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Trinotate / Trinotate.github.io

web documentation for Trinotate
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problem with sqlite #27

Open JiaZhong28 opened 4 years ago

JiaZhong28 commented 4 years ago

Hi Brian, i want to use the annotation pipline for 6 files simultaneously, then I put all the involved commands within pipline into one shell script. i have 6 such shell scripts in total, and I found all the shell used the same within the sam path. I do not know if it is because the same sqlite.db I used to load all files. it's turned out that such error occurred in one of the six script: .import tmp.ORF.bulk_load ORF" | sqlite3 /stor9000/apps/users/NWSUAF/2013130172/database/trinotate/Trinotate.sqlite tmp.ORF.bulk_load:1: INSERT failed: database is locked tmp.ORF.bulk_load:2: INSERT failed: database is locked tmp.ORF.bulk_load:3: INSERT failed: database is locked tmp.ORF.bulk_load:4: INSERT failed: database is locked

I find nothing but column name in final report, and I do not know how to deal with it.

best ruoxi,jing

brianjohnhaas commented 4 years ago

sqlite doesn't allow for concurrency, afaik. You can only load one at a time.

On Wed, Aug 21, 2019 at 11:49 PM JiaZhong28 notifications@github.com wrote:

Hi Brian, i want to use the annotation pipline for 6 files simultaneously, then I put all the involved commands within pipline into one shell script. i have 6 such shell scripts in total, and I found all the shell used the same

within the sam path. I do not know if it is because the same sqlite.db I used to load all files. it's turned out that such error occurred in one of the six script: .import tmp.ORF.bulk_load ORF" | sqlite3 /stor9000/apps/users/NWSUAF/2013130172/database/trinotate/Trinotate.sqlite tmp.ORF.bulk_load:1: INSERT failed: database is locked tmp.ORF.bulk_load:2: INSERT failed: database is locked tmp.ORF.bulk_load:3: INSERT failed: database is locked tmp.ORF.bulk_load:4: INSERT failed: database is locked I find nothing but column name in final report, and I do not know how to deal with it. best ruoxi,jing — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub , or mute the thread .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas