Trinity assembly Error

Question

[iamtuttu5]

Hello everyone

I was trying to run trinity tool

I tried this command for assembly

perl Trinity \
  --seqType fq \
  --single /home/tuttu/ngs/trinityrnaseq-2.1.1/011.fq \
  --CPU 4 \
  --max_memory 10G \
  --output /home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_data

It outputs the following error

tuttu@kau:~/ngs/trinityrnaseq-2.1.1$ perl Trinity --seqType fq --single /home/tuttuu/ngs/trinityrnaseq-2.1.1/011.fq --CPU 4 --max_memory 10G --output /home/jinu/ngs/trinityrnaseq-2.1.1/trinity_output_data
Trinity version: v2.1.1
-currently using the latest production release of Trinity.

Thursday, November 26, 2015: 17:22:25   CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/tuttu/ngs/trinityrnaseq-2.1.1/util/support_scripts/ExitTester.jar 0
Thursday, November 26, 2015: 17:22:25   CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/tuttu/ngs/trinityrnaseq-2.1.1/util/support_scripts/ExitTester.jar 1
Thursday, November 26, 2015: 17:22:26   CMD: mkdir -p /home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_data
mkdir: cannot create directory '/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_data': Permission denied
Error, cmd: mkdir -p /home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_data died with ret 256 at Trinity line 2183.

Thank you

[iamtuttu5]

I don't know whether it is right or wrong when I give sudo before that command now its running .. I am new to linux , if I am doing anything wrong, please let me know , as I am working on my institute server system through SSH,

Thank you

[ka6AjxQY]

It's a permissions problem on the perl script. You shouldn't have to use sudo to run anything besides administration tasks. I'd recommend asking your system administrator to allow execution of this script by a group ID (gid) that you are a part of, else make it executable by all.

Answer 1

[JC]

Directory permission is your problem:

"mkdir: cannot create directory ‘/home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_data’: Permission denied"

Check permissions (ls -lh) where are you trying to create the directory and add them with "chmod +w dir"

[iamtuttu5]

ls -lh gives the following result

tuttu@kau~/ngs/trinityrnaseq-2.1.1$ ls -lh
total 6.6G
-rwxr-xr-x  1 root root 3.1G Nov 13 16:42 011.fq
-rwxr-xr-x  1 root root 3.4G Nov 13 16:46 012.fq
drwxrwxr-x  5 root root 4.0K Oct 15 17:37 Analysis
drwxrwxr-x  4 root root 4.0K Oct 15 17:37 Butterfly
drwxrwxr-x  9 root root 4.0K Nov 20 19:27 Chrysalis
drwxrwxr-x  3 root root 4.0K Oct 15 17:37 galaxy-plugin
drwxrwxr-x  3 root root 4.0K Oct 15 17:37 hpc_conf
drwxrwxr-x  4 root root 4.0K Nov 25 19:33 Inchworm
-rw-rw-r--  1 root root 1.5K Oct 15 17:37 LICENSE
-rw-rw-r--  1 root root 1.5K Oct 15 17:37 LICENSE.txt
-rw-rw-r--  1 root root 1.7K Oct 15 17:37 Makefile
-rw-rw-r--  1 root root  443 Oct 15 17:37 notes
drwxrwxr-x  7 root root 4.0K Oct 15 17:37 PerlLib
-rw-rw-r--  1 root root  105 Oct 15 17:37 README
-rw-rw-r--  1 root root   76 Oct 15 17:37 README.md
-rw-rw-r--  1 root root  51K Oct 15 17:37 Release.Notes
-rw-r--r--  1 root root  56M Sep 18  2014 rstudio-0.98.1062-amd64.deb
drwxrwxr-x 12 root root 4.0K Oct 15 17:37 sample_data
-rwxrwxr-x  1 root root 106K Oct 15 17:37 Trinity
drwxrwxr-x 13 root root 4.0K Nov 23 19:03 trinity-plugins
drwxrwxr-x  2 root root 4.0K Oct 15 17:37 trinityrnaseq.wiki
drwxrwxr-x  7 root root 4.0K Oct 15 17:37 util

[iamtuttu5]

I don't know whether it is right or wrong when I give sudo before that command now its running .. I am new to linux , if i am doing anything wrong , please let me know , as I am working on my institute server system through SSH,

now the command which is running is

sudo perl Trinity --seqType fq --single /home/tuttu/ngs/trinityrnaseq-2.1.1/011.fq --CPU 4 --max_memory 10G --output /home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_data

Thank you

[JC]

Actually using sudo to run a program that doesn't require admin level is wrong. Check commands chown and chgrp to change ownership of your directories and files.