debugging "Error: Error during trajectory inference"

[celinesin]

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!

[zouter]

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?

[celinesin]

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

[celinesin]

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:

1. launch console.app, search for "docker" and in the dropdown menu choose "Process"
2. 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

[celinesin]

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>

[rcannood]

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.