I have a maybe naive question. I am trying to use your tool, but I am getting the following error:
"
setting up MToolBox environment variables...
...done
setting up MToolBox variables in config file ...
...done
sample 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 sam.
output files will be placed in test_out
cat: test.lst: No such file or directory
EXECUTING READ MAPPING WITH MAPEXOME...
cat: test.lst: No such file or directory
Compression of fastq files from bam/sam input files...
Done.
/home/sp2037/apps/NGS/MToolBox/MToolBox/MToolBox.sh: line 337: cd: test_out: No such file or directory
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
Skipping Mark Duplicates...
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/sp2037/apps/NGS/MToolBox/MToolBox/VCFoutput.py", line 36, in
VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read())
IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp'
PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
/home/sp2037/apps/NGS/MToolBox/MToolBox/MToolBox.sh: line 472: cd: testout: No such file or directory
Haplogroup predictions based on RSRS Phylotree build 17
ls: cannot access OUT*: No such file or directory
Heteroplasmy 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
"
I am not sure if I need to generate a list beforehand with the names of my samples?
Hello,
Hope you are well.
I have a maybe naive question. I am trying to use your tool, but I am getting the following error:
" setting up MToolBox environment variables... ...done
setting up MToolBox variables in config file ... ...done
sample 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 sam. output files will be placed in test_out
cat: test.lst: No such file or directory
EXECUTING READ MAPPING WITH MAPEXOME...
cat: test.lst: No such file or directory
Compression of fastq files from bam/sam input files... Done. /home/sp2037/apps/NGS/MToolBox/MToolBox/MToolBox.sh: line 337: cd: test_out: No such file or directory
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 Skipping Mark Duplicates... 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/sp2037/apps/NGS/MToolBox/MToolBox/VCFoutput.py", line 36, in
VCF_dict = ast.literal_eval(open('VCF_dict_tmp', 'r').read())
IOError: [Errno 2] No such file or directory: 'VCF_dict_tmp'
PREDICTING HAPLOGROUPS AND ANNOTATING/PRIORITIZING VARIANTS...
/home/sp2037/apps/NGS/MToolBox/MToolBox/MToolBox.sh: line 472: cd: testout: No such file or directory Haplogroup predictions based on RSRS Phylotree build 17 ls: cannot access OUT*: No such file or directory Heteroplasmy 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 "
I am not sure if I need to generate a list beforehand with the names of my samples?
Thank you in advance, Stavroula