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I'm using Python 2.7 to run the MToolBox but I have an issue in assembling mtDNA with ASSEMBLEMGENOME.
Although it seems that pandas is not installed in the python version used by the script when I checked pandas I saw the versions installed in python environment.
Could this problem related to 'mtVariantCaller.py' or other script called 'assembleMTgenome.py'?
I'm sharing my run screen and errors I had below.
If you could help me this issue?
Thanks a lot!
Bengisu
##### ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...
WARNING: values of tail < 5 are deprecated and will be replaced with 5
Traceback (most recent call last):
File "/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/assembleMTgenome.py", line 10, in <module>
from mtVariantCaller import mtvcf_main_analysis, get_consensus_single
File "/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/mtVariantCaller.py", line 15, in <module>
import pandas as pd
ImportError: No module named pandas
Traceback (most recent call last):
File "/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/assembleMTgenome.py", line 10, in <module>
from mtVariantCaller import mtvcf_main_analysis, get_consensus_single
File "/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/mtVariantCaller.py", line 15, in <module>
import pandas as pd
ImportError: No module named pandas
##### GENERATING VCF OUTPUT...
Traceback (most recent call last):
File "/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/VCFoutput.py", line 4, in <module>
from mtVariantCaller import VCFoutput
File "/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/mtVariantCaller.py", line 15, in <module>
import pandas as pd
ImportError: No module named pandas
##### PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
/home/bengisu/Documents/MToolBox-1.2.1/MToolBox/MToolBox.sh: line 472: cd: T1: No such file or directory
Haplogroup predictions based on RSRS Phylotree build 17
Your best results file is mt_classification_best_results.csv
Loading contig sequences from file BRAIN_3_S25_R1_001-contigs.fasta
Unable to compute haplogroup. ExitYour best results file is mt_classification_best_results.csv
Loading contig sequences from file BRAIN_3_S25_R2_001-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
The text was updated successfully, but these errors were encountered:
Hello,
I'm using Python 2.7 to run the MToolBox but I have an issue in assembling mtDNA with ASSEMBLEMGENOME.
Although it seems that pandas is not installed in the python version used by the script when I checked pandas I saw the versions installed in python environment.
Could this problem related to 'mtVariantCaller.py' or other script called 'assembleMTgenome.py'?
I'm sharing my run screen and errors I had below.
If you could help me this issue?
Thanks a lot!
Bengisu
The text was updated successfully, but these errors were encountered: