differential expression analysis, trinity error
1
0
Entering edit mode
6.5 years ago

Hello,

Im trying to generate a heat map in trinity of differentially expressed transcripts. However, when I run this command, I get back an error. Any thoughts on how to fix this? Thank you, Nikelle

[npetrill@trogdor DifferentialExpression]$  perl run_DE_analysis.pl --matrix /home/npetrill/aligning/final/countmatrix/matrix.counts.matrix --method edgeR --output edger_trans
Got 36 samples, and got: 37 data fields.
Header: 22  29  34  39  42  49  60  6   13  18  1   33  46  57  59  5   62  116 20  26  31  54  14a 23  25  54a 58  6a  9   19  28  33a 4   54b 8
Next: TR214882|c0_g1    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    1.00    1.00    0.00    1.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00

$VAR1 = {
          '33' => 12,
          '26' => 21,
          '1' => 11,
          '18' => 10,
          '16' => 19,
          '25' => 26,
          '28' => 32,
          '54a' => 27,
          '57' => 14,
          '20' => 20,
          '14' => 18,
          '59' => 15,
          '49' => 6,
          '54b' => 35,
          '31' => 22,
          '33a' => 33,
          '42' => 5,
          '22' => 1,
          '46' => 13,
          '13' => 9,
          '23' => 25,
          '29' => 2,
          '6' => 8,
          '39' => 4,
          '14a' => 24,
          '9' => 30,
          '58' => 28,
          '8' => 36,
          '4' => 34,
          '60' => 7,
          '34' => 3,
          '6a' => 29,
          '19' => 31,
          '62' => 17,
          '5' => 16,
          '54' => 23
        };
$VAR1 = {
          '33' => [
                    '33'
                  ],
          '26' => [
                    '26'
                  ],
          '1' => [
                   '1'
                 ],
          '18' => [
                    '18'
                  ],
          '16' => [
                    '16'
                  ],
          '25' => [
                    '25'
                  ],
          '28' => [
                    '28'
                  ],
          '54a' => [
                     '54a'
                   ],
          '57' => [
                    '57'
                  ],
          '20' => [
                    '20'
                  ],
          '14' => [
                    '14'
                  ],
          '59' => [
                    '59'
                  ],
          '49' => [
                    '49'
                  ],
          '54b' => [
                     '54b'
                   ],
          '31' => [
                    '31'
                  ],
          '33a' => [
                     '33a'
                   ],
          '42' => [
                    '42'
                  ],
          '22' => [
                    '22'
                  ],
          '46' => [
                    '46'
                  ],
          '13' => [
                    '13'
                  ],
          '23' => [
                    '23'
                  ],
          '29' => [
                    '29'
                  ],
          '6' => [
                   '6'
                 ],
          '39' => [
                    '39'
                  ],
          '14a' => [
                     '14a'
                   ],
          '9' => [
                   '9'
                 ],
          '58' => [
                    '58'
                  ],
          '8' => [
                   '8'
                 ],
          '4' => [
                   '4'
                 ],
          '60' => [
                    '60'
                  ],
          '34' => [
                    '34'
                  ],
          '6a' => [
                    '6a'
                  ],
          '19' => [
                    '19'
                  ],
          '62' => [
                    '62'
                  ],
          '5' => [
                   '5'
                 ],
          '54' => [
                    '54'
                  ]
        };
Error, cannot mkdir edger_trans at run_DE_analysis.pl line 185.
DE RNA RNA-Seq trinity • 1.5k views
ADD COMMENT
1
Entering edit mode
6.5 years ago

Does the edger_trans directory already exist? If so, what happens if you delete it and then rerun the analysis?

Are you even allowed to write in the directory you're trying to create edger_trans?

ADD COMMENT
0
Entering edit mode

Hi Philipp,

Thanks for your reply, I am having a hard time figuring out where my edger_trans directory would exist. Do you know where I could find this? Thanks so much for your help, Nikelle

ADD REPLY
0
Entering edit mode

You seem to run your analysis in the DifferentialExpression folder, is that correct? Is there an edger_trans directory in there?

When you set the output directory you give it a "relative" path only: --output edger_trans, you don't give it an "absolute" path which would be something like /home/npetrill/DifferentialExpression/edger_trans

When you use a relative path then the system will add the current path to the front of it, so by giving --output edger_trans the system will put the directory "where you currently are" in front of that

ADD REPLY
0
Entering edit mode

Thank you, I understand now. However, I do not have an edger_trans directory in my DifferentialExpression directory. However, I created a new directory and added that to my absolute path, seems to be working now! Thanks for the help!

ADD REPLY
0
Entering edit mode

glad to hear it's fixed!

ADD REPLY

Login before adding your answer.

Traffic: 1540 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6