I tried to re-run a DESeq2 using settings that previously worked and also ran annotateMyID on an expression file with Entrez ID. Both runs gave me similar “Error in file(file, “rt”) : cannot open the connection”
Specifically for DESeq2
“Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in file(file, “rt”) : cannot open the connection
Calls: get_deseq_dataset → lapply → lapply → FUN → read.table → file
Warning message:
In file(file, “rt”) :
cannot open file ‘/galaxy-repl/main/files/057/262/dataset_57262771.dat’: No such file or directory”
And for annotateMyID:
“Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in file(file, “rt”) : cannot open the connection
Calls: read.table → file
Warning message:
In file(file, “rt”) :
cannot open file ‘/galaxy-repl/main/files/059/601/dataset_59601606.dat’: No such file or directory”
This part of the error, and your description, appears to be related to a problem that impacted a few others a short time ago today.
Message from our admin @nate at about those types of errors.
This error was caused by an accidental deployment of an incorrect Galaxy configuration file that has now been fixed. Please try running the job again and let us know if you’re still encountering issues.
Please try the rerun and thanks for reporting the problem!
For others reading, if a job failed today, please try at least one rerun now to eliminate this same configuration issue as a contributing factor. The error message can vary but usually involves some file not found by the tool during processing. If that rerun job fails again, and you cannot sort out why, then the problem is likely inputs and/or parameter issues. Review/search prior Q&A, GTN tutorials, and ask new questions as needed (in new topics, not as replies to this topic please).