MGI MegaBOLT Assembly instructions

M G I Tech Co., Ltd.
[email protected]E-mail:
Main Building and Second floor of No.11 Building, Beishan Industrial Zone, Yantian District,
518083 Shenzhen, Guangdong, P.R.China
https://en.mgi-tech.com/Website:
Address:
Research Use
Only
5.0
Version
AdvancedUser Manual

About this user manual
This user manual is applicable to MegaBOLT Bioinformatics Analysis
Accelerator (MegaBOLT). The edition is 5.0 and the software version
is V2.4.0.0
This manual and the information contained within are proprietary
to MGI Tech Co., Ltd. (hereinafter called MGI), and are intended
solely for the contractual use of its customer in connection with the
use of the product described herein and for no other purpose. Any
person or organization can not entirely or partially reprint, copy,
revise, distribute or disclose to others the manual without the prior
written consent of 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. However, MGI is not responsible for
any mistakes or missing parts in the manual, and reserves the right
to revise the manual and Device, so as to improve the reliability,
performance or design.
Figures in this manual are all illustrations. The contents might be
slightly different from the software, please refer to the software
purchased.
The company, product names, and trademarks are the property of
their respective owners.
©
2019-2022 MGI Tech Co., Ltd. All rights reserved.

Manufacturer information
Manufacturer MGI Tech Co., Ltd.
Manufacturer address
Main Building and Second floor of No.11
Building, Beishan Industrial Zone, Yantian
District, 518083 Shenzhen, Guangdong,
P.R.China
Technical support provider MGI Tech Co., Ltd.
Technical support
telephone [phone]
Technical support E-mail MGI-servic[email protected]
Revision history
Date Version
RevisionRevision
June 1, 2022 5.0
July 1, 2021 4.0
December 30, 2020 3.0
July 17, 2020 2.0
Initial releaseInitial release November 30, 2019 1.0

I
Contents
Overview
11
Overview .................................................. 2
Learning about MegaBOLT
11
MegaBOLT storage and directory structure ...... 4
System storage structure ��������������������������������������������4
MegaBOLT software directory architecture ���������������������4
Reference directory structure and description�����������������5
bed file��������������������������������������������������������������������6
11
MegaBOLT sub-module ................................7
Program and tools ����������������������������������������������������� 7
Source code of open source software ����������������������������8
11
MegaBOLT Server and client ......................... 9
Introduction of server and client ����������������������������������9
MegaBOLT system service�������������������������������������������9
11
MegaBOLT traffic........................................ 11
Introduction of traffic ������������������������������������������������ 11
Traffic threshold������������������������������������������������������� 11
Querying MegaBOLT traffic ����������������������������������������12

Contents
II
11
MegaBOLT logs ......................................... 13
Log structure�����������������������������������������������������������13
Server logs ����������������������������������������������������������������� 13
Client logs ������������������������������������������������������������������ 13
Task log ��������������������������������������������������������������������� 14
Log level explanation ����������������������������������������������� 14
General Linux operation guide
11
Portable storage device mounting................. 16
Mounting storage through the graphical interface ����������16
Mounting storage through the command line ���������������� 17
11
Network configuration ................................ 19
Enabling network setup ���������������������������������������������19
Setting network connection��������������������������������������� 20
User verification ������������������������������������������������������ 22
Automatic network connection ���������������������������������� 23
11
RAID5......................................................24
Introduction of RAID5����������������������������������������������� 24
Resync checking ����������������������������������������������������� 24
Redundant backup and data security��������������������������� 25
0101
Changing password of storage device ............ 26
Data storage device encryption and decryption ������������� 26
Passphrase ������������������������������������������������������������� 26
Disclaimer�������������������������������������������������������������� 28

Contents
III
Appendixes
Device related FAQs������������������������������������������������� 30
Workflow related FAQs����������������������������������������������31
Error related FAQs ��������������������������������������������������� 33

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Overview

Overview
2
1
Overview
This manual is intended for users that are familiar with the basic use
of MegaBOLT and need further details and features.
Firstly, this manual introduces the structure of MegaBOLT
storage, software directory, and ZLIMS analysis results directory;
the structure of the 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. Secondly, this
manual introduces the Server-Client structure and system services,
which guides you to inquire and control MegaBOLT running status
through system services.
Thirdly, this manual provides guidance on the general operation
under the Linux operating system, including portable storage device
mounting and network settings.
Finally, this manual provides quick solutions for common problems
and errors when using MegaBOLT.

Learning about Mega-
BOLT

MegaBOLT storage and directory structure
4
2
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
functions are described in the table below:
Storage Mounting
directory Function
SSD /Operating system and software
SSD /mnt/ssd MegaBOLT software
Sata HDD /data User data storage
MegaBOLT software directory
architecture
The root directory of the MegaBOLT software is /mnt/ssd/
MegaBOLT/, and its contents strcuture is shown as follows:

MegaBOLT storage and directory structure
5
Directory Items stored
bin Executable files
config Configuration files
docs User guides
env Runtime environment dependencies
lib Libraries
lic License files
log Item
test Test cases
tmpDir 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.* Hg19 reference file and index
dbsnp
_
151.vcf.* Associated dbsnp files of hg19
1000G
_
phase1.* KnownSites files. Its associated reference can be
identified by label hg19 or hg38 in the file name.
Mills
_and_1000G_
gold_
standard.
indels.*
KnownSites files. Its associated reference can be
identified by the label hg19 or hg38 in the file name
hg38.* Hg38 reference file and index
hs37d5/ hs37d5 reference file and index, associated dbsnp
and knownSites files
ReadMe Introduces the reference and download link of its
associated files
build.sh Script programs for building all reference indexes
automatically
db The bed file of WES data analysis

MegaBOLT storage and directory structure
6
The hg19, hg38, and their associated files can be downloaded from NCBI.
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

MegaBOLT sub-module
7
3
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
described in the table below:
Program Description
MegaBOLT MegaBOLT client program, used to submit tasks
MegaBOLT
_
server MegaBOLT server program, used to run the
tasks submitted by the client
hc4HaplotypeCaller.jar Germline variant calling procedure
BQSR.jar Base quality score recalibration program
gatk4
_
mutect2
_
acc.jar Somatic variant calling program
bwa BWA alignment program
mm2Alignment Minimap2 alignment program
picard.jar Picard program
samtools Samtools program
Sort Sorting program
SortMarkDup Sorting and duplicate marking program
In spite of the submodules above, MegaBOLT also provides some
third-party applications, which are installed in the following directory
for unified management:
/mnt/ssd/MegaBOLT/tools/

MegaBOLT sub-module
8
Software tools under this directory are described in the table below:
Directory Description
GATK GATK software, including GATK3.8 and GATK4.0
biobambam2 Biobambam2 tool kit
DeepVariant Variant calling procedure based on deep learning
DNApipe 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/

MegaBOLT Server and client
9
4
MegaBOLT Server and
client
Introduction of server and client
MegaBOLT adopts the Server-Client structure. The server program
resides in the background. When the client submits a task, the
server parses and then executes the task.
The MegaBOLT server is monitored by the MegaBOLT system
service. This service starts with the operating system and
automatically starts the MegaBOLT server. You do not need to
pay attention to the running status of the server program when
submitting tasks.
MegaBOLT system service
The MegaBOLT system service is used to monitor the server
program, ensuring that the server program runs normally and
stably. Through the MegaBOLT system service, you can query the
server running status, and start, shut down, or restart the server
program.
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.
1. Querying the server running status
To query the server running status, execute the following
command:
service megaboltd status
A sample of the results generated is shown below:
●megaboltd.service - SYSV: start/stop/restart/reload
daemon of MegaBOLT server
Loaded: loaded (/etc/rc.d/init.d/megaboltd; bad;
vendor preset: disabled)

MegaBOLT Server and client
10
Active: active (running) since Mon 2019-11-04
09:58:40 CST; 7h ago
Docs: man:systemd-sysv-generator(8)
Memory: 63.9 GB
CGroup: /system.slice/megaboltd.service
├─ 1972 /usr/bin/megaboltd
└─ 2024 /mnt/ssd/MegaBOLT_scheduler/bin/
MegaBOLT_server –restart
“active (running)” in the results indicates that the server is
running.
2. Stopping the server
To stop the server, execute the following command:
sudo service megaboltd stop
Enter the SU passwords and the following information is
displayed:
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
following command:
sudo service megaboltd start
Enter the SU passwords and the following information is
displayed:
Starting megaboltd (via systemctl): [ OK ]
The MegaBOLT system service and server are started.
4. Restarting the server
Modification on MegaBOLT configuration files only takes effect
after restarting the server. To restart MegaBOLT system service
and server, execute the following command:
sudo service megaboltd restart
Enter the SU passwords and the following information is
displayed:
Restarting megaboltd (via systemctl): [ OK ]
The MegaBOLT system service and server are restarted.

MegaBOLT traffic
11
5
MegaBOLT traffic
Introduction of traffic
Analysis traffic is a license and is limited, counting in base numbers.
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. When the traffic runs out, MegaBOLT is unable to analyze
any data until new traffic is installed.
Take a standard 100 Gbp WGS data set as an example. MegaBOLT
will deduct 100 Gbp from available traffic after analyzing the data
set. If the amount of traffic available before analyzing the data set is
100 Tbp, then 99.9 Tbp of traffic will be left.
Traffic threshold
To ensure that the user continuously uses MegaBOLT, when
remaining traffic is less than 10% of the initial value, a traffic
threshold warning is triggered, and MegaBOLT will be temporarily
unavailable. In this case, contact your local sales representative
or technical support to buy new traffic license and reactivate
MegaBOLT. When MegaBOLT traffic reaches the threshold, the user
could readjust the threshold to activate the remaining 10% traffic by
performing the following operations:
1. Get access to the following directory through Linux resource
manager:
/mnt/ssd/MegaBOLT_scheduler/config/
2. Open the following file:
MegaBOLT.Resources.Configuration.xml
3. Change MAX_TRAFFIC_USAGE_RATIO to 1.0.
4. Directly reboot the server or execute the following command to
restart the MegaBOLT service program:
sudo systemctl restart megaboltd.service

MegaBOLT traffic
12
Querying MegaBOLT traffic
MegaBOLT traffic can be queried by command. After you open a
terminal, execute the following command:
MegaBOLT --trafc
The example output is as follows:
TrafcStatistics:
Total Trafc: 100500000000000 bp
Used Trafc: 4998200 bp
Left Trafc: 100499995001800 bp.
Output interpretation:
Total Traffic: Initial traffic
Used Traffic: Consumed traffic
Left Traffic: Remaining traffic

MegaBOLT logs
13
6
MegaBOLT logs
Log structure
Three types of logs are generated when MegaBOLT is running, which
are server logs, client logs, and task logs. The logs record different
types of running information, which are recorded in different levels
to help you quickly view task information or locate errors.
Server logs
Server logs are divided into four log files. Which are stored in
the following directory: /mnt/ssd/MegaBOLT
_
scheduler/log The
functions of the log files are described in the table below:
Item Description
megabolt
_
server.err
Standard output stream/standard error stream
of the server program
megabolt
_
server.log Server program runtime log
megabolt
_
rockey.log Dongle data traffic log
megabolt
_
task.log Server task log
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 Description
megabolt.out
Standard output/error stream of the client
program
megabolt.log Client program running log