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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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KeyError in line 38 of snakePipes/workflows/HiC/internals.snakefile: 'MboI' #292

Closed mictadlo closed 6 years ago

mictadlo commented 6 years ago

Hi, While running this command HiC dbg2olc40x -i /work/waterhouse_team/All_RawData/Benth/USA_ABombarely/Nbenthamiana_HiC/ -o /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes I got:

Failed to create temp dir under temp path prefix (/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes-tmp)! Try fallback: /scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/ ...
KeyError in line 38 of /lustre/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/internals.snakefile:
'MboI'
  File "/lustre/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/Snakefile", line 34, in <module>
  File "/lustre/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/shared/rules/hicexplorer.snakefile", line 8, in <module>
  File "/lustre/scratch/waterhouse_team/benth/dbg2olc-40x/snakepipes/snakePipes/workflows/HiC/internals.snakefile", line 38, in get_restriction_seq
Error: snakemake returned an error code of 1, so processing is incomplete!

How to I specify Mbol as enzyme?

Thank you in advance,

Michal

LeilyR commented 6 years ago

You don't need to always change the config files. almost all you need could be possible to be altered from the command line. MboI is the same as DpnII which is already in the dictionary, also in case in future you had an enzyme which was not in the dictionary you would be able to add it to it. For the moment just add --enzyme DpnII to your command line

mictadlo commented 6 years ago

Thank you.