Error in running MToolBox

Question

[adarsh]

Hi,

I have tried running different versions of the tool MToolBox. But I am continuously getting following error at the vcf generation:

#### GENERATING VCF OUTPUT...
Reference sequence used for VCF: RCRS
Traceback (most recent call last):
  File "/data/ngs/programs/MToolBox/MToolBox-1.2.1/MToolBox/VCFoutput.py", line 38, in <module>
    VCFoutput(VCF_dict, reference=reference_sequence, name=sample_vcf_name)
  File "/data/ngs/programs/MToolBox/MToolBox-1.2.1/MToolBox/mtVariantCaller.py", line 868, in VCFoutput
    i._sample_indexes[sample][0].append(aplotype)
AttributeError: 'int' object has no attribute 'append'

When I tried running a single sample, it generated vcf. It even worked for two samples together and generated vcf. But when I gave more than two samples, it is not generating multisample vcf. However, the tool finished its running and generated all other files including the final annotation files. I am unable to solve this error as, because it was written in Python2.7 and I am not very sure why this is happening. I have tried running v1.2.1, v1.1 and v1.0. The same error was reported by other people in the GitHub page. But there is no response from the team.

Has anyone came across this issue and found out any solution? Please help.

I have around 70 samples to be processed and the requirement is to use this specific tool

Thanks

[GenoMax]

it was written in Python2.7 and I am not very sure why this is happening

Are you make sure the python available for this job is v.2.7 or above (especially if you are using a job scheduler and/or modules etc)? At this point default python is likely set to v.3.x on current OS.

[adarsh]

Yes, I have created a separate conda environment for this tool with python2.7. All the python scripts from the tool are running, except for the one wich is merging the vcf.