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, 12:23, 19 May 2015
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| == Thursday == | | == Thursday == |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
− | === Checking if SnpCall Completed === | + | === Checking if INDEL Completed === |
| ==== Logging Back in to Check Jobs ==== | | ==== Logging Back in to Check Jobs ==== |
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| Did you get a "completed successfully" message? | | Did you get a "completed successfully" message? |
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− | If yes, how long did SNP calling take? Look at the log message - time in seconds. | + | If yes, how long did INDEL calling take? Look at the log message - time in seconds. |
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| If no, are you running on seqshop-server? If so, KILL it. ssh -X to one of the seqshop machines and run on there. | | 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 | | Ctrl-c |
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− | Detach from screen. We will resume it again later when we restart SNPCall (if necessary). | + | Detach from screen. We will resume it again later. |
| Ctrl-a d | | Ctrl-a d |
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| === Ancestry Tutorial === | | === Ancestry Tutorial === |
− | Now we are going to run the Structural Variation Practical | + | Now we are going to run the Ancestry Practical |
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| Please go to: [[SeqShop: Estimates of Genetic Ancestry Practical, May 2015]] | | Please go to: [[SeqShop: Estimates of Genetic Ancestry Practical, May 2015]] |
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− | We will Resume SNP Calling (if necessary) after the practical.
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− | === Restart SnpCall ===
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− | ==== Resume screen ====
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− | ;How do you log back into screen?
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− | screen -r
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− | This will resume an already running screen.
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− | Your screen session still has your environment variables set, so you do not need to reset them.
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− | ==== Running SnpCall ====
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− | Run GotCloud snpcall with 6 jobs running in parallel
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− | ${GC}/gotcloud snpcall --conf $SAMPLE/gotcloud.conf --numjobs 6
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− | * GotCloud will pick up after the last completed step from before.
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− | This will run overnight. We will check if it completed at the practical in the morning.
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| ==== Log Out ==== | | ==== Log Out ==== |