Activity for BPGA

Milena Trabert posted a comment on ticket #9

Milena Trabert — Thu, 18 Nov 2021 12:15:21 -0000

Hello! I also had this error, and it was a problem with usearch. There still was an older version of usearch on my current computer (with the same version name as the one I downloaded, but a different checksum than the one listed on the website). BPGA step 2 works perfectly with the older version from Feb 10th 2021, but when I try to run it with a current version, I experience the error listed above every time.

Xiaorui Chen posted a comment on a wiki page

Xiaorui Chen — Mon, 20 Sep 2021 16:31:24 -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.

Narendrakumar Chaudhari posted a comment on ticket #9

Narendrakumar Chaudhari — Wed, 02 Dec 2020 07:22:39 -0000

Dear user, Thanks for using BPGA. If you don't mind, please email the Input_all.seq file to bpgatool@gmail.com rather than publicly. We will post the problem and solution if it is solved.

WANG created ticket #9

WANG — Wed, 02 Dec 2020 07:10:27 -0000

Error about "Illegal modulus zero" and can't be fixed after relaunching BPGA

Narendrakumar Chaudhari posted a comment on ticket #8

Narendrakumar Chaudhari — Thu, 12 Nov 2020 09:18:01 -0000

Dear User, Look for file gi_name in the bin directory after running BPGA analysis. This file contains gene identifiers with their names (if you use gbk or gbff as input). You can just match the accession numbers in Sequences\REPSEQ_core.txt with gi_name to find their names. Alternatively, if you want the KEGG or COG gene family classification for the same core genome, you can look for K###### numbers or COG#### in Supporting_files\CORE_kegg_hits3.txt or Supporting_files\CORE_COG_hits3.txt, and search...

Narendrakumar Chaudhari modified a wiki page

Narendrakumar Chaudhari — Fri, 30 Oct 2020 09:51:08 -0000

Results

Ran AJ created ticket #8

Ran AJ — Wed, 06 Nov 2019 14:30:08 -0000

List of core genes

Narendrakumar Chaudhari modified ticket #7

Narendrakumar Chaudhari — Tue, 24 Sep 2019 15:31:33 -0000

All outputs removed

Narendrakumar Chaudhari posted a comment on ticket #7

Narendrakumar Chaudhari — Tue, 24 Sep 2019 15:31:00 -0000

You are welcome.

Ran AJ posted a comment on ticket #7

Ran AJ — Tue, 24 Sep 2019 15:28:28 -0000

Ok sorry thank you mea culpa. It appears in my computer as empty folders... but when I clicked it was not empty... Thank you again it help me in all cases for the intermediate files! Best, Rania

Narendrakumar Chaudhari posted a comment on ticket #7

Narendrakumar Chaudhari — Tue, 24 Sep 2019 15:18:40 -0000

They are moved to Results folder and other files are moved to sequence folder or Supporting_files folder created inside bin.

Ran AJ posted a comment on ticket #7

Ran AJ — Tue, 24 Sep 2019 14:59:16 -0000

Thank you very much for your rapid answer. So, yes, I can run directly from step 2. Then I choose "Draw pan-core plot with combinations". I can see that it is "DONE", but when I exit, the pdf plots, are also removed. So do I have to copy them also? Thank you very much Best, Rania

Narendrakumar Chaudhari modified a comment on ticket #7

Narendrakumar Chaudhari — Tue, 24 Sep 2019 14:33:05 -0000

Hello, Rania, The intermediate files are deleted and output is moved to respective folders formed inside bin. However, you can rerun the analsis step 2 directly. If you want to see intermediate files then copy them before exit.

Narendrakumar Chaudhari modified a comment on ticket #7

Narendrakumar Chaudhari — Tue, 24 Sep 2019 14:32:27 -0000

Hello, Rania, The intermediate files are deleted and output is moved to respective folders formed inside bin. However, you can rerun the analsysi step 2 directly. If you want to see intermediate files then copy them before exit.

Narendrakumar Chaudhari posted a comment on ticket #7

Narendrakumar Chaudhari — Tue, 24 Sep 2019 14:32:05 -0000

Hello, Rania, The intermediate file are deleted and output is moved to respective folders formed inside bin. However, you can rerun the analsysi step 2 directly. If you want to see intermediate files then copy them before exit.

Ran AJ created ticket #7

Ran AJ — Tue, 24 Sep 2019 14:23:56 -0000

All outputs removed

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Narendrakumar Chaudhari — Tue, 30 Jul 2019 12:23:57 -0000

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Narendrakumar Chaudhari — Tue, 30 Jul 2019 12:22:50 -0000

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Narendrakumar Chaudhari — Tue, 30 Jul 2019 11:59:35 -0000

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Idowu Olawoye posted a comment on ticket #6

Idowu Olawoye — Mon, 01 Jul 2019 14:45:16 -0000

Please Help with the above

Narendrakumar Chaudhari posted a comment on ticket #2

Narendrakumar Chaudhari — Mon, 01 Jul 2019 11:14:44 -0000

Then, close BPGA. Relaunch it and then directly run to step 2.

Idowu Olawoye created ticket #6

Idowu Olawoye — Mon, 01 Jul 2019 10:46:14 -0000

Input Clustering Error

Idowu Olawoye modified a comment on ticket #2

Idowu Olawoye — Tue, 16 Apr 2019 14:40:57 -0000

I am having the same error and restarting step 2 doesnt solve it. What can I do? The input_all.seq file is not empty.

Idowu Olawoye posted a comment on ticket #2

Idowu Olawoye — Tue, 16 Apr 2019 14:10:11 -0000

I am having the same error and restarting step 2 doesnt solve it. What can I do?

Narendrakumar Chaudhari modified ticket #4

Narendrakumar Chaudhari — Tue, 02 Apr 2019 06:27:57 -0000

Functional Analysis

Narendrakumar Chaudhari posted a comment on ticket #3

Narendrakumar Chaudhari — Tue, 02 Apr 2019 06:26:16 -0000

Please refer to closed ticket #2 Linux Illegal modulus zero

Narendrakumar Chaudhari modified ticket #2

Narendrakumar Chaudhari — Tue, 02 Apr 2019 06:24:59 -0000

Linux Illegal modulus zero

Narendrakumar Chaudhari modified ticket #1

Narendrakumar Chaudhari — Tue, 02 Apr 2019 06:24:08 -0000

A few issues on Linux and PC

Narendrakumar Chaudhari posted a comment on ticket #5

Narendrakumar Chaudhari — Tue, 02 Apr 2019 05:52:34 -0000

For MLST analysis, BPGA will halt and allow the user to make required changes. For MLST analysis, on user defined housekeeping genes Check "mlst_core.txt" for gene details and copy the respective cluster IDs from the first column to "CORE_MLST.txt". CORE_MLST file has core gene family IDs , If you keep only desired IDs phylogeny will run on only those present in CORE_MLST file. You can select by looking at the gene names in mlst_core.txt file. and copy only desired IDs from mlst_core.txt to CORE_MLST...

jacastillo created ticket #5

jacastillo — Tue, 02 Apr 2019 02:41:47 -0000

MLST based core phylogeny

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Narendrakumar Chaudhari — Sat, 19 Jan 2019 06:36:48 -0000

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Narendrakumar Chaudhari — Tue, 11 Sep 2018 09:12:18 -0000

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jacastillo posted a comment on ticket #4

jacastillo — Fri, 31 Aug 2018 18:31:56 -0000

Hi BPGA team: I appreciate your answer about KEGG/COG problem. I followed your instruction and it worked! I have another question: BPGA doesn’t seem to work with unfinished/unclosed genomes, I mean, sequences at contigs or scaffold level. Do you have a new version of BPGA for WGS/incomplete genomes? José

Narendrakumar Chaudhari posted a comment on ticket #4

Narendrakumar Chaudhari — Wed, 22 Aug 2018 06:30:39 -0000

Just check from usearch.exe file properties that it is not actually usearch.exe.exe due to hidden file extension. If so remove .exe from file name. Always run bpga from command line or terminal to know more detailed errors. Some systems with Win 10 OS may not allow dll dependaent usearch to run properly. If none of this works re-extract the bpga package from downloaded zip and start over in another location.

jacastillo created ticket #4

jacastillo — Wed, 22 Aug 2018 00:08:29 -0000

Functional Analysis

Codie posted a comment on ticket #2

Codie — Fri, 16 Feb 2018 21:50:27 -0000

I was receiving the same error. I followed Narendrakumar's advice and it worked for me!!

Pablo Cruz Morales created ticket #3

Pablo Cruz Morales — Wed, 31 Jan 2018 21:16:10 -0000

Illegal modulus zero at /BPGA/lib/std/cavaexecscript/BPGA-Version-1.3.pl line 2193, line 1.

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 10:02:37 -0000

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:58:54 -0000

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:58:13 -0000

Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:57:36 -0000

Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:55:45 -0000

FAQs

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:30:10 -0000

Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:28:18 -0000

Description of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:27:10 -0000

Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 09:15:39 -0000

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Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 08:47:18 -0000

Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 07:48:15 -0000

Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 07:42:12 -0000

Interpretation of Results

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Interpretation of Results

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Interpretation of Results

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Interpretation of Results

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Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 06:50:41 -0000

Interpretation of Results

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Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 06:37:16 -0000

Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 06:33:39 -0000

Interpretation of Results

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 06:18:12 -0000

General Instructions

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Narendrakumar Chaudhari — Fri, 14 Jul 2017 06:16:20 -0000

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BPGA released /BPGA-1.3-mswin-x86-0-0-0.zip

BPGA — Sat, 13 May 2017 07:47:02 -0000

BPGA released /BPGA-1.3-mswin-x64-0-0-0.zip

BPGA — Sat, 13 May 2017 07:45:03 -0000

BPGA released /BPGA-1.3-linux-x86_64-0-0-0.tar.gz

BPGA — Sat, 13 May 2017 07:45:03 -0000

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BPGA released /Latest Release/BPGA-1.3.0/Update_history.txt

BPGA — Fri, 12 May 2017 12:55:03 -0000

Boahemaa Adu-Oppong posted a comment on ticket #2

Boahemaa Adu-Oppong — Wed, 03 May 2017 15:18:17 -0000

Thank you for the response. I'll go ahead and try that. Thank you.

Narendrakumar Chaudhari modified a comment on ticket #2

Narendrakumar Chaudhari — Wed, 03 May 2017 05:47:56 -0000

Check if Input_all.seq is not empty. If all are files generated during peparation, relaunch BPGA and start from step 2.

Narendrakumar Chaudhari posted a comment on ticket #2

Narendrakumar Chaudhari — Wed, 03 May 2017 05:47:30 -0000

Check if Input_all.seq is not empty. if all files generated during peparation relaunch BPGA and start from step 2.

Boahemaa Adu-Oppong modified a comment on ticket #2

Boahemaa Adu-Oppong — Tue, 02 May 2017 16:30:16 -0000

Also, before clustering fails this is what is printed out: ./usearch -sortbylength INPUT_all.seq -fastaout INPUT_all_sorted.faa -minseqlength 20 ---Fatal error--- Missing --output

Boahemaa Adu-Oppong posted a comment on ticket #2

Boahemaa Adu-Oppong — Tue, 02 May 2017 16:30:00 -0000

Alsom before clustering fails this is what is printed out: ./usearch -sortbylength INPUT_all.seq -fastaout INPUT_all_sorted.faa -minseqlength 20 ---Fatal error--- Missing --output

Boahemaa Adu-Oppong created ticket #2

Boahemaa Adu-Oppong — Tue, 02 May 2017 16:25:55 -0000

Linux Illegal modulus zero

Ben Vezina posted a comment on ticket #1

Ben Vezina — Wed, 29 Mar 2017 03:56:07 -0000

Thanks!

Ben Vezina posted a comment on ticket #1

Ben Vezina — Wed, 29 Mar 2017 03:55:42 -0000

Hi Narendrakumar, Thanks for the response. I'll give that a go then

Narendrakumar Chaudhari posted a comment on ticket #1

Narendrakumar Chaudhari — Sat, 25 Mar 2017 04:57:58 -0000

Ben, If you select any fasta option we must ignore your headers because it may not...

Narendrakumar Chaudhari posted a comment on ticket #1

Narendrakumar Chaudhari — Sat, 25 Mar 2017 04:55:33 -0000

Sorry, @Ben Vezina, We did not get any notification about your post. Check out the...

Ben Vezina modified a comment on ticket #1

Ben Vezina — Tue, 10 Jan 2017 03:49:17 -0000

Sorry don't know how to edit original post, but another feature that is missing is...

Ben Vezina posted a comment on ticket #1

Ben Vezina — Tue, 10 Jan 2017 03:49:07 -0000

Sorry don't know how to edit original post, but another featuer that is missing is...

Ben Vezina created ticket #1

Ben Vezina — Tue, 10 Jan 2017 02:59:54 -0000

A few issues on Linux and PC

BPGA released /Latest Release/BPGA-1.3.0/BPGA-1.3-mswin-x86-0-0-0.zip

BPGA — Mon, 19 Dec 2016 07:42:02 -0000

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