Hi,

Dear Community,

I am unable to generate the the VCF file from MToolBox. However, except this I able to generate all the output files, including VCF_dict_tmp.

When I run the command:

MToolBox.sh -i ~/software/MToolBox-master/test_config.sh

I got this error:

..................

##### ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...

WARNING: values of tail < 5 are deprecated and will be replaced with 5

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

##### GENERATING VCF OUTPUT...
Reference sequence used for VCF: RCRS
Traceback (most recent call last):
File "/home/wuk/software/MToolBox-master/MToolBox/VCFoutput.py", line 32, in <module>
VCFoutput(VCF_dict, reference=reference_sequence)
File "/home/wuk/software/MToolBox-master/MToolBox/mtVariantCaller.py", line 1198, in VCFoutput
i._sample_indexes[sample][0].append(aplotype)
AttributeError: 'int' object has no attribute 'append'

...........................

The rest of the analysis runs well. Also see this:

command:

python /home/wuk/software/MToolBox-master/MToolBox/VCFoutput.py -r RSRS VCF_dict_tmp

Error:

Reference sequence used for VCF: RSRS
Traceback (most recent call last):
File "/home/wuk/software/MToolBox-master/MToolBox/VCFoutput.py", line 32, in <module>
VCFoutput(VCF_dict, reference=reference_sequence)
File "/home/wuk/software/MToolBox-master/MToolBox/mtVariantCaller.py", line 1198, in VCFoutput
i._sample_indexes[sample][0].append(aplotype)
AttributeError: 'int' object has no attribute 'append'

The environment is already set. Kindly guide me where I am doing wrong.

Regards,

Waqas.