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MetaErg with default options does not running

Open PavelKiryanov opened this issue 3 years ago • 0 comments

After installation MetaErg with docker, I tried to run it with default options as in Readme, but error appears:

docker run --shm-size 2g --rm -u $(id -u):$(id -g) -it -v my_local_dir:/data/ xiaolidong/docker-metaerg metaerg.pl --dbdir /data/db --outdir /data/my_metaerg_output /data/contig.fasta
[Wed Jul 21 10:58:18 2021] Creating new output folder: /data/my_metaerg_output
[Wed Jul 21 10:58:18 2021] Running: mkdir -p \/data\/my_metaerg_output
mkdir: cannot create directory '/data/my_metaerg_output': Permission denied
[Wed Jul 21 10:58:18 2021] Could not run command:mkdir -p \/data\/my_metaerg_output, No such file or directory``

If I run it without -u $(id -u):$(id -g) other error appears:

sudo docker run --shm-size 2g --rm -it -v my_local_dir:/data/ xiaolidong/docker-metaerg metaerg.pl --dbdir /data/db --outdir /data/my_metaerg_output /data/contig.fasta
[Wed Jul 21 11:05:41 2021] Creating new output folder: /data/my_metaerg_output
[Wed Jul 21 11:05:41 2021] Running: mkdir -p \/data\/my_metaerg_output
[Wed Jul 21 11:05:41 2021] Running: mkdir -p \/data\/my_metaerg_output\/tmp
[Wed Jul 21 11:05:41 2021] Running: mkdir -p \/data\/my_metaerg_output\/data
[Wed Jul 21 11:05:41 2021] Using filename prefix: metaerg.pl_07212021.XXX
[Wed Jul 21 11:05:41 2021] metaerg.pl --dbdir /data/db --mincontiglen 200 --minorflen 180 --prefix metaerg.pl_07212021 --outdir /data/my_metaerg_output --locustag metaerg.pl --increment 1 --cpus 8 --evalue 1e-05 --identity 20 --coverage 70 -hmmcutoff --cut_ga -hmmevalue 1e-5 /data/contig.fasta

[Wed Jul 21 11:05:41 2021] Loading and checking input file: /data/my_metaerg_output/metaerg.pl_07212021.fna

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '/data/contig.fasta': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.28.1/Bio/Root/Root.pm:447
STACK: Bio::Root::IO::_initialize_io /usr/local/share/perl/5.28.1/Bio/Root/IO.pm:268
STACK: Bio::SeqIO::_initialize /usr/local/share/perl/5.28.1/Bio/SeqIO.pm:513
STACK: Bio::SeqIO::fasta::_initialize /usr/local/share/perl/5.28.1/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /usr/local/share/perl/5.28.1/Bio/SeqIO.pm:389
STACK: Bio::SeqIO::new /usr/local/share/perl/5.28.1/Bio/SeqIO.pm:435
STACK: main::filter_fasta /NGStools/metaerg/bin/metaerg.pl:763
STACK: /NGStools/metaerg/bin/metaerg.pl:92

What is wrong?`

PavelKiryanov avatar Jul 21 '21 12:07 PavelKiryanov