[sklages]

/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45

Where have you put the new java? When you have put it into 'newbler2.9/java' as suggested, then the version used by your gsAssembler is not correct (wrong path).

You haven't changed the APP vars in the script, as you have shown in one of your posts?

Just go remove everything (in the unedited gsAssembler or a copy of that!) after:

# ---------------------------------------------------------------------
# Before you run the application specify the location of the
# java runtime base directory which will be used for running
# ---------------------------------------------------------------------

and replace it by:

export JAVA_HOME="/package/sequencer/Java/6"
export JAVA="$JAVA_HOME"/bin/java

echo "Using package java in $JAVA_HOME"
$JAVA -version
echo ""


# ---------------------------------------------------------------------
# Start
# ---------------------------------------------------------------------
exec "$JAVA" "${finalJavaArgs[@]}" com.simontuffs.onejar.Boot $enableVersion $enableVerbose $*

Adjust JAVA_HOME to point to the correct path of your fresh Oracle Java installation.

This must work :-)

[yifangt]

Thanks Sven!
I must have missed something important.

Where have you put the new java?

It was /home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45
That is parrallel to the Newbler2.9 JAVA which is: /home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_33
I had thought jre already included JAVA. Am I right? Or, how to get simple JAVA instead of JRE?
Here is the whole replacement of the part I made according to your last post:

# ---------------------------------------------------------------------
# Before you run the application specify the location of the
# java runtime base directory which will be used for running
# ---------------------------------------------------------------------
# modified according to Sven from seqanswer forum 2013-12-20
## (1) Roche 454 Suite is NOT compatible with Java 7
## -> Install newest Oracle Java 6, 1.6.0_45

export JAVA_HOME="/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45"
export JAVA="$JAVA_HOME"/bin/java

echo "Using package java in $JAVA_HOME"
$JAVA -version
echo ""

# ---------------------------------------------------------------------
# Start
# ---------------------------------------------------------------------
exec "$JAVA" "${finalJavaArgs[@]}" com.simontuffs.onejar.Boot $enableVersion $enableVerbose $*

Anything wrong?
Thank you!

[sklages]

OK, apart from the PM I sent you, can you please specify what "cannot add sequences" really means?
How do your file(name)s look like?
Where did you click?
What did (not) happen? What have you expected?
Did you get an error?

[yifangt]

Thanks!

what "cannot add sequences" really means?

Under Project menu after newbler started, at FASTA and FASTQ reads options, on the left sight there is + icon to add sequences. After finding the fasta sequence, I clicked the + icon. Nothing happened, no error or warning message.
Same with the GS reads menu. By the way when newbler is started, the Project icon always has a exclamation mark withing a yellow triangle. I assume it is a warning or error.

How do your file(name)s look like?

They are standard FASTA/FASTQ format or SFF format from 454 FLX sequencer. The sequence names are like sequence.fasta, QWR_2013_I.fastq, HZR5FRR01.sff.

Where did you click?

After I created new project (New) or open existing project (Open), I clicked the project menu, then FASTA and FASTQ reads bar, then the + bar and follow the GUI windows to get the file location. then click "OK"

What did (not) happen? What have you expected?

Nothing happened on the GUI window!, as I was expecting the sequence will appear in the window as indicated in the main screen for Name, Read Type etc...

Did you get an error?

I did not see any error at the GUI, but lots with strace, e.g. a few examples:

open("/home/yifang/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yifang/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yifang/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)

which seems a lots of libraries are missing. Before I go for those libraries issue, I thought I may have missed something very basic as your solution is quite simple and straight forward.
Thanks a lot!

[sklages]

strange ...

OK, let's put together:
- you have a 64bit Ubuntu system
- you have only replaced the final section in gsAssembler as proposed
- you have started "gsAssembler" and you do not get an open dialog for importing sequence files

The libraries are "missed" are pretty core libaries and should be available on your system, just check with e.g.:

locate libm.so.6

You can probably ignore these warnings ..

You should also start gsAssembler without strace just to easier see if gsAssembler itself spits out a warning/error.

Can you send me (PM) the altered "gsAssembler" and the complete strace output? I could have a look if we have overseen something very fundamental ..

The exclamation mark on the project tab just wants to tell you "Warning: One or more read files must be added before the analysis can be started.". So pretty normal, just a reminder :-)

[yifangt]

Thanks Sven!
I have sent you a couple of PM about the gsAssembler, as the forum does not alow PM more than 5000 char long.

locate libm.so.6
/lib/i386-linux-gnu/libm.so.6
/lib/x86_64-linux-gnu/libm.so.6

Also I tried putting java in

 /home/yt/download-software/newbler2.9/jre1.6.0_45

This is the output after I ran gsAssembler

Using package java in /home/yt/download-software/newbler2.9/jre1.6.0_45

The problem is still the same.
Thank you so much for all your help. I will try to call Roche to see if I can get some idea, although I was warned not to expect too much.
All the best,

[dsenalik]

SOLVED
I too had the same problem.
When I ran strace, I noticed that there were no messages after program startup.
I also noticed another java process running (with htop), and did a strace -p to trace that process number.

I found that there were many attempts to find the file MIDConfig.parse.
It tried 36 times, 15 different locations:

/opt/454-2.8/apps/assembly/bin/com/fourfivefour/assembly/MIDConfig.parse
/opt/454-2.8/apps/assembly/bin/com/fourfivefour/assembly/view/MIDConfig.parse
/opt/454-2.8/apps/assembly/bin/com/fourfivefour/assembly/view/projectdata/MIDConfig.parse
/opt/454-2.8/apps/assembly/bin/com/fourfivefour/MIDConfig.parse
/opt/454-2.8/apps/assembly/bin/MIDConfig.parse
/opt/454-2.8/apps/assembly/config/com/fourfivefour/assembly/MIDConfig.parse
/opt/454-2.8/apps/assembly/config/com/fourfivefour/assembly/view/MIDConfig.parse
/opt/454-2.8/apps/assembly/config/com/fourfivefour/assembly/view/projectdata/MIDConfig.parse
/opt/454-2.8/apps/assembly/config/com/fourfivefour/MIDConfig.parse
/opt/454-2.8/apps/assembly/config/MIDConfig.parse
/opt/454-2.8/apps/assembly/libexec/com/fourfivefour/assembly/MIDConfig.parse
/opt/454-2.8/apps/assembly/libexec/com/fourfivefour/assembly/view/MIDConfig.parse
/opt/454-2.8/apps/assembly/libexec/com/fourfivefour/assembly/view/projectdata/MIDConfig.parse
/opt/454-2.8/apps/assembly/libexec/com/fourfivefour/MIDConfig.parse
/opt/454-2.8/apps/assembly/libexec/MIDConfig.parse

And what do you know, it never tried the actual location, which was

/opt/454-2.8/apps/gsSeqTools/config

I did the simplest thing I could think of, made symlinks to all files in the actual config directory to one of the directories that was actually searched for. I did all the files in the config directory, in case it needed some of the other ones also.

cd /opt/454-2.8/apps/assembly/config
for file in ../../gsSeqTools/config/* ; do sudo ln -s $file ; done

I did the same for the other programs (I didn't test these)

cd /opt/454-2.8/apps/mapper/config
for file in ../../gsSeqTools/config/* ; do sudo ln -s $file ; done
cd /opt/454-2.8/apps/amplicons/config
for file in ../../gsSeqTools/config/* ; do sudo ln -s $file ; done

Now it works!

Edit:
On another installation, the symlinks were already there, but pointed to the wrong location (since I had renamed /opt/454/ to /opt/454-2.8 and the links were absolute instead of relative). I added a -f to each of the ln commands to force overwrite with correct locations.

[sklages]

Funny though, .. :-)
I didn't see any attempts to read the parse file in yifangt's strace output. Nevertheless, if that was the problem in your case, you should report that back to Roche, as this error should be catched when starting gsAssembler or the mapper.

[dsenalik]

Yeah, the same with my first strace, because Java somehow launches an independent process that strace doesn't follow. That made it hard to find.

[Leandrofm]

Thanks a lot dsenalik! It is working now! newbler 2.9 - Biolinux 7.