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Trinotate / Trinotate.github.io

web documentation for Trinotate
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import_expression_and_DE_results #14

Open abdo3a opened 5 years ago

abdo3a commented 5 years ago

Hi Brian I did following command, import_expression_and_DE_results.pl --sqlite Trinotate_cvel.sqlite --transcript_mode --samples_file ../cvel_sample.txt --count_matrix ../cvel_trans.isoform.counts.matrix --fpkm_matrix ../cvel_trans.isoform.TMM.EXPR.matrix

Samples and replicates: $VAR1 = {}; Sample and replicate database identifiers: $VAR1 = {}; -parsing counts matrix: ../cvel_trans.isoform.counts.matrix Can't use an undefined value as a HASH reference at /home/nemo/miniconda3/envs/bio/bin/import_expression_and_DE_results.pl line 379, <$fh> line 1. Issuing rollback() due to DESTROY without explicit disconnect() of DBD::SQLite::db handle Trinotate_cvel.sqlite at /home/nemo/miniconda3/envs/bio/bin/import_expression_and_DE_results.pl line 379.

. How to resolve it? Regards

brianjohnhaas commented 5 years ago

Hi

It looks like there might be something off with the samples file you're using. Trinotate doesn't seem to be parsing it according to expectations. Can you compare yours to the sample data and see if there's anything obvious?

I'm happy to look at your files if needed.

-via googleFi

On Sun, Dec 16, 2018, 7:35 AM Abdoallah Sharaf <notifications@github.com wrote:

Hi Brian I did following command, import_expression_and_DE_results.pl --sqlite Trinotate_cvel.sqlite --transcript_mode --samples_file ../cvel_sample.txt --count_matrix ../cvel_trans.isoform.counts.matrix --fpkm_matrix ../cvel_trans.isoform.TMM.EXPR.matrix

  • and it give me following error.

Samples and replicates: $VAR1 = {}; Sample and replicate database identifiers: $VAR1 = {}; -parsing counts matrix: ../cvel_trans.isoform.counts.matrix Can't use an undefined value as a HASH reference at /home/nemo/miniconda3/envs/bio/bin/import_expression_and_DE_results.pl line 379, <$fh> line 1. Issuing rollback() due to DESTROY without explicit disconnect() of DBD::SQLite::db handle Trinotate_cvel.sqlite at /home/nemo/miniconda3/envs/bio/bin/import_expression_and_DE_results.pl line 379.

. How to resolve it? Regards

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abdo3a commented 5 years ago

Thanks Brian for the quick reply, as you mentioned it was something related to my sample data, i figure out what is the problem..i have tabs and spaces mixes samples file.. Thanks for the hint