brianjohnhaas
commented
1 year ago This message was cross posted across a number of different forums/sites. Responded to.
On Sat, May 27, 2023 at 6:24 AM nisntraj @.***> wrote:
Hi, I wanted to create Trinotate sqlite database, but facing an issue while using the first Trinotate command. Please help me in solving the issue and guide me what to do. I am attaching the command used as well as the error message received.
Thank you in advance
COMMAND USED:
./Trinotate --db /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite --create --trinotate_data_dir /home/workstation2/Trinotate-Trinotate-v4.0.0
ERROR MESSAGE:
Use of uninitialized value $blast_type in concatenation (.) or string at ./Trinotate line 200. -CREATING /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite and populating data dir: /home/workstation2/Trinotate-Trinotate-v4.0.0 WARNING: SQLITE database /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite already exists and wont be replaced. -sqlite db /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite already exists and is not being replaced. If a new boilerplate is required, copy db from: /home/workstation2/Trinotate-Trinotate-v4.0.0/TrinotateBoilerplate.sqlite -- Skipping CMD: /home/workstation2/Trinotate-Trinotate-v4.0.0/util/admin/Build_Trinotate_Boilerplate_SQLite_db.pl TrinotateBoilerplate, checkpoint [/home/workstation2/Trinotate-Trinotate-v4.0.0/__chckpts/build_boilerplate.ok] exists.
- [Sat May 27 15:37:32 2023] Running CMD: mv TrinotateBoilerplate.sqlite pfam2go go-basic.obo pfam2go.tab NOG.annotations.tsv.gz /home/workstation2/Trinotate-Trinotate-v4.0.0/ mv: 'TrinotateBoilerplate.sqlite' and '/home/workstation2/Trinotate-Trinotate-v4.0.0/TrinotateBoilerplate.sqlite' are the same file mv: 'pfam2go' and '/home/workstation2/Trinotate-Trinotate-v4.0.0/pfam2go' are the same file mv: 'go-basic.obo' and '/home/workstation2/Trinotate-Trinotate-v4.0.0/go-basic.obo' are the same file mv: 'pfam2go.tab' and '/home/workstation2/Trinotate-Trinotate-v4.0.0/pfam2go.tab' are the same file mv: 'NOG.annotations.tsv.gz' and '/home/workstation2/Trinotate-Trinotate-v4.0.0/NOG.annotations.tsv.gz' are the same file Error, cmd: mv TrinotateBoilerplate.sqlite pfam2go go-basic.obo pfam2go.tab NOG.annotations.tsv.gz /home/workstation2/Trinotate-Trinotate-v4.0.0/ died with ret 256 No such file or directory at /home/workstation2/Trinotate-Trinotate-v4.0.0/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x55f807279d58)) called at ./Trinotate line 426 main::run_Trinotate_create("/home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite", "/home/workstation2/Trinotate-Trinotate-v4.0.0") called at ./Trinotate line 237
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
Hi, I wanted to create Trinotate sqlite database, but facing an issue while using the first Trinotate command. Please help me in solving the issue and guide me what to do. I am attaching the command used as well as the error message received.
Thank you in advance
COMMAND USED:
./Trinotate --db /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite --create --trinotate_data_dir /home/workstation2/Trinotate-Trinotate-v4.0.0
ERROR MESSAGE:
Use of uninitialized value $blast_type in concatenation (.) or string at ./Trinotate line 200. -CREATING /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite and populating data dir: /home/workstation2/Trinotate-Trinotate-v4.0.0 WARNING: SQLITE database /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite already exists and wont be replaced. -sqlite db /home/workstation2/Trinotate-Trinotate-v4.0.0/Trinotate.sqlite already exists and is not being replaced. If a new boilerplate is required, copy db from: /home/workstation2/Trinotate-Trinotate-v4.0.0/TrinotateBoilerplate.sqlite -- Skipping CMD: /home/workstation2/Trinotate-Trinotate-v4.0.0/util/admin/Build_Trinotate_Boilerplate_SQLite_db.pl TrinotateBoilerplate, checkpoint [/home/workstation2/Trinotate-Trinotate-v4.0.0/__chckpts/build_boilerplate.ok] exists.