debugging "Error: Error during trajectory inference"
Opened this issue · 5 comments
I'm having trouble running dynwrap::infer_trajectory() on my data.
My installation seems to be okay, the methods work fine on the toy data.
However, on my data (and verbose=TRUE), I get a lot of package loading messages and:
1. dynwrap::infer_trajectory(dataset, method = ti_monocle_ddrtree(reduction_method = "DDRTree",
. max_components = 5, norm_method = "log", filter_features_mean_expression = 0.1),
. verbose = TRUE)
2. stop("Error during trajectory inference \n", crayon::bold(error),
. call. = FALSE)
As my data was running as expected through Monocle in the past, I followed
https://github.com/dynverse/ti_monocle_ddrtree/blob/master/run.R
line by line, and everything runs up to line 79.
Do you have any tips on how I can debug this? (I tried several other ti_ methods as well, with similar results)
Thanks for this really cool package!
Hi @celinesin
Sorry for the late reply, I was on holidays.
Do you get the same type of error with other TI methods? It's a bit bizarre that verbose=TRUE
does not produce an error.
This might also be a running out of memory issue. Does the memory usage spike when running the method?
Hi @zouter,
Thanks for your reply! I get the same error with ti_slice(), ti_monocle_ddrtree(), and ti_comp1(). Ah, running out of memory could be the culprit, since it's inside the Docker? How can I check this?
Thanks again!
Celine
Hello!
Just an update, in case someone else runs into the same problem. I'm using MacOS Mojave.
First, to check if i was running out of memory:
- launch console.app, search for "docker" and in the dropdown menu choose "Process"
- look for events such as "oom_kill_process" and "out_of_memory"
(if you haven't run your script in the last 24 hours, run it first)
To increase the memory, I followed this:
https://stackoverflow.com/questions/44533319/how-to-assign-more-memory-to-docker-container
Now, I have a new error to follow :)
27366555: RECEIVED OUT-OF-SEQUENCE NOTIFICATION: 857 vs 1560, 512, <private>
Failed to forward unexpected ICMP datagram with type 5
OK, another update:
I don't know what the above error is about, but by restarting everything, it fixed itself.
I now have a new error:
Error in igraph::as_data_frame(gr, "edges") : Not a graph object
Calls: %>% -> eval -> eval -> <Anonymous>
Hey Celine! Is there no more output than this, even when verbose is TRUE? Could you provide a minimum reproducible example?
This reminds me of a problem that I thought I had fixed a long time ago.. I will try to remember what it was again.