Description
all the .py files are present in the directory and are executable yet while running the command it says "no command found" please help me
user@user:~/Desktop/MToolBox-master/MToolBox$ ./MToolBox.sh -i test_rCRS_config.sh
setup.sh file not found. Setting MToolBox environment sourcing conf.sh file
setting up MToolBox variables in config file ...
...done
/home/user/Desktop/MToolBox-master/MToolBox/vcf will be used as vcf file name...
Check python version... (2.7 required)
OK.
Checking files to be used in MToolBox execution...
Checking mapExome parameters...
OK.
Checking assembleMTgenome parameters...
OK.
Checking mt-classifier parameters...
OK.
Input type is fastq.
output files will be placed in /home/user/Desktop/MToolBox-master/MToolBox/test_out/
EXECUTING READ MAPPING WITH MAPEXOME...
mapExome for sample PD11, files found: PD11.R1.fastq PD11.R2.fastq
./MToolBox.sh: line 250: mapExome.py: command not found
mapExome for sample PM11, files found: PM11.R1.fastq PM11.R2.fastq
./MToolBox.sh: line 250: mapExome.py: command not found
SAM files post-processing...
SORTING OUT.sam FILES WITH PICARDTOOLS...
ls: cannot access 'OUT_*': No such file or directory
Success.
ls: cannot access 'OUT_': No such file or directory
Skip Indel Realigner...
ls: cannot access 'OUT_': No such file or directory
ELIMINATING PCR DUPLICATES WITH PICARDTOOLS MARKDUPLICATES...
ls: cannot access 'OUT_': No such file or directory
ls: cannot access 'OUT_': No such file or directory
ls: cannot access 'OUT_*': No such file or directory
ASSEMBLING MT GENOMES WITH ASSEMBLEMTGENOME...
WARNING: values of tail < 5 are deprecated and will be replaced with 5
ls: cannot access 'OUT_*': No such file or directory
GENERATING VCF OUTPUT...
Traceback (most recent call last):
File "/home/user/Desktop/MToolBox-master/MToolBox/VCFoutput.py", line 4, in
from mtVariantCaller import VCFoutput
File "/home/user/Desktop/MToolBox-master/MToolBox/mtVariantCaller.py", line 13, in
import vcf
File "/home/user/Desktop/MToolBox-master/MToolBox/vcf/init.py", line 175, in
from vcf.parser import Reader, Writer
File "/home/user/Desktop/MToolBox-master/MToolBox/vcf/parser.py", line 4, in
import gzip
File "/usr/local/lib/python2.7/gzip.py", line 9, in
import zlib
ImportError: No module named zlib
PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
Haplogroup predictions based on RSRS Phylotree build 17
./MToolBox.sh: line 479: mt-classifier.py: command not found
./MToolBox.sh: line 483: variants_functional_annotation.py: command not found
./MToolBox.sh: line 484: variants_functional_annotation.py: command not found
No annotation.csv found. Exit
user@user:~/Desktop/MToolBox-master/MToolBox$
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