nmquijada
commented
4 years ago Dear @m-ocejo Really thanks for your words, I am glad you like the software. Thank you also for openning different threads for your issues, it will be easier to focus in each problem and also it is more helpful for other users with the sames issues. I looked into the attached file. The error is not related to the final report, as the code there is OK. However, the report found problems by trying to show some of your data. If you correct (or change) the files that are giving errors by files with the proper data, and you re-run the report generation (https://github.com/nmquijada/tormes#rendering-customized-reports) you will get the appropiate report. If you see, your "fimH_typing" file is empty, and so they are all the PointFinder results. No pangenome outputs are available neither... Are fymtyper, pointfinder and roary software properly working in your environment? If you need some code for making them run, please let me know and I'll share it. I see in https://github.com/nmquijada/tormes/issues/13 that you were able to correct the problem with kraken. It's the first time I got a report with that issue, so I'll work on that... If you add the correct kraken information to your "sequencing_assembly_report.txt" file, and you re-run the report generation, you will get it in the report. The problem with the "Antibiotic resistance genes (ResFinder) count" is the same that was reported in https://github.com/nmquijada/tormes/issues/2 , and it's a bug in the code that I think I solved in the new version (will be released soon). Please find attached your corrected "resfinder_gene_per_isolate.txt" file that you can use for your new report.
resfinder_gene_per_isolate.txt
Could you please also tell me which system are you using? We will make it run :) Best, Narciso
Dear Narciso, first of all, congratulations and a big thank you for developing this useful and handy pipeline. We have run the pipeline with several strains of E. coli (using the default settings, with no reference genome and option --genera Escherichia) but unfortunately we encountered several issues. To maintain one thread conversation for each query, I am going to create one issue for each question.
In Antibiotic resistance genes (ResFinder) count and Point mutations, we concluded that the error might be in the generation of the final report, as each tool seem to have worked well because individual expected results were generated. To correct this, we attempted to edit the Rmd (approx 3000 lines in R generated) as suggested in issue #2 however we have over 40 samples and find it a bit unreasonable to edit the lines for each samples. Perhaps you can suggest a more practical solution for this?
Please find attached these report files in the case you need them:
report_files.zip
Thanks in advance!