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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Error Java not installed when using illumiprocessor #192

Closed Lostinthecodingsauce closed 3 years ago

Lostinthecodingsauce commented 4 years ago

Hi Brant,

I am having trouble getting illumiprocessor to run. I am encountering the error that "java does not appear to be installed", but I am using Java 8 and have updated illumiprocessor. I have been trying to use the work-arounds you posted here; https://github.com/faircloth-lab/phyluce/issues/100 but I cannot get illumiprocessor to update from 2.0.8 to version 2.0.9. I have tried getting it to run on both a cluster and my lab computer where someone has used the phyluce pipeline for a previous project and have received the same result. Do you have suggestions to force illumiprocessor to recognize java?

brantfaircloth commented 4 years ago

Have you tried conda update --force-reinstall illumiprocessor. That may get 2.0.9 for you. Also, is the correct version of java in your $PATH when you run illumiprocessor? Finally, you could try to create just an environment for illumiprocessor and see if that fixes the issue:

# create new environment
conda create -n illumiprocessor python=2.7 illumiprocessor
[does stuff]
conda activate illumiprocessor

# then run
illumiprocessor...

# exit this environment
conda deactivate
Lostinthecodingsauce commented 4 years ago

Thanks for your quick response! I think it is a problem with my $PATH, I just looked and its using Java 1.0. Thanks so much for your help!

Ben

On Wed, May 20, 2020 at 9:59 AM Brant Faircloth notifications@github.com wrote:

Have you tried conda update --force-reinstall illumiprocessor. That may get 2.0.9 for you. Also, is the correct version of java in your $PATH when you run illumiprocessor? Finally, you could try to create just an environment for illumiprocessor and see if that fixes the issue:

create new environment

conda create -n illumiprocessor python=2.7 illumiprocessor [does stuff] conda activate illumiprocessor

then run

illumiprocessor...

exit this environment

conda deactivate

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/faircloth-lab/phyluce/issues/192#issuecomment-631600956, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOMO2LMLK7GQQ3TAEOXZN3RSQD57ANCNFSM4NGD5KNQ .

--

Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University

brantfaircloth commented 4 years ago

No problem. It may be that your conda setup isn't quite correct... if activated correctly, it should modify your path so that the conda binaries come before anything else. You can re-run that with:

source <path to conda>/bin/activate
conda init
Lostinthecodingsauce commented 4 years ago

Hi Brant,

It seems that I am using the correct version on Java, illumiprocessor (2.0.9), I set up a brand new conda environment (test_illumi), and I am using the most up todate version of trimmomatic. Everything is in the correct $PATH, but I am now getting the permission denied error. Do you have any ideas?

Traceback (most recent call last):

File "/Users/kburns/anaconda3/envs/test_illumi/bin/illumiprocessor", line 17, in 

sys.exit(main())

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/site-packages/illumiprocessor/cli/main.py", line 121, in main

main(args)

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/site-packages/illumiprocessor/main.py", line 22, in main

core.check_dependencies(args)

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/site-packages/illumiprocessor/core.py", line 241, in check_dependencies

java.test_trimmomatic(args.trimmomatic)

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/site-packages/illumiprocessor/core.py", line 229, in test_trimmomatic

stderr=subprocess.PIPE

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/subprocess.py", line 394, in init

errread, errwrite)

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/subprocess.py", line 1047, in _execute_child

raise child_exception

OSError: [Errno 13] Permission denied

On Wed, May 20, 2020 at 10:32 AM Brant Faircloth notifications@github.com wrote:

No problem. It may be that your conda setup isn't quite correct... if activated correctly, it should modify your path so that the conda binaries come before anything else. You can re-run that with:

source /bin/activate conda init

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/faircloth-lab/phyluce/issues/192#issuecomment-631618547, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOMO2OUV37HEZYEAYRIFFLRSQHZLANCNFSM4NGD5KNQ .

--

Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University

brantfaircloth commented 4 years ago

Looks like something is off with permissions on your installation (somehow). can you just run trimmomatic? If you get a permissions error there, it may be because trimmomatic is not executable - so you'd need to:

# input correct path to wherever trimmomatic is
chmod 0755 /path/to/conda/bin/trimmomatic

PS: also be sure that the correct conda env is activated - that could also cause a problem.

Lostinthecodingsauce commented 4 years ago

Hi Brant,

Sorry for not replying, I needed a break and was camping for the past few days. I have tried your recommendations but am still having the same issue. Do you have any recommendations for my code? illumiprocessor \ --input Users/kburns/Ben_Card_UCEs/RawReads \ --output Users/kburns/Ben_Card_UCEs/Cleanreads \ --config Users/kburns/Ben_Card_UCEs/illumi.Card.conf \ --cores 12 \ --trimmomatic ~anaconda3/envs/test_illumi/share/trimmomatic-0.39-1/trimmomatic.jar ## Run in test_illumi environment, I have made sure everything is executable using chmod 0775 )

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/subprocess.py", line 1047, in _execute_child

raise child_exception

OSError: [Errno 2] No such file or directory

(test_illumi) bash-3.2$ I have also tried using; --trimmomatic ~anaconda3/envs/phyluce/jar/trimmomatic.jar # experiences java not install error, run in phyluce environment. I cant get illumiprocessor to update to 2.0.9 in this environment. I have used force-install, uninstalled, and reinstalled. The only way I am able to get to version 2.0.9 of illumiprocessor is in test_illumi

On Wed, May 20, 2020 at 1:45 PM Brant Faircloth notifications@github.com wrote:

Looks like something is off with permissions on your installation (somehow). can you just run trimmomatic? If you get a permissions error there, it may be because trimmomatic is not executable - so you'd need to:

input correct path to wherever trimmomatic is

chmod 0755 /path/to/conda/bin/trimmomatic

PS: also be sure that the correct conda env is activated - that could also cause a problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/faircloth-lab/phyluce/issues/192#issuecomment-631716554, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOMO2NMNYLASNEOQ6NH2OTRSQ6NXANCNFSM4NGD5KNQ .

--

Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University

Lostinthecodingsauce commented 4 years ago

Hi Brant,

I was able to get it run properly once I switched over to miniconda. Thank you for your help,

Ben

On Sat, May 23, 2020 at 4:22 PM Ben Scott bfscott1906@gmail.com wrote:

Hi Brant,

Sorry for not replying, I needed a break and was camping for the past few days. I have tried your recommendations but am still having the same issue. Do you have any recommendations for my code? illumiprocessor \ --input Users/kburns/Ben_Card_UCEs/RawReads \ --output Users/kburns/Ben_Card_UCEs/Cleanreads \ --config Users/kburns/Ben_Card_UCEs/illumi.Card.conf \ --cores 12 \ --trimmomatic ~anaconda3/envs/test_illumi/share/trimmomatic-0.39-1/trimmomatic.jar ## Run in test_illumi environment, I have made sure everything is executable using chmod 0775 )

File "/Users/kburns/anaconda3/envs/test_illumi/lib/python2.7/subprocess.py", line 1047, in _execute_child

raise child_exception

OSError: [Errno 2] No such file or directory

(test_illumi) bash-3.2$ I have also tried using; --trimmomatic ~anaconda3/envs/phyluce/jar/trimmomatic.jar # experiences java not install error, run in phyluce environment. I cant get illumiprocessor to update to 2.0.9 in this environment. I have used force-install, uninstalled, and reinstalled. The only way I am able to get to version 2.0.9 of illumiprocessor is in test_illumi

On Wed, May 20, 2020 at 1:45 PM Brant Faircloth notifications@github.com wrote:

Looks like something is off with permissions on your installation (somehow). can you just run trimmomatic? If you get a permissions error there, it may be because trimmomatic is not executable - so you'd need to:

input correct path to wherever trimmomatic is

chmod 0755 /path/to/conda/bin/trimmomatic

PS: also be sure that the correct conda env is activated - that could also cause a problem.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/faircloth-lab/phyluce/issues/192#issuecomment-631716554, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALOMO2NMNYLASNEOQ6NH2OTRSQ6NXANCNFSM4NGD5KNQ .

--

Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University

--

Benjamin Scott Graduate Student/Teaching Assistant M.S. Evolutionary Biology student San Diego State University