search

mitoNGS / MToolBox

A bioinformatics pipeline to analyze mtDNA from NGS data
http://sourceforge.net/projects/mtoolbox/?source=navbar
GNU General Public License v3.0
86 stars 37 forks source link

"No module named pandas" although pandas installed #111

Open bengisukb opened 9 months ago

bengisukb commented 9 months ago

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

##### 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