When running MToolBox on the example dataset (sim_data) provided, i met with the following error:
**
I##### 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
Set max per-file depth to 8000
##### GENERATING VCF OUTPUT...
Reference sequence used for VCF: RCRS
##### PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
Haplogroup predictions based on RSRS Phylotree build 17
Your best results file is mt_classification_best_results.csv
Loading contig sequences from file simulation100X-contigs.fasta
Loaded 1 contig sequences
Aligning Contigs to mtDNA reference genome...
Sequence haplogroup assignment
Classification according to tree: /home/iti.gupta/archive/MToolBox/MToolBox/data/phylotree_r17.pickle
genome_state is incomplete
OrderedDict()
====================
------------------------------
Contig alignment to MHCS and rCRS
Unable to compute haplogroup. ExitParsing pathogenicity table...
Parsing variability data...
Parsing info about haplogroup-defining sites...
Parsing info about haplogroup assignments...
No annotation.csv found. Exit
**
clody23
commented
5 years ago
When running MToolBox on the example dataset (sim_data) provided, i met with the following error: **
I##### 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