MGI MegaBOLT Advanced User's Manual

Bioinformatics analysis accelerator

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Page 1 Main Building and Second floor of No.11 Building, Beishan Industrial Zone, Yantian District, Research Use 518083 Shenzhen, Guangdong, P.R.China Only Ve r s io n E-mail: MGI-service@mgi-tech.com 5 . 0 M G I T e c h C o . , L t d . Website: https://en.mgi-tech.com/...
Page 2 MGI. Any unauthorized person should not use this manual. MGI does not make any promise of this manual, including (but not limited to) any commercial of special purpose and any reasonable implied guarantee. MGI has taken measures to guarantee the correctness of this manual.
Page 3 Manufacturer information Manufacturer MGI Tech Co., Ltd. Main Building and Second floor of No.11 Building, Beishan Industrial Zone, Yantian Manufacturer address District, 518083 Shenzhen, Guangdong, P.R.China Technical support provider MGI Tech Co., Ltd. Technical support 4000-966-988 telephone Technical support E-mail MGI-service@mgi-tech.com...
Page 4: Table Of Contents
Contents Overview Overview ..........2 Learning about MegaBOLT MegaBOLT storage and directory structure ..4 System storage structure ��4 MegaBOLT software directory architecture ��4 Reference directory structure and description ��5 bed file ��6 MegaBOLT sub-module ........7 Program and tools �� 7 Source code of open source software ��8...
Page 5 MegaBOLT logs ......... 13 Log structure ��13 Server logs �� 13 Client logs �� 13 Task log �� 14 Log level explanation �� 14 General Linux operation guide Portable storage device mounting ....16 Mounting storage through the graphical interface ��16 Mounting storage through the command line ��...
Page 6 Appendixes Device related FAQs �� 30 Workflow related FAQs ��31 Error related FAQs �� 33...
Page 7 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...
Page 8 Overview...
Page 9: Overview
MegaBOLT submodules; default reference and relevant information of bed interval files used by WES data analysis and the MegaBOLT log system, so that you can understand MegaBOLT in-depth and use MegaBOLT for diverse data analysis and downstream analysis more conveniently and flexibly.
Page 10: Learning About Megabolt
Learning about Mega- BOLT...
Page 11: Megabolt Storage And Directory Structure
System storage structure MegaBOLT is equipped with two SSDs, which are used to store the operating system and MegaBOLT software respectively. In addition, the MegaBOLT workstation is equipped with a large-capacity data storage (Sata HDD). The hardware mounting structure and its...
Page 12: Reference Directory Structure And Description
Temporary files and intermediate files tools Third party software tools Reference directory structure and description MegaBOLT provides three references: hg19 (default), hg38, and hs37d5. The storage diretory is : /mnt/ssd/MegaBOLT/reference/ . Major files and their explanation are shown in the table below: Item Description hg19.*...
Page 13: Bed File
The bed file for WES data analysis is stored in the following directory: /mnt/ssd/MegaBOLT/reference/db/db _ BED/ Use of the abbreviation of bed files are supported by command line argument --bed . You can check the relations between the abbreviations and their actual bed file by viewing the file below: /mnt/ssd/MegaBOLT/reference/db/db _ BED/db.list...
Page 14: Megabolt Sub-Module
MegaBOLT sub- module Program and tools The executable files of MegaBOLT are stored in the following directory: /mnt/ssd/MegaBOLT/ bin/ Subprograms that can be invoked by MegaBOLT are stored in this directory. You can invoke the submodules independently for customized analysis pipeline development. Major subprograms are...
Page 15: Source Code Of Open Source Software
Took kit relevant to bioinformatics analysis Source code of open source software Part of the subprograms are customized and optimized in performance and accuracy by the MegaBOLT R&D team. The original source code of these subprograms are stored in the following directory: /mnt/ssd/MegaBOLT/tools/src/...
Page 16: Megabolt Server And Client
The MegaBOLT server is essential for the normal operation of the MegaBOLT system. Operate under the instruction of the technical support or local distributor unless you are sure about the results of the following operations.
Page 17 Stopping megaboltd (via systemctl): [ OK ] Both the MegaBOLT system service and the server are stopped and the MegaBOLT tasks submitted at this time will fail. 3. Starting the server To start MegaBOLT system service and server, execute the...
Page 18: Megabolt Traffic
It permits normal running of MegaBOLT. Each MegaBOLT product is equipped with some traffic before delivery. After analyzing an input data set, MegaBOLT will count the total number of bases in the input data set, and deduct the same number of traffic from available traffic.
Page 19: Querying Megabolt Traffic
Querying MegaBOLT traffic MegaBOLT traffic can be queried by command. After you open a terminal, execute the following command: MegaBOLT --traffic The example output is as follows: TrafficStatistics: Total Traffic: 100500000000000 bp Used Traffic: 4998200 bp Left Traffic: 100499995001800 bp.
Page 20: Megabolt Logs
Client logs Client logs are divided into two log files, that is, megabolt.log and megabolt.out , which are stored under the output directory of MegaBOLT analysis tasks. The functions of the two log files are described in the table below: Item...
Page 21: Task Log
Log level explanation MegaBOLT log information is divided into different levels according to the severity. Higher level indicates higher severity. The log levels are described in the order of low severity to high severity in the...
Page 22: General Linux Operation Guide
General Linux operation guide...
Page 23: Portable Storage Device Mounting
Portable storage device mounting The MegaBOLT server uses the CentOS7 operating system and the hard disk is mounted differently from the Windows operating system. The following sections introduce the CentOS portable storage devices mounting from the aspects of graphical interface and the command line respectively.
Page 24: Mounting Storage Through The Command Line
M o u n t i n g s t o ra g e t h ro u g h t h e command line When mounting portable storage devices in exFAT, ext4 format through the non-graphical interface or when required, you need to mount the portable storage devices through the command line.
Page 25 The output result shows that the U disk is named “ /dev/sda ”, the file system is in NTFS format, and only one partition “/dev/sda1” exists. 2. Mounting disks to the operating system If the disk uses the exFAT file system, execute the following command to mount the disk: mkdir /mnt/usb mount.exfat /dev/sda1 /mnt/usb...
Page 26: Network Configuration
Network configuration The MegaBOLT server adopts the CentOS7 operating system. You can set up the network by following the guidance provided in this chapter. Enabling network setup 1. Click the message icon on the upper right corner and select Ethernet >...
Page 27: Setting Network Connection
2. In the Wired Settings window, available Ethernet ports for the current device are displayed on the left; the Ethernet port connected to network is shown on the right with network bandwidth and the network connection switch can be turned on or off.
Page 28 2. Static network connection To configure the static network, open the IPv4 window, set Addresses to Manual, and input the static IP address of the target network in the Address box, fill out the Netmask and Gateway boxes, and apply the changes, as shown in Figure 4. Turn on the network connection switch again to validate the settings.
Page 29: User Verification
User verification If the target network requires user verification, click the setup icon on the bottom right of the Settings interface to enter the network security setup window. Figure 5 Online user verification Select Security, turn on the switch, select the user verification method next to Authentication according to the user verification mode of the target network, input the user name and password, and click Apply to validate the modification.
Page 30: Automatic Network Connection
Automatic network connection The CentOS 7 operating system supports automatic network connection after startup. After network user authentication, enter the network security settings window again. Click Identity on the left side of the window, and select Connect automatically at the bottom of the window.
Page 31: Raid5
Introduction of RAID5 In order to balance storage performance, data security, and costs, MegaBOLT workstation adopts RAID 5 to build storage arrays for scattered HDDs. After a RAID5 array is built, the total volume of the workstation is around 21 TB. The RAID5 array is mounting to /data.
Page 32: Redundant Backup And Data Security
/usr/sbin/raid-check & Redundant backup and data security ® MegaBOLT workstation adopts Intel VROC to build a RAID5 array. The stability of the RAID5 array is directly related to the motherboard and each hard disk. If the motherboard or one of the hard disks is damaged, the data on the RAID5 array may be damaged or lost.
Page 33: Changing Password Of Storage Device
Page 24 . The initial passphrase of data storage is: megabolt To ensure your data security, please change the initial passphrase on your first entrance to MegaBOLT system, and perform the following operations: 1. Open linux disks tool by the following steps:...
Page 34 2. Choose the encrypted disk data, click the setting button, and then click Change Passphrase on the prompted menu. Figure 7 Change PWD 1...
Page 35: Disclaimer
Disclaimer The data security of storage device needs to be maintained by both MGI and customers. As the manufacturer of MegaBOLT, MGI provides support services for the security of MegaBOLT. As the controller or processor of using MegaBOLT to process and store...
Page 36 Appendixes...
Page 37 Device related FAQs Does the device provide storage of large capacity? The MegaBOLT workstation provides 30 TB data storage by default. What is the amount of data that can be analyzed by using the temporary computing storage? The maximum amount of data that can be analyzed highly efficient is “...
Page 38 MegaBOLT provides administrator privileges. Add “ sudo ” before the command and input the password to execute the command in administrator mode. Can the operating system be updated? I t i s n o t re co m m e n d e d . M e g a B O L T p ro v i d e s t h e b e s t performance and stability in the current operating system version.
Page 39 Can I input multiple vcf files (dbSNP) by setting --vcf multiple times? It is not supported currently. If you input multiple vcf files, only the last vcf file will be used. Can multiple bam files be used as input for HaplotypeCaller? It is not supported in this version.
Page 40 The number is not limited. All the samples listed in the sample list file will be processed in order. Error related FAQs How to locate errors in failed MegaBOLT analysis task: a) Check states of megaboltd service and MegaBOLT_server; b) Determine whether the exception is caused by client or task , based on the first appearing “warning/error/critical”...
Page 41 “ Socket exception - Client connect server failed, strerror: Connection refused ” The MegaBOLT sever program is not started. You can restart the analysis in one minute. If the problem persists, execute sudo service megaboltd restart to start the MegaBOLT server program, and submit the task again.
Page 42 The raw reads are incomplete, please check the original file. The following error occurs when running a MegaBOLT task: “ERROR: Sample-name.bam_stats.sh error” There are two reasons for this problem, please check them separately: a) Combining multiple libraries data with different insert size.
Page 43 - - - T h i s p a g e i s i n t e n t i o n a l l y l e f t b l a n k . - - -...

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