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barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
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no output.html file #339

Closed SoGUILL closed 1 year ago

SoGUILL commented 1 year ago

Hello, I have installed Breseq on my mac to do polymorphism analysis. Everything seems to work fine. But I don't have the output.html file. I only have the independent files for each observed modification. How can I get this output.html file ? Thank you for your help!

jeffreybarrick commented 1 year ago

If you have no output.html then there was an error near the end of the run. Check the output to the terminal or a log file if you are running it on a cluster. Most likely there is something missing with your install of R that prevents it from being able to generate plots. It's also possible your computer ran out of hard drive space in the middle of the run. Let us know that the error is and also details about how you installed breseq and R.

SoGUILL commented 1 year ago

Thank you for your feedback. There is no mention of an execution error. The log file is empty (there is just the execution command). I have all the html files independently. I just need to compile these files into an output.html file. I installed Breseq via Conda : "conda install breseq". I have a Mac book Pro macOS Monterey version 12.5. The version of R is R4.2.2 GUI 1.79 Big on ARM build (R-4.2.2-arm64.pkg). Thank for your help

jeffreybarrick commented 1 year ago

There should be some output to the terminal when you run breseq. That would have been where the error showed up. Can you check for that, or run the same command in the same directory and share the terminal output?

SoGUILL commented 1 year ago

Hello, I have a message that appears at the end of the execution at each of my attempts that I had not seen. zsh: killed breseq -r GCF_000756125.1_ASM75612v1_genomic.gbk BP125_S36_R1_001.fastq -p So the program stops before the end. In the output folder, I have log.txt, output.gd, output.vcf and summary.json files + calibration and evidence folders. I also get this message when I test your dataset (SRR030257). Is there a memory problem? I have a fairly powerful Mac with 32GB of memory / 1TB of flash storage (700GB available). Thanks a lot

evolvomics commented 1 year ago

That's odd. It is an error that usually occurs when resources are running out, but that shouldn't be the case. I see some reports that this kind of thing can happen after MacOS updates on M1 macs, and that the solution is to re-install conda. Maybe that will work?

https://github.com/tensorflow/tensorboard/issues/5658