SeqShop: Calling Your Own Genome, May 2015
Login instructions for seqshop-server
Login to the seqshop-server Linux Machine
This section will appear redundantly in each session. If you are already logged in or know how to log in to the server, please skip this section
- Login to the windows machine
- The username/password for the Windows machine should be written on the right-hand monitor
- Start->Enter "Xming" in the search and select "Xming" from the program list
- Nothing will happen, but Xming was started.
- Start->Enter "putty" in the search and select "PuTTY" from the program list
- Host Name:
seqshop-server.sph.umich.edu
- Setup to allow you to open external windows:
- In the left pannel: Connection->SSH->X11
- Add a check mark in the box next to
Enable X11 forwarding
- Click
Open
- If it prompts about a key, click
OK
You should now be logged into a terminal on the seqshop-server and be able to access the test files.
- If you need another terminal, repeat from step 3.
Login to the seqshop Machine
So you can each run multiple jobs at once, we will have you run on 4 different machines within our seqshop setup.
- You can only access these machines after logging onto seqshop-server
3 users logon to:
ssh -X seqshop1
3 users logon to:
ssh -X seqshop2
2 users logon to:
ssh -X seqshop3
2 users logon to:
ssh -X seqshop4
Tuesday - Start SNP Calling
Setup Screen
The snpcall pipeline will run overnight, but you'll want to log out.
- How do I leave something running on the server even if I log out?
- One solution is screen!
- How do I use screen?
- Before running your command, you need to start screen:
screen
As it says, press Space
or Return
.
- It should now look basically the same as your normal command line.
Setup Variables
Set these values. Also, be sure to specify your sample name instead of SampleXX
export SAMPLE=SampleXX
or
export SAMPLE=NA12878
Point to your GotCloud & your output directory:
export GC=~/seqshop/gotcloud export OUT=~/$SAMPLE/output
List of BAMs
The list of BAMs has already been created (just 1 BAM, your sample).
- But it is simply SAMPLE\tBAM_name, so easy to figure out
cat ~/$SAMPLE/output/bam.list
SampleXX SampleXX/output/bams/SampleXX.recal.bam
- Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
Configuring SNPCALL
cat ~/$SAMPLE/gotcloud.conf
You will see this:
# References SS_DIR = /net/seqshop-server/home/mktrost/seqshop/singleSample REF_DIR = $(SS_DIR)/ref/gotcloud.ref/ ######### ALIGNMENT ######## MAP_TYPE = BWA_MEM FASTQ_LIST = fastq.list BATCH_TYPE = BATCH_OPTS = BWA_THREADS = -t 6 # SNP Call Settings UNIT_CHUNK = 20000000 # Chunk size of SNP calling : 20Mb VCF_EXTRACT = $(SS_DIR)/snpOnly.vcf.gz MODEL_GLFSINGLE = TRUE MODEL_SKIP_DISCOVER = FALSE MODEL_AF_PRIOR = TRUE EXT_DIR = $(SS_DIR)/ext EXT = $(EXT_DIR)/ALL.chrCHR.phase3.combined.sites.unfiltered.vcf.gz $(EXT_DIR)/chrCHR.filtered.sites.vcf.gz
Running SNP Calling
Run GotCloud snpcall with 8 jobs running in parallel
- Why 8?
- You want to run as many as you can.
- 2-3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine
${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 8 --outdir $OUT
- Only need the configuration, number of threads, and the output directory, rest is specified within the configuration.
This will run overnight. We will check if it completed at the practical in the morning.
Log Out
- Want to log out and leave your job running?
In the screen window, type:
Ctrl-a d
(Hold down Ctrl and type 'a', let go of both and type 'd')
- This will "detach" from your screen session while your alignment continues to run.
If you have not detached from screen:
Ctrl-a d
exit PuTTY
FEEDBACK!
Please provide feedback on today:
https://docs.google.com/forms/d/1ADTkBjzT-QNj2lrejyqGqDaahTponrw20kSgDNwqwH4/viewform
Thursday
Checking if snpcall Completed
Resume screen to Check Jobs
- How do you log back into screen?
screen -r
This will resume an already running screen.
Your screen session still has your environment variables set, so you do not need to reset them.
Verify you got a "completed successfully" message.
How long did snpcall calling take? Look at the log message - time in seconds.
List of BAMs
The list of BAMs has already been created (just 1 BAM, your sample).
- But it is simply SAMPLE\tBAM_name, so easy to figure out
cat ~/$SAMPLE/output/bam.list
SampleXX SampleXX/output/bams/SampleXX.recal.bam
- Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path).
GotCloud INDEL Configuration
cat ~/$SAMPLE/gotcloud.conf
Same as it looked the other day with no special Configuration settings for INDEL calling.
Running INDEL
Run GotCloud indel with 6 jobs running in parallel
${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 --outdir $OUT
- Only need the configuration, number of threads, and the output directory, rest is specified within the configuration.
This will run overnight. We will check if it completed at the practical in the morning.
Log Out
- Want to log out and leave your job running?
In the screen window, type:
Ctrl-a d
(Hold down Ctrl and type 'a', let go of both and type 'd')
- This will "detach" from your screen session while your alignment continues to run.
exit PuTTY
FEEDBACK!
Please provide feedback for today. https://docs.google.com/a/umich.edu/forms/d/1iES6usHxLB7Ec9hRxtqYgH7v05lU3Ume4VJcksx8Ogg/viewform