Running the System Check
After turning on the server, you can make sure that your DRAGEN server is functioning properly by running /opt/edico/self_test/self_test.sh, which does the following:
| • | Automatically indexes chromosome M from the hg19 reference genome |
| • | Loads the reference genome and index |
| • | Maps and aligns a set of reads |
| • | Saves the aligned reads in a BAM file |
| • | Asserts that the alignments exactly match the expected results |
Each server ships with the test input FASTQ data for this script, which is located in /opt/edico/self_test. The system check takes approximately 25–30 minutes.
The following example shows how to run the script and shows the output from a successful test.
[root@edico2 ~]# /opt/edico/self_test/self_test.sh
---------------------------------
test hash creating
test hash created
---------------------------------
reference loading /opt/edico/self_test/ref_data/chrM/hg19_chrM
reference loaded
---------------------------------
real0m0.640s
user0m0.047s
sys0m0.604s
not properly paired and unmapped input records percentages: PASS
---------------------------------
md5sum check dbam sorted: PASS
---------------------------------
SELF TEST COMPLETED
SELF TEST RESULT : PASS
If the output BAM file does not match expected results, then the last line of the above text is as follows:
SELF TEST RESULT : FAIL
If you experience a FAIL result after running this test script immediately after turning on your DRAGEN server, contact Illumina Technical Support.