search

jaleesr / TrendCatcher

TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255
9 stars 3 forks source link

"Error reading from connection" #11

Closed PetrosRoth closed 5 months ago

PetrosRoth commented 5 months ago

Hi,

I am working on the analysis of a time-course RNA-seq in wheat and I would love to apply your package to identify expression patterns over time.

While trying to run TrendCatcher, the job is aborted and I got this error message:

"Read count table. Passed Format Check. Count table is 24 Samples, 63351 Genes Found 1352 low count genes. Count table format correct, finished loading. gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates Run TrendCatcher. |======== | 5%Error in unserialize(socklist[[n]]) : error reading from connection Timing stopped at: 2.41 0.33 82.64"

Note that preprocess_TrendCatcher works without any problem. Could it be due to resource limitations (CPU, RAM)?

When I ran the demo it also worked without any issue.

Any thoughts on that?

wangxinge commented 5 months ago

Hi @PetrosRoth, thanks for using TrendCatcher! The error looks like coming from your PC limitation. By default, TrendCatcher will detect your CPUs to run jobs parallel. You can try to set rebose to TRUE, so it will use only 1 CPU to run the job, it will be slow though.