Juicer on AWS - running, but what's up with that message?

[devon....@gmail.com]

I've been following the tutorial on running Juicer on an AWS Instance. Things mostly seem to be going to plan, but as I started the `juicer.sh` script, I am getting these messages:

ubuntu@ip-172-31-66-49 /opt/juicer/work/EXP1> /opt/juicer/scripts/myjuicer.sh -g LUr3p1 -d /opt/juicer/work/EXP1 -D /opt/juicer -s Sau3AI -p /opt/juicer/work/EXP1/references/LUr3p1.chrom.sizes -y /opt/juicer/work/EXP1/references/LUr3p1_Sau3AI.txt -z /opt/juicer/work/EXP1/references/LUr3p1.fasta

Sau3AI not listed as recognized enzyme. Using /opt/juicer/work/EXP1/references/LUr3p1_Sau3AI.txt as site file

Ligation junction is undefined

(-: Looking for fastq files...fastq files exist

LSF daemon (LIM) not responding ... still trying

I'm guessing the Sau3AI enzyme wasn't updated on the AWS scripts (as the same `juicer.sh` commands on our compute cluster using the SLURM-directory of Juicer scripts didn't throw this message). Nevertheless, it looks like that's not a problem as it's recognizing the site file anyway.

It's the second one I have no idea about: the `LSF deamon` line. It keeps getting added every few seconds. Is there something in the `juicer.sh` script where it's trying to connect but failing? I updated the local IP address (following your tutorial; plus you can see the command prompt change when that part of modifying the local IP address is complete). 

Thanks for helping,

Devon

[Muhammad Saad Shamim]

Hey Devon,

Hope you're doing well!

Was this instance launched using the juicer AWS image or a custom installation of juicer on AWS?

Can you try restarting the services (open lava, networking)

sudo hostname HEADNODE
sudo service openlava restart
sudo /etc/init.d/networking restart

If that doesn't work, can you reboot the instance, and redo the first-time tweaks?

This is an unusual error that I haven't seen before.

Best,

- Muhammad Saad Shamim

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[devon....@gmail.com]

I think the suggested reboot solved it. Here's what I did:

ubuntu@ip-172-31-66-49 /opt/juicer/work> sudo hostname HEADNODE
ubuntu@ip-172-31-66-49 /opt/juicer/work> sudo service openlava restart
Stopping daemons...
Starting daemons...
lim started
res started
sbatchd started
ubuntu@ip-172-31-66-49 /opt/juicer/work> sudo /etc/init.d/networking restart
 * Running /etc/init.d/networking restart is deprecated because it may not enable again some interfaces
 * Reconfiguring network interfaces...                                                                                                                                                                                      ssh stop/waiting
ssh start/running, process 2675

Here's what I'm seeing upon launching the command:

ubuntu@HEADNODE /opt/juicer/work> /opt/juicer/scripts/myjuicer.sh \

> -g LUr3p1 \
> -d /opt/juicer/work/EXP1 \
> -D /opt/juicer \
> -s Sau3AI \
> -p /opt/juicer/work/EXP1/references/LUr3p1.chrom.sizes \
> -y /opt/juicer/work/EXP1/references/LUr3p1_Sau3AI.txt \
> -z /opt/juicer/work/EXP1/references/LUr3p1.fasta

Sau3AI not listed as recognized enzyme. Using /opt/juicer/work/EXP1/references/LUr3p1_Sau3AI.txt as site file
Ligation junction is undefined
(-: Looking for fastq files...fastq files exist

Job <9371> is submitted to queue <normal>.
(-: Aligning files matching /opt/juicer/work/EXP1/fastq/*_R*.fastq*
 in queue normal to genome LUr3p1 with site file /opt/juicer/work/EXP1/references/LUr3p1_Sau3AI.txt
(-: Created /opt/juicer/work/EXP1/splits and /opt/juicer/work/EXP1/aligned. Splitting files
Job <9372> is submitted to queue <Split>.
<<Waiting for dispatch ...>>

I think what happened before was that I set up an EC2 instance, but had to close it (my Terminal kept freezing only on the EC2 instance and no other machine's I was connected to). I then detached the 2.5Tb AWS Volume I created for that Instance, and started a brand new EC2. I then attached that original Volume back to the new Instance and found all the same contents there, and then entered the command that was generating that weird prompt.

Perhaps even when the Volume is recognized, the issue here was that the new EC2 instance generated a new local IP address? I didn't think so, because the earlier IP address matched what I had between both EC2 instances.... at least, the output from 

/sbin/ifconfig | grep "inet addr" | awk -F: '{print $2}' | awk '{print $1}' |head -1

generated the same IP address between the original EC2 instance and the new one I had created... Writing that sentence doesn't sound right to me, but I swear that's what I saw.

Anyway, after stopping that second Instance, then executing the three lines of command to restart the networking bit, the job launched and my reads are currently getting split. Fingers crossed this all works.

...

While I'm on topic, can you confirm that this pipeline works for reads generated with Phase Genomics? I'm doing a bit of a facepalm today realizing that I shouldn't have invested all this time without asking if your group has seen success with folks who have used that specific protocol.

Thanks again for your insights. Happy Friday.