SantosJGND
commented
1 year ago Hello,
This seems to have been a successful installation of televir software. forgive the "cp: cannot stat 'utility.db': No such file or directory" error, that command should have been removed, it does not impact installation.
Could you run ./up.sh, and confirm that televir projects and settings are accessible through the main Projects / Settings pages respectively?
Thank you, Joao
$ ./up_televir.sh
postgres is up-to-date
docker_officer_1 is up-to-date
postgres_backup is up-to-date
Starting televir-server ... done
Attaching to televir-server
televir-server | ---> Create televir dbs in /televir/mngs_benchmark/ ...
televir-server | True
televir-server | False
televir-server | False
televir-server | 19-May-23 13:57:42 - Environment directory: /televir/mngs_benchmark/mngs_environments/
televir-server | 19-May-23 13:57:42 - Fasta directory: /televir/mngs_benchmark/ref_fasta/
televir-server | 19-May-23 13:57:42 - refseq_viral.genome.fna found.
televir-server | 19-May-23 13:57:42 - swissprot.gz found.
televir-server | 19-May-23 13:57:42 - hg38.fa.gz found.
televir-server | 19-May-23 13:57:42 - virosaurus90_vertebrate_20200330.fas found.
televir-server | 19-May-23 13:57:42 - Downloading databases and software
televir-server | 19-May-23 13:57:42 - acc2taxid map file /televir/mngs_benchmark/metadata/swissprot_acc2taxid.tsv exists, continuing.
televir-server | 19-May-23 13:57:42 - accession to taxid mapping done. You can now delete the directory /televir/mngs_benchmark/metadata/prot.accession2taxid/
televir-server | 19-May-23 13:57:42 - refseq_prot not found.
televir-server | 19-May-23 13:57:42 - protein_acc2taxid.tsv file found.
televir-server | False
televir-server | 19-May-23 13:57:42 - Environment directory: /televir/mngs_benchmark/mngs_environments/
televir-server | 19-May-23 13:57:42 - Fasta directory: /televir/mngs_benchmark/ref_fasta/
televir-server | 19-May-23 13:57:42 - refseq_viral.genome.fna found.
televir-server | 19-May-23 13:57:42 - swissprot.gz found.
televir-server | 19-May-23 13:57:42 - hg38.fa.gz found.
televir-server | 19-May-23 13:57:42 - virosaurus90_vertebrate_20200330.fas found.
televir-server | 19-May-23 13:57:42 - Downloading databases and software
televir-server | 19-May-23 13:57:42 - acc2taxid map file /televir/mngs_benchmark/metadata/swissprot_acc2taxid.tsv exists, continuing.
televir-server | 19-May-23 13:57:42 - accession to taxid mapping done. You can now delete the directory /televir/mngs_benchmark/metadata/prot.accession2taxid/
televir-server | 19-May-23 13:57:42 - refseq_prot not found.
televir-server | 19-May-23 13:57:42 - protein_acc2taxid.tsv file found.
televir-server | 19-May-23 13:57:42 - database directory /televir/mngs_benchmark/ref_db/
televir-server | 19-May-23 13:57:42 - install prepped
televir-server | 19-May-23 13:57:42 - Centrifuge db viral index is installed.
televir-server | 19-May-23 13:57:42 - clark db viruses is installed.
televir-server | 19-May-23 13:57:42 - Kraken2 db viral k2d file exists. Kraken2 is installed.
televir-server | 19-May-23 13:57:42 - kraken2 database fasta not found.
televir-server | 19-May-23 13:57:42 - Krakenuniq viral taxDB present. prepped.
televir-server | 19-May-23 13:57:42 - Kaiju viral is installed.
televir-server | 19-May-23 13:57:42 - BWA db hg38 is installed.
televir-server | 19-May-23 13:57:42 - bowtie2 index for hg38 is installed.
televir-server | 19-May-23 13:57:42 - FastViromeExplorer index for /televir/mngs_benchmark/ref_fasta/refseq_viral.genome.fna.gz is installed.
televir-server | 19-May-23 13:57:42 - blast index for refseq_viral_genome is installed.
televir-server | 19-May-23 13:57:42 - deSAMBA db refseq is installed.
televir-server | 19-May-23 13:57:42 - FastViromeExplorer index for /televir/mngs_benchmark/ref_fasta/virosaurus90_vertebrate-20200330.fas.gz is installed.
televir-server | 19-May-23 13:57:42 - deSAMBA db virosaurus is installed.
televir-server | 19-May-23 13:57:42 - FastViromeExplorer index for /televir/mngs_benchmark/ref_fasta/refseq-viral.dust.fna.gz is installed.
televir-server | 19-May-23 13:57:42 - deSAMBA db centrifuge is installed.
televir-server | 19-May-23 13:57:42 - acc2taxid.tsv found for all nuc files.
televir-server | False
televir-server | /televir/mngs_benchmark/mngs_environments/trimmomatic/classes/trimmomatic.jar True
televir-server | copying files
televir-server | dir: /televir/mngs_benchmark/app/
televir-server | cp: cannot stat 'utility.db': No such file or directory
televir-server | ---> Finshed creating televir dbs in /televir/mngs_benchmark/ ... done
televir-server exited with code 0