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nmquijada / tormes

Making whole bacterial genome sequencing data analysis easy
GNU General Public License v3.0
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WARNING: html report file could not be created #35

Closed valery-shap closed 3 years ago

valery-shap commented 3 years ago

Hello, Narciso,

I have reads that I've filtered all 16s before and run tormes with these filtered reads. And seems that tormes couldn't create report file because 16S-rRNA folder Fasta files are empty. I'm not sure of this) Could it be so? I attached .err file.

Best regards, Valery 87565_filt copy_err.txt

nmquijada commented 3 years ago

Hi Valery,

It looks very much that that was the problem, yes. The generation of the report relies in the tormes_report.Rmd file, that is stored in the report_files directory and that it is able for user manipulation. We can make R to "ignore" this problem and keep rendering the report by just throwing a "warning". For doing so:

  1. uncompress the report_files directory: tar xzf report_files.tgz and cd report_files
  2. open the tormes_report.Rmd file in your favorite text editor.
  3. in the line 221 you will find: ```{r, echo=FALSE}
  4. change it to: ```{r, echo=FALSE, error=TRUE}
  5. save the document and re-run the tormes-report generation: ./render_report.sh

This script will use the information contained in the "new" tormes_report.Rmd file for the generation of your report.

Please try it out and let me know if it works. If you find troubles modifying the tormes_report.Rmd file, you can also share it with me.

All the best, Narciso

nmquijada commented 3 years ago

Hi Valery,

We just released the new version of TORMES (v1.3.0). This issue is solved in this newer version. Therefore, please consider updating to TORMES v.1.3.0.

Best, Narciso

valery-shap commented 3 years ago

Hello, Narciso,

Thank you very much! I'm still an active user of TORMES, but I've updated all databases.

Best regards, Valery