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Xiaorui Chen — Mon, 20 Sep 2021 16:31:23 -0000

Dear Sir or madam,
I couldn' t process my default pangenome analysis in BPGA second step, I don't know whats' wrong for that? I emailed BPGAtool@gmail.com, after I send my input data from last Friday, until now nobody reply me back, please contact me soon, thanks.

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 30 Jul 2019 12:23:54 -0000

--- v94
+++ v95
@@ -20,8 +20,6 @@
 **Usearch: ** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Windows executables to "**usearch.exe**"  [case sensitive, also mind that Windows file extensions are visible] 
 **gnuplot:** [Download Gnupot_Win-64bit_Version](http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/gp466-win64-setup.exe/download)  or [Download_Gnupot_Win-32bit_Version](http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/gp466-win32-setup.exe/download) 
 **WARNING (for Windows only) :** Please check “vcomp100.dll” system file in the system32 or system64 folder, path of this folder is as “C:\Windows\System32”. If not present copy it into above said folder. This file is required for USEARCH to function properly. This dll is available [at this link](http://www.drive5.com/usearch/manual/vcomp100.html) 
-* * 
-* *

 * **Linux Requirements:**
 **Usearch :** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Linux executable to "**usearch**". [case sensitive]

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 30 Jul 2019 12:22:47 -0000

--- v93
+++ v94
@@ -20,7 +20,8 @@
 **Usearch: ** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Windows executables to "**usearch.exe**"  [case sensitive, also mind that Windows file extensions are visible] 
 **gnuplot:** [Download Gnupot_Win-64bit_Version](http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/gp466-win64-setup.exe/download)  or [Download_Gnupot_Win-32bit_Version](http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/gp466-win32-setup.exe/download) 
 **WARNING (for Windows only) :** Please check “vcomp100.dll” system file in the system32 or system64 folder, path of this folder is as “C:\Windows\System32”. If not present copy it into above said folder. This file is required for USEARCH to function properly. This dll is available [at this link](http://www.drive5.com/usearch/manual/vcomp100.html) 
- 
+* * 
+* *

 * **Linux Requirements:**
 **Usearch :** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Linux executable to "**usearch**". [case sensitive]

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 30 Jul 2019 12:02:38 -0000

--- v92
+++ v93
@@ -11,17 +11,17 @@
 \*In BPGA-1.3.0 or later, there is minor change in pathway calculations. It considers one enzyme involved in more than one pathways. Earlier versions used to consider one enzyme in only one pathway.      | Last update on 12/May/2017 : introduced pan profile plot with combinations from matrix input. 
 [Older versions below this are not available]      |    [Do not download]    |  [Do not download]
 bpga-version-1.3-mswin-x64-0-0-0 or **Higher**      | Work with upcoming GBK files having "accession.version" gene identifier (e.g YP_281368.1 ) as well as old NCBI GBK files.       | NCBI is planning to eliminate GI ids from all its files from Nov. 2016.
-
+ 
 **PREREQUISITES** 
-
-
+ 
+ 
 * **Windows Requirements:** 
 **System:** Windows XP or latter
 **Usearch: ** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Windows executables to "**usearch.exe**"  [case sensitive, also mind that Windows file extensions are visible] 
 **gnuplot:** [Download Gnupot_Win-64bit_Version](http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/gp466-win64-setup.exe/download)  or [Download_Gnupot_Win-32bit_Version](http://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/gp466-win32-setup.exe/download) 
 **WARNING (for Windows only) :** Please check “vcomp100.dll” system file in the system32 or system64 folder, path of this folder is as “C:\Windows\System32”. If not present copy it into above said folder. This file is required for USEARCH to function properly. This dll is available [at this link](http://www.drive5.com/usearch/manual/vcomp100.html) 
-
-
+ 
+ 
 * **Linux Requirements:**
 **Usearch :** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Linux executable to "**usearch**". [case sensitive]  
 **gnuplot:** Linux users need to download exact version of gnuplot for linux from this [SourceForge Page](https://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/)

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 30 Jul 2019 12:00:52 -0000

--- v91
+++ v92
@@ -26,7 +26,11 @@
 **Usearch :** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Linux executable to "**usearch**". [case sensitive]  
 **gnuplot:** Linux users need to download exact version of gnuplot for linux from this [SourceForge Page](https://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/)
 Extract gnuplot 4.6.6. files by  `tar -xzf FILENAME.tar.gz` 
-cd to gnuplot 4.6.6 directory simply install `sudo ./configure` ,  `sudo make`,  `sudo make install`  to install gnuplot manually. 
+cd to gnuplot 4.6.6 directory simply run: 
+`sudo ./configure` , 
+`sudo make`, 
+`sudo make install` 
+to install gnuplot manually. 
 **ghostscript:** run `sudo apt-get install ghostscript`
 **wine (Ubuntu):** `sudo add-apt-repository ppa:ubuntu-wine/ppa -y && sudo apt-get update && sudo apt-get install wine` 
 **WARNING (for Debian only) :** Make sure you have 'glibc 2.15' or higher (the C library in Debian).If not, you can carefully install higher version of glibc in parallel to 'glibc 2.14' or less. [Do not try to remove original glibc, as other binaries may not work properly.]  As the post on one of the debian forum says: "One can install NEW glibc in parallel to OLD in some different place, e.g., in /opt. In fact, this is a common technique to make Google Chrome work on CentOS.   I'm not saying this is as easy as 1-2-3, but it is certainly both doable and, if done properly, safe."

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 30 Jul 2019 11:59:29 -0000

--- v90
+++ v91
@@ -24,7 +24,9 @@

 * **Linux Requirements:**
 **Usearch :** Get it from [http://www.drive5.com/usearch/](http://www.drive5.com/usearch/). Download and rename the Linux executable to "**usearch**". [case sensitive]  
-**gnuplot:** run  `sudo apt-get install gnuplot-4.6.6` or simply `sudo apt-get install gnuplot` 
+**gnuplot:** Linux users need to download exact version of gnuplot for linux from this [SourceForge Page](https://sourceforge.net/projects/gnuplot/files/gnuplot/4.6.6/)
+Extract gnuplot 4.6.6. files by  `tar -xzf FILENAME.tar.gz` 
+cd to gnuplot 4.6.6 directory simply install `sudo ./configure` ,  `sudo make`,  `sudo make install`  to install gnuplot manually. 
 **ghostscript:** run `sudo apt-get install ghostscript`
 **wine (Ubuntu):** `sudo add-apt-repository ppa:ubuntu-wine/ppa -y && sudo apt-get update && sudo apt-get install wine` 
 **WARNING (for Debian only) :** Make sure you have 'glibc 2.15' or higher (the C library in Debian).If not, you can carefully install higher version of glibc in parallel to 'glibc 2.14' or less. [Do not try to remove original glibc, as other binaries may not work properly.]  As the post on one of the debian forum says: "One can install NEW glibc in parallel to OLD in some different place, e.g., in /opt. In fact, this is a common technique to make Google Chrome work on CentOS.   I'm not saying this is as easy as 1-2-3, but it is certainly both doable and, if done properly, safe."

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Sat, 19 Jan 2019 06:36:46 -0000

--- v89
+++ v90
@@ -1,5 +1,5 @@
 # BPGA - Bacterial Pan Genome Analysis pipeline
-> Follow BPGA  ![](https://abs.twimg.com/favicons/win8-tile-144.png) [@bpgatool](http://twitter.com/bpgatool) 
+> Follow BPGA  on Twitter [@bpgatool](http://twitter.com/bpgatool) 
 > Also see  [Results](Results)    [FAQs](FAQs)

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Sat, 19 Jan 2019 06:34:16 -0000

--- v88
+++ v89
@@ -1,5 +1,5 @@
 # BPGA - Bacterial Pan Genome Analysis pipeline
-> Follow BPGA  ![](https://s22.postimg.org/kdzhplg5d/image1s.jpg) [@bpgatool](http://twitter.com/bpgatool) 
+> Follow BPGA  ![](https://abs.twimg.com/favicons/win8-tile-144.png) [@bpgatool](http://twitter.com/bpgatool) 
 > Also see  [Results](Results)    [FAQs](FAQs)

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 11 Sep 2018 09:17:32 -0000

--- v87
+++ v88
@@ -108,7 +108,7 @@

 * **HMP Protein FASTA files sample:(.pep.fsa)**
 ~~~
- >HMPREF9420_0006 protein name [Organism Name]
+>HMPREF9420_0006 protein name [Organism Name]
 MRTNFKVSFYLRSNYENKEGKSPVMLRVFLNGEMSNFG
 MTENEQIFWNRVLELAQSQLKQATYEFFVHDARLLKVD
 ~~~

Home modified by Narendrakumar Chaudhari

Narendrakumar Chaudhari — Tue, 11 Sep 2018 09:12:10 -0000

--- v86
+++ v87
@@ -59,7 +59,7 @@
 This option includes the both 1 and 2 options together for whole pan-genome analysis using dafault settings (user friendly) but for more than 100 genomes this will not include subset analysis and KEGG/COG functional analysis.
 * **Important: To use BPGA with cd-hit and OrthoMCL outputs, follow these steps:**
 **1) CD-HIT:**
-Do step 1 of BPGA using your gbk or protein fasta files. Use the **INPUT_all.faa/.seq** file generated here as input for cd-hit (Set your own identity and coverage values). You can either use [online cd-hit web server](http://weizhongli-lab.org/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit) or standalone in linux.
+Do step 1 of BPGA using your gbk or protein fasta files. Use the **INPUT_all.faa/.seq** file generated here as input for cd-hit (Set your own identity and coverage values). You can either use [online cd-hit web server](http://weizhong-lab.ucsd.edu/cdhit_suite/cgi-bin/index.cgi?cmd=cd-hit) or standalone in linux.
 Now use ***\*.clstr** or **\*.sorted*** files from the cd-hit output in Step 2 of BPGA. (copy the file in bin folder and enter full name when asked). You are done.
 **2) OrthoMCL: **
 For users new to OrthoMCL get a preinstalled virtual Operating System from [this link](https://wiki.itap.purdue.edu/display/BioCoreFacility/Phylogenomics+workshop)
@@ -104,7 +104,7 @@
 MTENEQIFWNRVLELAQSQLKQATYEFFVHDARLLKVD
 MRTNFKVSFYLRSNYENKEGKSPVMLRVFLNGEMSNFG
 ~~~
-
+***(Note that new NCBI faa files may not have the above format, they may match the following .pep.fsa format. In that case, user needs to use the pep.fsa option while using BPGA and rename the files accordingly before proceeding.)***

 * **HMP Protein FASTA files sample:(.pep.fsa)**
 ~~~