rafinhacp
commented
3 years ago Ah, solved!
I found the same error here https://sourceforge.net/p/trinotate/mailman/trinotate-users/?viewmonth=201312 (you have to dig a bit, there are a bunch of messages here referring to different errors/issues)
The samples_file had a few spaces in it, instead of being separated by tab...thus the error!
Hello all!
I'm have been using Trinotate Web in my projects, but this time I ran into an error that I'm not being able to figure it out. Any help is welcome!
I followed the order of uploads present in the Trinotate web page, but when I tried to upload the isoform information using the following command: /Users/rafaelaperez/Trinotate-Trinotate-v3.2.1/util/transcript_expression/import_expression_and_DE_results.pl \ --sqlite Trinotate.sqlite \ --samples_file RMCassembly.txt \ --count_matrix RSEM-RMC3.isoform.counts.matrix \ --fpkm_matrix RSEM-RMC3.isoform.TMM.EXPR.matrix \ --DE_dir RMC-voom-isoform-diff/ \ --transcript_mode > load_diffexpiso.txt 2>&1
I ran into this issue: Samples and replicates: $VAR1 = {}; Sample and replicate database identifiers: $VAR1 = {}; -parsing counts matrix: RSEM-RMC3.isoform.counts.matrix Can't use an undefined value as a HASH reference at /Users/rafaelaperez/Trinotate-Trinotate-v3.2.1/util/transcript_expression/import_expression_and_DE_results.pl line 379, <$fh> line 1. Issuing rollback() due to DESTROY without explicit disconnect() of DBD::SQLite::db handle Trinotate.sqlite at /Users/rafaelaperez/Trinotate-Trinotate-v3.2.1/util/transcript_expression/import_expression_and_DE_results.pl line 379.
Does anyone knows how to fix it? I'm populating the database using my personal computer, a Macbook, so unix is the OS. I've done it before with a smaller dataset from another project and everything went fine...I don't know why I'm getting this issue now.
Thank you for your attention and help!