Running DE module with unknowingly incorrectly named table file
I have pre-normalized data and want to start my analysis at the DE miRNA module. I created my own table of read counts as shown in the documentation.
The module ran "successfully" but no output was generated. After digging through the code a bit, I found that the module is looking for a specific file name: $projectdir.$output_dir.$name.".tab
However this naming convention isn't mentioned in the documentation, and I originally named my tabular file something else. I believe the correct behaviour should be for the module to fail if the expected file does not exist (preferably with a statement about the naming convention), and not exit successfully.
Script output shown below and config file used is attached.
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miARma, miRNA and RNASeq Multiprocess Analysis
miARma v 1.5 (Apr-2016)
Created at Computational Biology and Bioinformatics Group (CbBio)
Institute of Biomedicine of Seville. IBIS (Spain)
Copyright (c) 2016 IBIS. All rights reserved.
mail : miARma-devel@cbbio.es
[Mon Sep 5 19:13:22 2016] Starting a miARma analysis for miRNA [Mon Sep 5 19:13:22 2016] Checking provided parameters for: DEAnalysis. [Mon Sep 5 19:13:22 2016] Checking General-output_dir parameter ... Exists! [Mon Sep 5 19:13:22 2016] The folder specified in (output_dir=/cluster3_dea/results/) already exists. [Mon Sep 5 19:13:22 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0 [Mon Sep 5 19:13:28 2016] Continue. [Mon Sep 5 19:13:28 2016] All parameters are correct. [Mon Sep 5 19:13:28 2016] Starting a differential expression analysis using edger software(s) [Mon Sep 5 19:13:28 2016] Differential expression analysis finished. [Mon Sep 5 19:13:28 2016] miARma finished. Job took 0 minutes miARma@Ubuntu:~/miARma$
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#60was marked as a duplicate of this issue. -
Dear Emilie, Did my answer helped you?
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reporter Yes it did, thank you!
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Dear Emilie, Thank you for using miARma.
If you want to start miARma in a different step from the beginning, then you need to make some changes. miARma for the DEAnalysis module reads from a folder called Readcount_results. So you have to create this folder inside your output_dir value . Then I recomend you to rename you file to: cut_bw1-ReadCount.tab.
Summary : save you file as : /cluster3_dea/results/Readcount_results/cut_bw1-ReadCount.tab
I hope that helps
Regards