DBD::SQLite::db do failed: attempt to write a readonly database

[xiaojing shi]

asta.clean

* Running CMD: /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/scripts/Load_Current_Gene_Annotations.dbi -c /project/uma_john_gibbons/shu_zhao/jing/temp/10-try-0211-3/update_misc/pasa/annotCompare.txt -g /project/uma_john_gibbons/shu_zhao/jing/temp/10-try-0211-3/update_misc/genome.fa -P /project/uma_john_gibbons/shu_zhao/jing/temp/10-try-0211-3/update_misc/genome.gff3  > pasa_run.log.dir/output.annot_loading.46644.out

DBD::SQLite::db do failed: attempt to write a readonly database at /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/PerlLib/DB_connect.pm line 221.

failed query: <insert into annotation_admin (date) values (CURRENT_TIMESTAMP)>  values: 

Errors: attempt to write a readonly database

 at /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/PerlLib/DB_connect.pm line 233.

        DB_connect::RunMod(DB_connect=HASH(0x563176d4e060), "insert into annotation_admin (date) values (CURRENT_TIMESTAMP)") called at /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/scripts/Annotation_store_preloader.dbi line 52

Sorry, couldn't retrieve an ID for the annotation version. :( 

Error, cmd: /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/scripts/Load_Current_Gene_Annotations.dbi -c /project/uma_john_gibbons/shu_zhao/jing/temp/10-try-0211-3/update_misc/pasa/annotCompare.txt -g /project/uma_john_gibbons/shu_zhao/jing/temp/10-try-0211-3/update_misc/genome.fa -P /project/uma_john_gibbons/shu_zhao/jing/temp/10-try-0211-3/update_misc/genome.gff3  > pasa_run.log.dir/output.annot_loading.46644.out died with ret 512 No such file or directory at /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/PerlLib/Pipeliner.pm line 186.

        Pipeliner::run(Pipeliner=HASH(0x55a103bf2568)) called at /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/Launch_PASA_pipeline.pl line 1044

[Brian Haas]

Hi,

The error DBD::SQLite::db do failed: attempt to write a readonly database at /share/pkg/condas/2018-05-11/envs/funannotate_1.7.1/opt/pasa-2.3.3/PerlLib/DB_connect.pm line 221.

failed query: <insert into annotation_admin (date) values (CURRENT_TIMESTAMP)>  values:
Errors: attempt to write a readonly database

suggests that the file permissions on the sqlite database are not allowing you to write to it.  You might check the unix permission settings.

best,

~b

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--
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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas