I'm getting the following error when trying to setup database.
Command used:
nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db /media/BRIANDATA2/sidd/viroprofiler_db --max_cpus 20 --max_memory 200GB
Error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
mkdir: cannot create directory ‘/media/BRIANDATA2/sidd/viroprofiler_db’: Permission denied
However, when I use the relative path in --db option I get some success but get another error:
Command used:
nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db viroprofiler_db --max_cpus 20 --max_memory 200GB
Error:
2023-06-20 19:47:51 (30.5 MB/s) - ‘taxdump.zip’ saved [58628855/58628855]
Archive: taxdump.zip
inflating: citations.dmp
inflating: delnodes.dmp
inflating: division.dmp
inflating: gencode.dmp
inflating: merged.dmp
inflating: names.dmp
inflating: nodes.dmp
inflating: gc.prt
inflating: readme.txt
viroprofiler_db/taxonomy/mmseqs_vrefseq.tar.gz: No such file or directory
Work dir:
/media/BRIANDATA2/sidd/work/a3/a1f7bb952801c534dba57b2aa6dec0
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for details
Command used and terminal output
# This is the command when using absolute path
nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db /media/BRIANDATA2/sidd/viroprofiler_db --max_cpus 20 --max_memory 200GB
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'
Caused by:
Process `VIROPROFILER:SETUP:DB_VIBRANT` terminated with an error exit status (1)
Command executed:
if [ ! -d /media/BRIANDATA2/sidd/viroprofiler_db/vibrant ]; then
mkdir -p /media/BRIANDATA2/sidd/viroprofiler_db/vibrant
executor > local (6)
[60/d37bfe] process > VIROPROFILER:SETUP:DB_CHECKV [100%] 1 of 1, failed: 1 ✘
[a2/f8216d] process > VIROPROFILER:SETUP:DB_VIBRANT [100%] 1 of 1, failed: 1 ✘
[8a/3b8bb6] process > VIROPROFILER:SETUP:DB_VIRSORTER2 [100%] 1 of 1, failed: 1 ✘
[b7/780b5b] process > VIROPROFILER:SETUP:DB_DRAM [100%] 1 of 1, failed: 1 ✘
[19/e6e121] process > VIROPROFILER:SETUP:DB_IPHOP [100%] 1 of 1, failed: 1 ✘
[6f/7e476f] process > VIROPROFILER:SETUP:DB_VREFSEQ [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:SETUP:DB_VIBRANT'
Caused by:
Process `VIROPROFILER:SETUP:DB_VIBRANT` terminated with an error exit status (1)
Command executed:
if [ ! -d /media/BRIANDATA2/sidd/viroprofiler_db/vibrant ]; then
mkdir -p /media/BRIANDATA2/sidd/viroprofiler_db/vibrant
export VIBRANT_DATA_PATH="/opt/conda/share/vibrant-1.2.1/db"
download-db.sh /media/BRIANDATA2/sidd/viroprofiler_db/vibrant
else
echo "VIBRANT database already exists"
fi
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
mkdir: cannot create directory ‘/media/BRIANDATA2/sidd/viroprofiler_db’: Permission denied
Work dir:
/media/BRIANDATA2/sidd/work/a2/f8216dcace4d0e2ef6e56c399b5c5a
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for details
Description of the bug
I'm getting the following error when trying to setup database.
Command used:
nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db /media/BRIANDATA2/sidd/viroprofiler_db --max_cpus 20 --max_memory 200GB
Error:
However, when I use the relative path in
--db
option I get some success but get another error:Command used:
nextflow run deng-lab/viroprofiler -r main -profile docker --mode "setup" --db viroprofiler_db --max_cpus 20 --max_memory 200GB
Error:
Command used and terminal output
Relevant files
nextflow_relativePath.log nextflow_absPath.log
System information
Nextflow version 23.04.1 nf-core/viroprofiler - revision: c2a1f1871b [main]. But while running the version displayed is ViroProfiler v0.2.4