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Trinotate / Trinotate.github.io

web documentation for Trinotate
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Get the report #13

Open Phinou opened 5 years ago

Phinou commented 5 years ago

Hi,

I'm trying to use Trinotate for different datasets and I'm stuck on the last step. When I generate the report I get the error below that I don't understand (for each of my datasets it processes a number of sequences before stopping - the one which doesn't pass is not different from the others). For each dataset, I have a transcriptome and a file Trinity.fasta.gene_trans_map. I used Transdecoder and I have results from blastp, blastx and hmmscan.

This last command give me the following errors :

CMD: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite //Trinotate.sqlite DBD::SQLite::st execute failed: disk I/O error at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 87. failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: disk I/O error Failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 102 eval {...} called at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 72 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x100de30)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 108 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x100de30)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite /projet/fr2424/sib/dnegre/Laminarionema/input/2.1.Trinotate/BinPacker/phaeo_strict/Trinotate.sqlite died with ret 30976 at //bin/Trinotate line 126'`

This sequence (TRINITY_17757t2_c0_g1_i1) is only presents into Transcriptome.fasta and Trinity.fasta.gene_transmap so I tried to remove it but the errors move to the next sequence, same line. I checked and into annotation*_report.xls, I have other sequences that are present only in these two files so I don't understand where is the error ?

NB : identical case, with others sequences, on my other three datasets

Thanks in advance for your answer

brianjohnhaas commented 5 years ago

Hi,

I'm seeing a lot of Errors: disk I/O error

which suggests a corruption of some sort.

Try rebuilding the initial database and then loading it with your results. It's a strange problem and I don't have other ideas at the moment.

best, ~b

On Tue, Dec 11, 2018 at 6:08 AM Phinou notifications@github.com wrote:

Hi,

I'm trying to use Trinotate for different datasets and I'm stuck on the last step. When I generate the report I get the error below that I don't understand (for each of my datasets it processes a number of sequences before stopping - the one which doesn't pass is not different from the others). For each dataset, I have a transcriptome and a file Trinity.fasta.gene_trans_map. I used Transdecoder and I have results from blastp, blastx and hmmscan.

Loading inputs into database Trinotate Trinotate.sqlite init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Transcriptome.fasta --transdecoder_pep Transcriptome.fasta.transdecoder.pep

Loading results into database Trinotate Trinotate.sqlite LOAD_swissprot_blastp blastp.outfmt6 Trinotate Trinotate.sqlite LOAD_swissprot_blastx blastx.outfmt6 Trinotate Trinotate.sqlite LOAD_pfam Trinity_PFAM.out

Visualisation Trinotate Trinotate.sqlite report > annotation_*_report.xls

This last command give me the following errors :

CMD: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite //Trinotate.sqlite DBD::SQLite::st execute failed: disk I/O error at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 87. failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: disk I/O error Failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 102 eval {...} called at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 72 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x100de30)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 108 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x100de30)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x100de30)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite /projet/fr2424/sib/dnegre/Laminarionema/input/2.1.Trinotate/BinPacker/phaeo_strict/Trinotate.sqlite died with ret 30976 at //bin/Trinotate line 126'`

This sequence (TRINITY_17757t2_c0_g1_i1) is only presents into Transcriptome.fasta and Trinity.fasta.gene_transmap so I tried to remove it but the errors move to the next sequence, same line. I checked and into annotation*_report.xls, I have other sequences that are present only in these two files so I don't understand where is the error ?

NB : identical case, with others sequences, on my other three datasets

Thanks in advance for your answer

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

Phinou commented 5 years ago

Hi,

Thank you for your quick answer but unfortunately, I always get the same error on the same sequence.

To be sure, I delete my Trinotate.sqlite and then I did the following cmd :

/*/Trinotate-3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate

Trinotate Trinotate.sqlite init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Transcriptome.fasta --transdecoder_pep Transcriptome.fasta.transdecoder.pep

Trinotate Trinotate.sqlite LOAD_swissprot_blastp blastp.outfmt6 Trinotate Trinotate.sqlite LOAD_swissprot_blastx blastx.outfmt6 Trinotate Trinotate.sqlite LOAD_pfam Trinity_PFAM.out

Trinotate Trinotate.sqlite report > annotation_*_report.xls

brianjohnhaas commented 5 years ago

Is it the disk i/o error?

-via googleFi

On Wed, Dec 12, 2018, 6:13 AM Phinou <notifications@github.com wrote:

Hi,

Thank you for your quick answer but unfortunately, I always get the same error on the same sequence.

To be sure, I delete my Trinotate.sqlite and then I did the following cmd :

/*/Trinotate-3.1.1/admin/Build_Trinotate_Boilerplate_SQLite_db.pl Trinotate

Trinotate Trinotate.sqlite init --gene_trans_map Trinity.fasta.gene_trans_map --transcript_fasta Transcriptome.fasta --transdecoder_pep Transcriptome.fasta.transdecoder.pep

Trinotate Trinotate.sqlite LOAD_swissprot_blastp blastp.outfmt6 Trinotate Trinotate.sqlite LOAD_swissprot_blastx blastx.outfmt6 Trinotate Trinotate.sqlite LOAD_pfam Trinity_PFAM.out

Trinotate Trinotate.sqlite report > annotation_*_report.xls

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/13#issuecomment-446551357, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX0OpSMI3xqrZi1GMdg2sLNMHPLicks5u4OTygaJpZM4ZNK-u .

Phinou commented 5 years ago

Yes, I have exactly the same errors

CMD: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite //Trinotate.sqlite DBD::SQLite::st execute failed: disk I/O error at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 87. failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: disk I/O error Failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 102 eval {...} called at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 72 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x1bad258)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 108 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x1bad258)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite/Trinotater.sqlite died with ret 30976 at //bin/Trinotate line 126.

brianjohnhaas commented 5 years ago

I'm not sure what these disk I/o errors are. If you want to share your trinotate sqlite database with me i can take a look and see if it's an issue with it

-via googleFi

On Wed, Dec 12, 2018, 7:42 AM Phinou <notifications@github.com wrote:

Yes, I have exactly the same errors

CMD: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite / /Trinotate.sqlite DBD::SQLite::st execute failed: disk I/O error at /

/Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 87. failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: disk I/O error Failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 102 eval {...} called at / /Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 72 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x1bad258)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at / /Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 at / /Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 108 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x1bad258)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at / /Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite/Trinotater.sqlite died with ret 30976 at //bin/Trinotate line 126.

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brianjohnhaas commented 5 years ago

Thx for sending the sqlite db. The report worked fine when I ran it on it from my mac. I wonder if it's an issue with your filesystem. Are you running it from a PC, or from a server?

On Wed, Dec 12, 2018 at 9:03 AM Brian Haas bhaas@broadinstitute.org wrote:

I'm not sure what these disk I/o errors are. If you want to share your trinotate sqlite database with me i can take a look and see if it's an issue with it

-via googleFi

On Wed, Dec 12, 2018, 7:42 AM Phinou <notifications@github.com wrote:

Yes, I have exactly the same errors

CMD: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite / /Trinotate.sqlite DBD::SQLite::st execute failed: disk I/O error at /

/Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 87. failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: disk I/O error Failed query: <select Featurestart, Featureend, Featurescore, FeatureStrand, FeatureFrame, Featureprediction from RNAMMERdata where TrinityQuerySequence = ? > values: TRINITY_17757t2_c0_g1_i1 Errors: at //Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 102 eval {...} called at / /Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 72 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x1bad258)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at / /Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 at / /Trinotate-3.1.1/util/../PerlLib/Sqlite_connect.pm line 108 Sqlite_connect::do_sql_2D('DBI::db=HASH(0x1bad258)', 'select Featurestart, Featureend, Featurescore, FeatureStrand,...', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/../PerlLib/Trinotate.pm line 424 Trinotate::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at / /Trinotate-3.1.1/util/Trinotate_report_writer.pl line 539 main::get_RNAMMER_info('DBI::db=HASH(0x1bad258)', 'TRINITY_17757t2_c0_g1_i1') called at //Trinotate-3.1.1/util/Trinotate_report_writer.pl line 139 Error, cmd: //Trinotate-3.1.1/util/Trinotate_report_writer.pl --sqlite/Trinotater.sqlite died with ret 30976 at //bin/Trinotate line 126.

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Phinou commented 5 years ago

Hi,

I use a cluster where Trinotate (Trinotate-3.1.1) is installed. Could it be a problem of memory or temporary files?

brianjohnhaas commented 5 years ago

I'm not sure. I've experienced weirdness on certain networked file systems. You might try copying the database to /tmp and running the report from there. The /tmp area tends to be on a direct drive and not the networked file system, in case that's part of the issue.

On Thu, Dec 13, 2018 at 3:50 AM Phinou notifications@github.com wrote:

Hi,

I use a cluster where Trinotate is installed. Could it be a problem of memory or temporary files?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Trinotate/Trinotate.github.io/issues/13#issuecomment-446888876, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVXwS7zVjWf4vWSoTmpHgddWEnS11Eks5u4hTBgaJpZM4ZNK-u .

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

Phinou commented 5 years ago

Hi,

Indeed, apparently this solved the problem. Thank you so much

Have a nice day

brianjohnhaas commented 5 years ago

great!

On Thu, Dec 13, 2018 at 12:25 PM Phinou notifications@github.com wrote:

Hi,

Indeed, apparently this solved the problem. Thank you so much

Have a nice day

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