DBD::SQLite::db do failed: disk I/O error

[Zinwinlatt]

Hello,

I'm running

$PASAHOME/Launch_PASA_pipeline.pl \
   -c alignAssembly.config -C -R -g /home/zwl/data/Iso_seq/Gbi_Genome_NFU/Gbi_chr.fa \
   -t LRSFmix.hq.fasta.clean -T -u LRSFmix.hq.fasta \
   --ALIGNERS blat,gmap --CPU 2

and set alignAssembly.config to

DATABASE=/home/zwl/rnaseq/06pasa/02assembly_Isoseq/mydb_pasa.sqlite validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=75 validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=95

But I got this error message,

-connecting to SQLite db: /home/zwl/rnaseq/06pasa/02assembly_Isoseq/mydb_pasa.sqlite -*** Running PASA pipeine: [Sun Jul 4 00:17:36 2021] Running CMD: /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S '/home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/schema/cdna_alignment_sqliteschema' DBD::SQLite::db do failed: disk I/O error at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi line 62. Error, invalid SQLite schema at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi line 62. Error, cmd: /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S '/home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/schema/cdna_alignment_sqliteschema' died with ret 9728 No such file or directory at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x2b54f55d3d30)) called at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/Launch_PASA_pipeline.pl line 1044

Could someone please help me to fix this issue?

[brianjohnhaas]

hi,

is file: /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/schema/cdna_alignment_sqliteschema

missing from your installation?

On Sat, Jul 3, 2021 at 12:25 PM Zinwinlatt @.***> wrote:

Hello,

I'm running

$PASAHOME/Launch_PASA_pipeline.pl \ -c alignAssembly.config -C -R -g /home/zwl/data/Iso_seq/Gbi_Genome_NFU/Gbi_chr.fa \ -t LRSFmix.hq.fasta.clean -T -u LRSFmix.hq.fasta \ --ALIGNERS blat,gmap --CPU 2

and set alignAssembly.config to

DATABASE=/home/zwl/rnaseq/06pasa/02assembly_Isoseq/mydb_pasa.sqlite validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=75 validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=95

But I got this error message,

-connecting to SQLite db: /home/zwl/rnaseq/06pasa/02assembly_Isoseq/mydb_pasa.sqlite -*** Running PASA pipeine:

• [Sun Jul 4 00:17:36 2021] Running CMD: /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S '/home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/schema/cdna_alignment_sqliteschema' DBD::SQLite::db do failed: disk I/O error at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi line 62. Error, invalid SQLite schema at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi line 62. Error, cmd: /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/create_sqlite_cdnaassembly_db.dbi -c alignAssembly.config -S '/home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/schema/cdna_alignment_sqliteschema' died with ret 9728 No such file or directory at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/PerlLib/Pipeliner.pm line 187. Pipeliner::run(Pipeliner=HASH(0x2b54f55d3d30)) called at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/Launch_PASA_pipeline.pl line 1044

Could someone please help me to fix this issue?

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[Zinwinlatt]

Hello Brian, @brianjohnhaas

I found that file in that directory.... It is not missing!

Actually I'm using PacBio Iso-seq data for mapping and assembling with GMAP, BLAT and I installed PASA with conda.

[brianjohnhaas]

it's peculiar.

You might try installing it separately by pulling the code from github (latest release) and using it directly.

On Sun, Jul 4, 2021 at 11:29 AM Zinwinlatt @.***> wrote:

Hello Brian,

I found that file in that directory.... It is not missing!

Actually I'm using PacBio Iso-seq data for mapping and assembling with GMAP, BLAT and I installed PASA with conda.

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[Zinwinlatt]

I think I got the answer for problem. I set database at /home/zwl/....../....../mydb_pasa.sqlite in alignAssembly.confi. Not in tmp/ dir as show in your example. So, I try to set in /tmp. It's Ok now.

But I got the same problem as in issue #136

https://github.com/PASApipeline/PASApipeline/issues/136

Error, cmd: gmap_build -D /home/zwl/data/Iso_seq/Gbi_Genome_NFU -T /home/zwl/data/Iso_seq/Gbi_Genome_NFU -d Gbi_chr.fa.gmap -k 13 /home/zwl/data/Iso_seq/Gbi_Genome_NFU/Gbi_chr.fa >&2 died with ret (32256) at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl line 115. Thread 1 terminated abnormally: Error, cmd: /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/process_GMAP_alignments_gff3_chimeras_ok.pl --genome /home/zwl/data/Iso_seq/Gbi_Genome_NFU/Gbi_chr.fa --transcripts LRSFmix.hq.fasta.clean --CPU 2 -N 1 -I 500000 > gmap.spliced_alignments.gff3 died with ret (512) at /home/zwl/miniconda3/envs/pasa/opt/pasa-2.4.1/scripts/../PerlLib/Process_cmd.pm line 18 thread 1.

[brianjohnhaas]

hopefully info in that long thread will guide you along to success.

On Sun, Jul 4, 2021 at 12:49 PM Zinwinlatt @.***> wrote:

I think I got the answer for problem. I set database at /home/zwl/....../....../mydb_pasa.sqlite in alignAssembly.confi. Not in tmp/ dir as show in your example. So, I try to set in /tmp. It's Ok now.

But I got the same problem as in isssue #136 https://github.com/PASApipeline/PASApipeline/issues/136

https://github.com/PASApipeline/PASApipeline/issues/136#issuecomment-569777640 http://url

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