Running and Verifying MEGAHIT

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to go to the source code installation directory:

   cd /path/to/MEGAHIT

3. Run the following command to create a test case folder and go to the folder:

   mkdir testcase && cd testcase

4. Upload the downloaded test case file to the current directory.
5. Run the following command to run the test case:

   megahit -t 128 --12 SRR1976948.abundtrim.subset.pe.fq.gz SRR1977249.abundtrim.subset.pe.fq.gz > megahit.log

   After the execution is complete, check the value of Time elapsed (unit: second) in the megahit.log file. A smaller value indicates better performance. The following is an example of the output result:

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   .
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   2020-11-19 16:21:34 - Merging to output final contigs
   2020-11-19 16:21:34 - 3227 contigs, total 10298772 bp, min 200 bp, max 301573 bp, avg 3191 bp, N50 6898 bp
   2020-11-19 16:21:35 - ALL DONE. Time elapsed: 126.348002 seconds