filter-bias test results in error

[JohnHadish]

When performing the filter-bias test, the following error happens:

This script uses KINC.R, a companion R library for KINC
https://github.com/SystemsGenetics/KINC.R
-------------------------------------------------------
Loading the expression matrix file...
Filtering the network for biased edges...
  Num threads: max allowed - 2
  GCE Welch's Anova test threshold: 0.001
  Missigness T-test threshold: 0.1
  Output file prefix: GEM-DAP-1-14_vs_Bartlett-v2_expression_matrix.-log-no-PAF.th0.0-p1e-06-rsqr0.30-gcn.tidy_qualitative
  Network Size: 11205067
  Chunk Size: 1e+06
  Number of chunks: 12

Working on chunk: 1. Edges 1 to 999999
  |++++++++++++++++++++++++++++++++++++++++++++++++++|  99%Error in checkForRemoteErrors(val) : 
  one node produced an error: not enough observations
Calls: filterBiasedEdges ... clusterApply -> staticClusterApply -> checkForRemoteErrors

SBATCH used:

#!/bin/sh
#SBATCH --partition=ficklin
#SBATCH --account=ficklin
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=20
#SBATCH --time=7-00:00:00
#SBATCH --job-name=08-filter-bias_qualitative
#SBATCH --output=logs/%x.log
#SBATCH --mail-type=ALL

module load gcc/7.3.0 openmpi/4.0.0 cuda/9.1.85 qt/5.10.1  blas/3.8.0 \
            gsl/2.4  statsLib/20190625 gcem/20190625 lapack/3.8.0 \
            ACE/3.2.0 openblas/0.3.0 KINC/3.4.1 R/3.6.1

kinc-filter-bias.R \
    --threads 40 \
    --net "GEM-DAP-1-14_vs_Bartlett-v2_expression_matrix.-log-no-PAF.th0.0-p1e-06-rsqr0.30-gcn.tidy_qualitative.txt" \
    --emx "/scidas/John/04-D.AnjouPear_TreeLocation/01-input_data/04-GEM-DAP-1-14_vs_Bartlett-v2_expression_matrix.txt.log-no.txt" \
    --out_prefix "GEM-DAP-1-14_vs_Bartlett-v2_expression_matrix.-log-no-PAF.th0.0-p1e-06-rsqr0.30-gcn.tidy_qualitative"

An improved error message would be useful for diagnosing this problem.

[JohnHadish]

This appears to be an issue with the network which was input. I fixed this by modifying the input file and re-running the script.

[spficklin]

@JohnHadish what was the issue?

[JohnHadish]

I believe that it was an issue with the input GEM containing additional information at the end of the file. After identifying this issue, I re-ran and the problem no longer happened.