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Error: sort(unique(c(cell_graph$from, cell_graph$to))) not equal to sort(names(to_keep)). Lengths differ: 119 is not 925 #4

Open pablommesas opened 5 years ago

pablommesas commented 5 years ago

When executing ti_monocle_ddrtree on

"dynbenchmark/derived/01-datasets/synthetic/dyngen/1/dataset.rds"

with:

## Compute Inferred Trajectory
trajectory <- wrap_expression(expression = dataset$expression, counts = dataset$counts) %>%
    add_prior_information(start_id = dataset$prior_information$start_id) %>%
    infer_trajectory(method="monocle_ddrtree", verbose = TRUE)
Executing 'monocle_ddrtree' on '20190708_123129__data_wrapper__QXj4M36onD'
With parameters: list(reduction_method = "DDRTree", max_components = 2L, norm_method = "log",     auto_param_selection = TRUE, filter_features = TRUE, filter_features_mean_expression = 0.1),
inputs: counts, and
priors : 
Input saved to /tmp/RtmpMCKufO/file355e3556b4f7/ti
Running method using babelwhale
Running /usr/bin/docker run -e 'TMPDIR=/tmp2' --workdir /ti/workspace -v '/tmp/RtmpMCKufO/file355e3556b4f7/ti:/ti' -v '/tmp/RtmpMCKufO/file355e1dfd32e8/tmp:/tmp2' \
  'dynverse/ti_monocle_ddrtree:v0.9.9.02' --dataset /ti/input.h5 --output /ti/output.h5

I got the following error 

Error: sort(unique(c(cell_graph$from, cell_graph$to))) not equal to sort(names(to_keep)).
Lengths differ: 119 is not 925
Execution halted

Thanks for your help!

pablommesas commented 5 years ago

I'm getting a similar error for some of the real data sets too. Do you have any idea what might be causing this?

Gold - Monocle Fails - Total number - 5

DATASET_NAMES_GOLD_MONOCLE_FAIL = ['aging-hsc-old_kowalczyk', 'germline-human-female-weeks_li', 'germline-human-male-weeks_li', 'pancreatic-beta-cell-maturation_zhang', 'stimulated-dendritic-cells-LPS_shalek']

Monocle Fails - Total number - 8

DATASET_NAMES_SILVER_MONOCLE_FAIL = ['embryonic-mesenchyme-stromal-cell-cxcl14-cxcl12-axis_mca', 'epidermis-hair-spatial_joost', 'germline-human-female_li', 'germline-human-male_li', 'hepatoblast-differentiation_yang', 'kidney-distal-convoluted-tubule_mca', 'mammary-gland-involution-endothelial-cell-aqp1-gradient_mca', 'planaria-phagocyte-differentiation_plass']

Thanks again!

andynkili commented 2 years ago

Hi all,

I am also having the same issue. Did anyone get a hint on a fix?

Best, Andy

bvaldebenitom commented 1 year ago

Hi @pablommesas and @andynkili ,

Just writing to report that this error stil occurs, and occurs regardless of the input dataset. It looks like it is not properly using the input object.

erzakiev commented 1 year ago

+1 also happened to me, after 2+ hours of computations on 24k cells