[lupid]

I do this

sudo ln -nsf /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents sudo ln -nsf /Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK
ln: /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK: Not a directory
Admins-iMac-2:~ crg-user$ export JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home"
Admins-iMac-2:~ crg-user$ java -version
-bash: java: command not found
Admins-iMac-2:~ crg-user$

and nothing, but it's weird for me at least because, this

Admins-iMac-2:~ crg-user$ /usr/libexec/java_home -VMatching Java Virtual Machines (1): 1.7.0_75, x86_64: "Java SE 7" /Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home
Admins-iMac-2:~ crg-user$

[lupid]

Any guess of what to do?

[GenoMax]

What output does this command produce (I don't have a 10.7 machine handy to check but this works with newer OS X)?

$ mdfind "kMDItemDisplayName == java"

or if that does not work then what about this

$ /usr/libexec/java_home -V

[lupid]

I get this, sorry for the delay.

Admins-iMac-2:test_Trinity_Assembly crg-user$ mdfind "kMDItemDisplayName == java"
/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/jre/bin/java
/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/bin/java
/usr/local/bin/Contents/Home/jre/bin/java
/usr/local/bin/Contents/Home/bin/java
/usr/local/Cellar/app-engine-java-sdk/1.9.18/libexec/demos/shardedcounter/src/com/google/appengine/demos/shardedcounter/java
/Users/crg-user/Desktop/Tomas/R-2.12.1/share/java
/Library/Frameworks/R.framework/Versions/3.1/Resources/share/java
/System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java
/usr/share/java
/usr/share/file/magic/java
/usr/lib/java
Admins-iMac-2:test_Trinity_Assembly crg-user$ /usr/libexec/java_home -V
Matching Java Virtual Machines (1):
1.7.0_75, x86_64: "Java SE 7" /Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home
Admins-iMac-2:test_Trinity_Assembly crg-user$

[GenoMax]

It is odd that you still do not seem to have Java 8 installed though the screenshot yesterday seemed to indicate that.

Anyway, if you do this (based on the post I linked in #3):

$ export JAVA_HOME=`/usr/libexec/java_home -v 1.7.0_75`

Those are backtick symbols (not single quotes).

See if trinity works now.

[lupid]

no, it say the same

Admins-iMac-2:test_Trinity_Assembly crg-user$ export JAVA_HOME=`/usr/libexec/java_home -v 1.7.0_75`
Admins-iMac-2:test_Trinity_Assembly crg-user$ ./runMe.sh #!/bin/bash -ve


if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
gunzip -c reads.left.fq.gz > reads.left.fq
fi

if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
gunzip -c reads2.right.fq.gz > reads2.right.fq
fi

if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
gunzip -c reads2.left.fq.gz > reads2.left.fq
fi



#######################################################
## Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
Use of uninitialized value $java_version in pattern match (m//) at ../../Trinity line 818.



********************************************************************
** Warning, Trinity cannot determine which version of Java is being used. Version 1.7 is required.

Attempting to continue in 30 seconds
********************************************************************


Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Error, cannot find 'java'. Please be sure it is available within your ${PATH} setting and then try again. at ../../Trinity line 2193.
Admins-iMac-2:test_Trinity_Assembly crg-user$

[GenoMax]

Based on the error in the last post.

$ export PATH="/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/bin:$PATH"

[lupid]

that last work, thanks, nevertheless it say

Admins-iMac-2:trinityrnaseq-2.0.6 crg-user$ perl Trinity --seqType fq --left /Users/crg-user/Desktop/Tomas/Carpa/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R1_001_-N_-a_-q20.fastq --right /Users/crg-user/Desktop/Tomas/Carpa/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R2_001_-N_-a_-q20.fastq --CPU 1 --max_memory 3G --verbose
Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Paired mode requires bowtie. Found bowtie at: /usr/local/bin/bowtie

and bowtie-build at /usr/local/bin/bowtie-build


Found samtools at: /usr/local/bin/samtools

-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
Thursday, April 16, 2015: 20:32:40 CMD: java -Xmx64m -jar /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
CMD finished (1 seconds)
Thursday, April 16, 2015: 20:32:41 CMD: java -Xmx64m -jar /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
-we properly captured the java failure status, as needed. Looking good.
Java tests succeeded.
###################################



----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------

----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

Thursday, April 16, 2015: 20:33:21 CMD: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 1 --PARALLEL_IWORM > /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp
bash: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm: cannot execute binary file
Error, cmd: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 1 --PARALLEL_IWORM > /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp died with ret 32256 at Trinity line 2116.



If it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.

Admins-iMac-2:trinityrnaseq-2.0.6 crg-user$

[GenoMax]

You need to add execute permissions to inchworm program.

$ chmod u+x /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm

If that does not work then do

$ sudo chmod u+x /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm

Other programs in the suite (chrysalis etc) may also need this modification.

[lupid]

And also don't work

Admins-iMac-2:trinityrnaseq-2.0.6 crg-user$ chmod u+x /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchwormAdmins-iMac-2:trinityrnaseq-2.0.6 crg-user$ perl Trinity --seqType fq --left /Users/crg-user/Desktop/Tomas/Carpa/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R1_001_-N_-a_-q20.fastq --right /Users/crg-user/Desktop/Tomas/Carpa/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R2_001_-N_-a_-q20.fastq --CPU 1 --max_memory 3G --verbose
Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Paired mode requires bowtie. Found bowtie at: /usr/local/bin/bowtie

and bowtie-build at /usr/local/bin/bowtie-build


Found samtools at: /usr/local/bin/samtools

-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
Friday, April 17, 2015: 16:22:18 CMD: java -Xmx64m -jar /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
CMD finished (0 seconds)
Friday, April 17, 2015: 16:22:18 CMD: java -Xmx64m -jar /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
-we properly captured the java failure status, as needed. Looking good.
Java tests succeeded.
###################################



----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------

----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

Friday, April 17, 2015: 16:22:54 CMD: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 1 --PARALLEL_IWORM > /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp
bash: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm: cannot execute binary file
Error, cmd: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 1 --PARALLEL_IWORM > /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp died with ret 32256 at Trinity line 2116.



If it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.

** The inchworm process failed.Admins-iMac-2:trinityrnaseq-2.0.6 crg-user$ sudo op/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm
Password:
Admins-iMac-2:trinityrnaseq-2.0.6 crg-user$ perl Trinity --seqType fq --left /Users/crg-user/Desktop/Tomas/Carpa/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R1_001_-N_-a_-q20.fastq --right /Users/crg-user/Desktop/Tomas/Carpa/c1/CarpaInviernoPool_S2_L001_R1.2_001/CarpaInviernoPool_S2_L001_R2_001_-N_-a_-q20.fastq --CPU 1 --max_memory 3G --verbose
Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Paired mode requires bowtie. Found bowtie at: /usr/local/bin/bowtie

and bowtie-build at /usr/local/bin/bowtie-build


Found samtools at: /usr/local/bin/samtools

-since butterfly will eventually be run, lets test for proper execution of java
#######################################
Running Java Tests
Friday, April 17, 2015: 16:23:17 CMD: java -Xmx64m -jar /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 0
CMD finished (1 seconds)
Friday, April 17, 2015: 16:23:18 CMD: java -Xmx64m -jar /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/util/support_scripts/ExitTester.jar 1
-we properly captured the java failure status, as needed. Looking good.
Java tests succeeded.
###################################



----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------

----------------------------------------------
--------------- Inchworm ---------------------
-- (Linear contig construction from k-mers) --
----------------------------------------------

Friday, April 17, 2015: 16:24:00 CMD: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 1 --PARALLEL_IWORM > /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp
bash: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm: cannot execute binary file
Error, cmd: /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1 --DS --keep_tmp_files --num_threads 1 --PARALLEL_IWORM > /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp died with ret 32256 at Trinity line 2116.



If it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set or run Trinity on a server with more memory available.

** The inchworm process failed.Admins-iMac-2:trinityrnaseq-2.0.6 crg-user$

[GenoMax]

It looks like you did not manage to change the permissions.

Post output of:

$ ls -l /Users/crg-user/Desktop/Tomas/trinityrnaseq-2.0.6/Inchworm/bin//inchworm