Its not running the analysis. I think there is something wrong with my samples file, but I used it fine to compare replicates with PtR. what is the samples versus data fields? My script:

/trinityrnaseq-v2.8.6/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix Trinity_kallisto.isoform.counts.matrix  --method edgeR --samples_file samples16_ed.txt

This is my samples file in tab delimited text:

APO kallisto_APO1_LO
APO kallisto_APO2_LO
APO kallisto_APO3_LO
ANG_LO  kallisto_Es1ANG 
ANG_LO  kallisto_Es2ANG
ANG_LO  kallisto_Es2LO
ANG_LO  kallisto_Es3ANG
ANG_LO  kallisto_Es3LO
ANG_LO  kallisto_WT_LO1
ANG_LO  kallisto_WT_LO3
ANG_LO  kallisto_WT_LO2
ANG_LO  kallisto_E16ANG
ANG_LO  kallisto_K3ANG
ANG_LO  kallisto_J1ANG
ANG_LO  kallisto_J8ANG
ANG_LO  kallisto_K7ANG

My output is:

Got 16 samples, and got: 17 data fields.
Header: kallisto_APO1_LO    kallisto_APO2_LO    kallisto_APO3_LO    kallisto_Es1ANG kallisto_Es2ANG kallisto_Es3ANG kallisto_K7ANG  kallisto_K3ANG  kallisto_J8ANG  kallisto_J1ANG  kallisto_E16ANG kallisto_WT_LO3 kallisto_WT_LO2 kallisto_WT_LO1 kallisto_Es3LO  kallisto_Es2LO
Next: TRINITY_GG_2139_c0_g1_i1  1   0   0   0   0   0   6   0   0   0   0   0   0   0

$VAR1 = {
          'kallisto_Es3LO' => 15,
          'kallisto_J8ANG' => 9,
          'kallisto_APO1_LO' => 1,
          'kallisto_WT_LO3' => 12,
          'kallisto_Es2LO' => 16,
          'kallisto_E16ANG' => 11,
          'kallisto_WT_LO2' => 13,
          'kallisto_K7ANG' => 7,
          'kallisto_K3ANG' => 8,
          'kallisto_Es1ANG' => 4,
          'kallisto_Es3ANG' => 6,
          'kallisto_WT_LO1' => 14,
          'kallisto_Es2ANG' => 5,
          'kallisto_APO3_LO' => 3,
          'kallisto_J1ANG' => 10,
          'kallisto_APO2_LO' => 2
        };
$VAR1 = {
          'APO' => [
                     'kallisto_APO1_LO'
                   ]
        };
Contrasts to perform are: $VAR1 = [];

It stops there and creates a folder with nothing. There is no "Error". All the R packages are installed and working.

When I include a contrasts file, I get the following Error:

Can't use an undefined value as an ARRAY reference at /isg/shared/apps/trinity/2.8.5/Analysis/DifferentialExpression/run_DE_analysis.pl line 568.