IMP error
Hi,
I have installed the IMP docker container and I am currently trying to test it on some sample data. I seem to have got IMP running but I am encountering some errors. They are below: It says it is missing the input files for rule trimming and then exits
[shabanb@thing1 IMP]$ ./IMP -m sample.100k.r1.fastq -m sample.100k.r2.fastq -o output --current
Executing " docker run -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP:/home/imp/data -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP/output:/home/imp/output -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP/db:/home/imp/databases -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP/conf:/home/imp/conf -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP:/home/imp/code -e MG="/home/imp/data/sample.100k.r1.fastq /home/imp/data/sample.100k.r2.fastq" -e CONFIGFILE=/home/imp/conf/userconfig.imp.json --rm -e "LOCAL_USER_ID=id -u $USER
" -e "LOCAL_GROUP_ID=id -g $USER
" --name data_Bioinfo_bioinfo_proj_bobbie_newProgs_IMP_output docker-r3lab.uni.lu/imp/imp:1.3 snakemake ALL -s /home/imp/code/Snakefile "
MissingInputException in line 1 of /home/imp/code/rules/Preprocessing/trimming.rules:
Missing input files for rule trimming:
/home/imp/databases/adapters/adapters.done
[shabanb@thing1 IMP]$ ./IMP -m sample.100k.r1.fastq -m sample.100k.r2.fastq -o output --current
Executing " docker run -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP:/home/imp/data -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP/output:/home/imp/output -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP/db:/home/imp/databases -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP/conf:/home/imp/conf -v /data/Bioinfo/bioinfo-proj-bobbie/newProgs/IMP:/home/imp/code -e MG="/home/imp/data/sample.100k.r1.fastq /home/imp/data/sample.100k.r2.fastq" -e CONFIGFILE=/home/imp/conf/userconfig.imp.json --rm -e "LOCAL_USER_ID=id -u $USER
" -e "LOCAL_GROUP_ID=id -g $USER
" --name data_Bioinfo_bioinfo_proj_bobbie_newProgs_IMP_output docker-r3lab.uni.lu/imp/imp:1.3 snakemake ALL -s /home/imp/code/Snakefile "
MissingInputException in line 1 of /home/imp/code/rules/Assembly/common/bwa.index.rule:
Missing input files for rule bwa_index:
/home/imp/databases/filtering/hg38.fa
Thanks, Bobbie.