IMP issues
https://git-r3lab.uni.lu/IMP/IMP/-/issues
2017-05-31T09:51:20+02:00
https://git-r3lab.uni.lu/IMP/IMP/-/issues/83
impy init
2017-05-31T09:51:20+02:00
castualwang
impy init
```
root@skywang:~# impy init
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4
IMP image found
Executing IMP command:
docker run --rm --name root_imp_db -v /root/imp-db:/home/imp/databases -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL...
```
root@skywang:~# impy init
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4
IMP image found
Executing IMP command:
docker run --rm --name root_imp_db -v /root/imp-db:/home/imp/databases -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" docker-r3lab.uni.lu/imp/imp:1.4 snakemake -s /home/imp/code/rules/ini/init
usermod: UID '0' already exists
groupmod: GID '0' already exists
Traceback (most recent call last):
File "/usr/local/lib/python3.4/dist-packages/snakemake/__init__.py", line 399, in snakemake
no_hooks=no_hooks)
File "/usr/local/lib/python3.4/dist-packages/snakemake/workflow.py", line 301, in execute
list_params_changes)
File "/usr/local/lib/python3.4/dist-packages/snakemake/persistence.py", line 24, in __init__
os.mkdir(self.path)
PermissionError: [Errno 13] Permission denied: '/home/imp/databases/.snakemake'
```
Yohan Jarosz
yohan.jarosz@uni.lu
Yohan Jarosz
yohan.jarosz@uni.lu
https://git-r3lab.uni.lu/IMP/IMP/-/issues/84
The job will stop after processing
2017-05-31T09:51:20+02:00
castualwang
The job will stop after processing
I imput the command:
```
impy run -m <input/MG.R1.fq> -m <input/MG.R2.fq> -t <input/MT.R1.fq> -t <input/MT.R2.fq> -o <output directory>
After the processing, the job stop!
Provided cores: 1
Rules claiming more threads will be scal...
I imput the command:
```
impy run -m <input/MG.R1.fq> -m <input/MG.R2.fq> -t <input/MT.R1.fq> -t <input/MT.R2.fq> -o <output directory>
After the processing, the job stop!
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 ALL
1 ANALYSIS
1 ASSEMBLY
1 BINNING
1 PREPROCESSING
1 REPORT
1 annotate
1 assembly_contig_length
3 bwa_index
2 call_contig_depth
2 call_gene_depth
2 cat_se_trimmed
1 collapse_hybrid_assemblies
1 diagramm
1 download_librairies_files
2 extract_unmapped_from_hybrid_assembly
1 extract_unmapped_from_megahit
2 fastqc_preprocessed
2 fastqc_raw
1 filter_rna
1 idba_hybrid_assembly_1
1 idba_hybrid_assembly_2
2 krona
1 local_librarie_files
1 make_report
2 mapping_on_assembly
1 maxbin
1 maxbin_contig2bin
1 megahit_assembly_from_preprocessing
1 megahit_assembly_from_unmapped
1 metaquast
1 mg_filtering
1 mt_filtering
1 prepare_input_data
3 reads_count
2 rename_stat_output
1 symlink_mg_preprocessed_files
1 symlink_mt_preprocessed_files
2 trimming
1 update_tbl2asn
2 variant_calling
1 visualize
1 visualize_maxbin
1 vizbin
59
rule prepare_input_data:
input: /home/imp/data/mg.r1.fq, /home/imp/data/mg.r2.fq, /home/imp/data/mt.r1.fq, /home/imp/data/mt.r2.fq
output: Preprocessing/mg.r1.fq, Preprocessing/mg.r2.fq, Preprocessing/mt.r1.fq, Preprocessing/mt.r2.fq
1 of 59 steps (2%) done
ProtectedOutputException in line 1 of /home/imp/code/rules/Assembly/common/bwa.index.rule:
Write-protected output files for rule bwa_index:
/home/imp/databases/filtering/hg38.fa.amb
/home/imp/databases/filtering/hg38.fa.bwt
/home/imp/databases/filtering/hg38.fa.pac
/home/imp/databases/filtering/hg38.fa.sa
/home/imp/databases/filtering/hg38.fa.ann
/home/imp/data/mg.r1.fq => Preprocessing/mg.r1.fq
/home/imp/data/mg.r2.fq => Preprocessing/mg.r2.fq
/home/imp/data/mt.r1.fq => Preprocessing/mt.r1.fq
/home/imp/data/mt.r2.fq => Preprocessing/mt.r2.fq
```