Line 7: |
Line 7: |
| </div> | | </div> |
| | | |
− | <div class="mw-collapsible" style="width:500px"> | + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| == Tuesday - Start SNP Calling == | | == Tuesday - Start SNP Calling == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
Line 102: |
Line 102: |
| </div> | | </div> |
| | | |
− | <div class="mw-collapsible mw-collapsed" style="width:500px"> | + | <div class="mw-collapsible" style="width:500px"> |
| | | |
− | == Wednesday == | + | == Thursday == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
| | | |
− | <div class="mw-collapsible" style="width:500px">
| |
| === Checking if snpcall Completed === | | === Checking if snpcall Completed === |
− | <div class="mw-collapsible-content">
| + | ==== Resume screen to Check Jobs ==== |
− | ==== Logging Back in to Check Jobs ==== | |
| | | |
| ;How do you log back into screen? | | ;How do you log back into screen? |
| screen -r | | screen -r |
| This will resume an already running screen. | | 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. | | Verify you got a "completed successfully" message. |
Line 120: |
Line 121: |
| How long did snpcall calling take? Look at the log message - time in seconds. | | How long did snpcall calling take? Look at the log message - time in seconds. |
| | | |
− | === Detach From screen===
| |
− | Detach from screen. We will resume it again later when we start SNPCall.
| |
− | Ctrl-a d
| |
− |
| |
− | </div>
| |
− | </div>
| |
− |
| |
− | === INDEL Tutorial ===
| |
− | Now we are going to run the INDEL Practical
| |
− |
| |
− | Please go to: [[SeqShop: Variant Calling and Filtering for INDELs Practical, May 2015]]
| |
− |
| |
− | We will Start INDEL Calling after the practical.
| |
− |
| |
− |
| |
− | <div class="mw-collapsible" style="width:500px">
| |
− |
| |
− | === Start INDEL Calling ===
| |
− | <div class="mw-collapsible-content">
| |
− | ==== Resume screen ====
| |
− |
| |
− | ;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.
| |
| | | |
| ==== List of BAMs ==== | | ==== List of BAMs ==== |
Line 155: |
Line 130: |
| :<code>SampleXX SampleXX/output/bams/SampleXX.recal.bam</code> | | :<code>SampleXX SampleXX/output/bams/SampleXX.recal.bam</code> |
| * Relative path, so assumes running from your home directory (I prefer absolute paths, but for simplicity of the workshop, we just use relative path). | | * 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 ==== | | ==== GotCloud INDEL Configuration ==== |
Line 160: |
Line 136: |
| cat ~/$SAMPLE/gotcloud.conf | | cat ~/$SAMPLE/gotcloud.conf |
| | | |
− | Same as it looked yesterday with no special Configuration settings for INDEL calling. | + | Same as it looked the other day with no special Configuration settings for INDEL calling. |
| | | |
| ==== Running INDEL ==== | | ==== Running INDEL ==== |
− | Run GotCloud indel with 8 jobs running in parallel | + | Run GotCloud indel with 6 jobs running in parallel |
− | * Why 8?
| + | ${GC}/gotcloud indel --conf $SAMPLE/gotcloud.conf --numjobs 6 --outdir $OUT |
− | ** You want to run as many as you can.
| |
− | ** 3 of you on the machine - 3*8 = 24 jobs will be running in parallel on that machine
| |
− | ${GC}/gotcloud indel --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. | | * Only need the configuration, number of threads, and the output directory, rest is specified within the configuration. |
| | | |
Line 187: |
Line 160: |
| </div> | | </div> |
| </div> | | </div> |
− | </div>
| |
− | </div>
| |
− |
| |
− | <div class="mw-collapsible mw-collapsed" style="width:500px">
| |
− |
| |
− | == Thursday ==
| |
− | <div class="mw-collapsible-content">
| |
− | === Checking if INDEL Completed ===
| |
− | ==== Logging Back in to Check Jobs ====
| |
− |
| |
− | ;How do you log back into screen?
| |
− | screen -r
| |
− | This will resume an already running screen.
| |
− |
| |
− | ==== Checking Completion ====
| |
− |
| |
− | Did you get a "completed successfully" message?
| |
− |
| |
− | If yes, how long did INDEL calling take? Look at the log message - time in seconds.
| |
− |
| |
− | If no, are you running on seqshop-server? If so, KILL it. ssh -X to one of the seqshop machines and run on there.
| |
− | Ctrl-c
| |
− |
| |
− | Detach from screen. We will resume it again later.
| |
− | Ctrl-a d
| |
− |
| |
− | === Ancestry Tutorial ===
| |
− | Now we are going to run the Ancestry Practical
| |
− |
| |
− | Please go to: [[SeqShop: Estimates of Genetic Ancestry Practical, May 2015]]
| |
− |
| |
− |
| |
− | ==== 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
| |
− |
| |
− |
| |
| </div> | | </div> |
| </div> | | </div> |