23, in joint_snv_mix.counters.joint_binary_quality_counter.JointBinaryQualityCounter.iter_ref (joint_snv_mix/counters/joint_binary_quality_counter.c:1505)
Exception: Invalid reference passed.