metaquast rule
Hello friends, probably a silly thing, but I cannot make IMP work following the example in your web page. Here is my .sh file:
#! /bin/bash -l
CONFIGFILE="/home/temp/software/IMP/IMP/src/config.imp.json"
MG="/home/temp/software/IMP/test/MT.R1.fq /home/temp/software/IMP/test/MT.R2.fq"
MT="/home/temp/software/IMP/test/MT.R1.fq /home/temp/software/IMP/test/MT.R2.fq"
OUTPUTDIR="/home/temp/software/IMP/test/output"
CONDAPATH="/home/temp/software/IMP/IMP/conda"
DBPATH="/home/temp/software/IMP/IMP/db"
FILTER="hg38"
SRCDIR="/home/temp/software/IMP/IMP/src"
LIBDIR="/home/temp/software/IMP/IMP"
IMP_ASSEMBLER="megahit"
snakemake -s /home/temp/software/IMP/IMP/Snakefile --use-conda -p
and when I run it I get: $ ./test.sh SyntaxError: Not all output, log and benchmark files of rule metaquast contain the same wildcards. This is crucial though, in order to avoid that two or more jobs write to the same file. File "/home/temp/software/IMP/IMP/Snakefile", line 36, in File "/home/temp/software/IMP/IMP/workflows/integrative/Analysis", line 18, in File "/home/temp/software/IMP/IMP/rules/Analysis/metaquast.rule", line 10, in
As I am new to snakemake, I do not know how to solve this problem. Could you please help me?
Best,
J