Expected Outcomes - JoshLoecker/MAPT GitHub Wiki

This page shows a list of (generally) expected outcomes when performing these tests.

If you are watching live-output when following this script, the first warning you will see is on that starts with [guppy/warning], or [guppy/error]. This is normal, as the rule that calls Guppy Basecaller first attempts to resume a previous run. Since it does not find any previous data, this error is shown. Assuming Guppy Basecaller restarts without an issue, this is nothing to be worried about.

There is a file under results/ named md5sum.results.txt. This contains an MD5 sum of any file in this directory. While we will not explain MD5 sums here, in short, they can be used to verify the contents of two files are identical. This is useful if you would like to compare your own results against the ones located here.
To do this,perform the following

  1. Navigate to your results directory (following the previous guide, this is /90daydata/brookings_minion/$USER_scratch/results)

  2. Execute find . -type f -exec md5sum {} \; > md5.results.$USER.txt a. find: Linux's find command
    b. .: Search in the currrent directory, and all subdirectories
    c. -type f: Find all files (ignore directories)
    d. -exec: Execute a command
    e. md5sum {}: Execute md5sum on the file found
    f. \;: This is required to tell find we are done executing commands
    g. > md5.results.$USER.txt: Export all results into a file called md5.results.$USER.txt, where $USER is your username

  3. Two options exist from this point a. Compare the md5sum list found at /project/brookings_minion/examples/results/md5sum.results.txt with the one you just created b. Compare the md5sum of each of the md5sum files that have already been created (i.e. 'going one level deeper')

  4. Compare lists directly a. Use the head command to view the first 10 lines of a file i. head /90daydata/brookings_minion/$USER_scratch/results/md5.results.$USER.txt ii. head /project/brookings_minion/examples/results/md5sum.results.txt

    b. Now your results are shown on top of the known results
    c. If these are not the same, something has gone wrong (unless you have changed additional parameters not found in the configuration file used to generate the results at /project/brookings_minion/examples/results)

  5. Compare md5sum of list of md5sum's a. Use the md5sum command on each list again
    i. md5sum /project/brookings_minion/examples/results/md5.results.txt
    ii. md5sum /90daydata/brookings_minion/$USER_scratch/results/md5.results.$USER.txt

    b. If these results are not the same, the results found in each of the two results folders are not the same i. However, just because the md5 sum of results are not the same does not mean they are not identical.
    ii. Assuming your job executed without any errors, it is safe to assume the correct output was created

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