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| Expand |
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| title | investigate the commands file to to determine what the piping command actually did (click for answer) |
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| Code Block |
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| language | bash |
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| title | Think about the commands that let you look at what the contents of a file are |
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| collapse | true |
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| cat commands |
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Executing the commands
| Warning |
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| title | Remember to make sure you are on an idev done |
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For reasons discussed numerous times throughout the course already, please be sure you are on an idev done. It is unlikely that you are currently on an idev node as copying the files while on an idev node seems to be having problems as discussed. Remember the hostname command and showq -u can be used to check if you are on one of the login nodes or one of the compute nodes. If you need more information or help re-launching a new idev node, please see this tutorial. |
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The easiest way to check if this is working is to use use ls and and see an explosion of new files. This will take quite a bit of time to complete running. You can check that things are running using the ps command, and looking at the new . As such, we have ALREADY log files which are created. As the commands take some time to run, pre-computed versions of these outputs are available so you can begin evaluating the results if you don't want to wait for them to finish.
Canned results
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Accessing pre-computed results
| Code Block |
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| language | bash |
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| title | Use this code block to copy the completed results to immediately begin evaluating the results. Additionally, when your results have completed running (likely >90 minutes as annovar not configured to use multiple processes), compare your results to these provided results |
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| Code Block |
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| collapse | true |
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| language | bash |
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| title | Use this code block to copy the completed results |
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mkdir provided_results
cd provided_results
cp $BI/ngs_course/human_variation/*chrom20.samtools* .
cp $BI/ngs_course/human_variation/*chrom20.GATK* . |
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