{"id":4610,"date":"2018-03-19T15:45:10","date_gmt":"2018-03-19T15:45:10","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4610"},"modified":"2018-03-19T17:29:08","modified_gmt":"2018-03-19T17:29:08","slug":"megahit","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/megahit\/","title":{"rendered":"MEGAHIT"},"content":{"rendered":"

Overview<\/h2>\n

MEGAHIT<\/a> is an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.<\/p>\n

Version 1.1.3 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing the software on the CSF. It is released under the GPU GPLv3 license and all usage must adhere to this license.<\/p>\n

Please cite your usage of MEGAHIT using the citation instructions<\/a>.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

\r\n# CPU-only executables\r\nmodule load apps\/gcc\/megahit\/1.1.3\r\n\r\n# CPU executables and GPU version of megahit_sdbg_build named megahit_sdbg_build_gpu.\r\n# This will load automatically the CUDA modulefile.\r\nmodule load apps\/gcc\/megahit\/1.1.3-gpu\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run megahit on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
Serial batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# $NSLOTS is automatically set to the number of cores (1 for a serial job)\r\nmegahit -t $NSLOTS args...<\/em> -o out_dir<\/em>\r\n                                 #\r\n                                 # If an output directory name is not given megahit will\r\n                                 # use 'megahit_out'. You should use a unique name if\r\n                                 # running more than one job in the same directory and you\r\n                                 # can use $JOB_ID to use the current job's unique number.\r\n                                 # For example: my_output_dir.$JOB_ID \r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores (can be 2--24).\r\n\r\n# $NSLOTS is automatically set to the number of cores given above\r\nmegahit -t $NSLOTS args...<\/em> -o out_dir<\/em>\r\n                                 #\r\n                                 # If an output directory name is not given megahit will\r\n                                 # use 'megahit_out'. You should use a unique name if\r\n                                 # running more than one job in the same directory and you\r\n                                 # can use $JOB_ID to use the current job's unique number.\r\n                                 # For example: my_output_dir.$JOB_ID \r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n