Need help with error: no VCF_dict_tmp

[dodoflyy]

Hi, I used install.sh to installed this sofeware, how ever when I test it by using test file of this software, it seems missing file/dir VCF-dict_tmp. I think there may be some installed problem that I don't know. Here is the error info:

GENERATING VCF OUTPUT...

Traceback (most recent call last): File "/ifs1/Reotech/user/pengguoyu/software/MToolBox-master/MToolBox/VCFoutput.py", line 36, in VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read()) IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp'

Loading contig sequences from file simulation100X-contigs.fasta Unable to compute haplogroup. ExitHeteroplasmy data file ('VCF_dict_tmp') not found. HF will not be reported in the output. Parsing pathogenicity table... Parsing variability data... Parsing info about haplogroup-defining sites... Parsing info about haplogroup assignments... No annotation.csv found. Exit

[sean-boothby]

Hey Matthew, been working on the same problem.

I think the issue has to do with the MToolBox.sh file calling for a file in the directory /bin/samtools-1.3 Seems like it the bash script calls for samtoolsexe which does not exist and from that point there are many issues that occur.

If you have solved this I would really appreciate your help. I will also keep anything I find out updated here.

[loganylchen]

I have the same question, but I found a few steps former for that

Traceback (most recent call last):
  File "/wes/chenyl/projects/MToolBox/MToolBox/assembleMTgenome.py", line 443, in <module>
    mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail)
  File "/wes/chenyl/projects/MToolBox/MToolBox/mtVariantCaller.py", line 856, in mtvcf_main_analysis
    qs1.append(median(qs2))
  File "/wes/chenyl/projects/MToolBox/MToolBox/mtVariantCaller.py", line 402, in median
    m1 = sorted(l)[(len(l)/2)+1-1]
IndexError: list index out of range