DBD::SQLite::db do failed: UNIQUE constraint failed:

[Juan Cerda-Herrera]

An error I am encountering when running the pipeline:

-connecting to SQLite db: /tmp/CuGr2

-*** Running PASA pipeine:

* [Wed Sep 20 14:31:15 2023] Running CMD: /usr/local/src/PASApipeline/scripts/create_sqlite_cdnaassembly_db.dbi -c /usr/local/src/work/alignAss

embly.config -S '/usr/local/src/PASApipeline/schema/cdna_alignment_sqliteschema'

* [Wed Sep 20 14:31:18 2023] Running CMD: /usr/local/src/PASApipeline/scripts/upload_transcript_data.dbi -M '/tmp/CuGr2' -t /usr/local/src/work

/transcripts.fasta -T /usr/local/src/work/tdn.accs -f NULL 

DBD::SQLite::db do failed: UNIQUE constraint failed: cdna_info.cdna_acc at /usr/local/src/PASApipeline/PerlLib/DB_connect.pm line 221, <$fileha

ndle> line 265730.

failed query: < insert into cdna_info (cdna_acc, is_assembly, is_fli, is_TDN, length, header) values (?,?,?,?,?,?) > values: TRINITY_DN21455

_c0_g1_i1 0 0 1 5873 TRINITY_DN21455_c0_g1_i1 len=5873 path=[1:0-587 4:588-3550 5:3551-4364 6:4365-4448 7:4449-5872]

Errors: UNIQUE constraint failed: cdna_info.cdna_acc

 at /usr/local/src/PASApipeline/PerlLib/DB_connect.pm line 233, <$filehandle> line 265730.

DB_connect::RunMod(DB_connect=HASH(0x56419c7471b8), " insert into cdna_info (cdna_acc, is_assembly, is_fli, is_TDN"..., "TRINITY_DN2145

5_c0_g1_i1", 0, 0, 1, 5873, "TRINITY_DN21455_c0_g1_i1 len=5873 path=[1:0-587 4:588-3550 5:"...) called at /usr/local/src/PASApipeline/scripts/u

pload_transcript_data.dbi line 97

Issuing rollback() due to DESTROY without explicit disconnect() of DBD::SQLite::db handle database=/tmp/CuGr2;host=localhost.

Error, cmd: /usr/local/src/PASApipeline/scripts/upload_transcript_data.dbi -M '/tmp/CuGr2' -t /usr/local/src/work/transcripts.fasta -T /usr/loc

al/src/work/tdn.accs -f NULL  died with ret 512 No such file or directory at /usr/local/src/PASApipeline/PerlLib/Pipeliner.pm line 187.

Pipeliner::run(Pipeliner=HASH(0x557ecea11648)) called at /usr/local/src/PASApipeline/Launch_PASA_pipeline.pl line 1061

Any ideas what this is an dhow to solve it?

[Brian Haas]

Hi Juan,

In your input transcripts.fasta file, are you finding the entry: "TRINITY_DN21455_c0_g1_i1" multiple times?

Note, if you have several Trinity assembly result files that you've combined into a single file for use with PASA, be sure that you first give each data set a unique prefix so that the identifiers will each be unique.

best,

~b

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Brian J. Haas
The Broad Institute
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[Juan Cerda-Herrera]

Hello,

Yes, it seems like that transcript name does appear multiple times in the file. I have given the different assemblies different prefixes. Are these sequences meant to be removed by the seqclean script? I did not run it because it was giving me some errors as well.  

[Brian Haas]

Hi Juan,

The name it's complaining about 'TRINITY_DN21455_c0_g1_i1' should probably not exist in your input as is, but rather have the prefix to this name that corresponds to whatever your sample was.

best,

~b

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