BPGA Activity
A tool for ultra-fast pan-genome analysis of microbes.
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Activity for BPGA
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Milena Trabert posted a comment on ticket #9
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.
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Xiaorui Chen posted a comment on a wiki page
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.
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Narendrakumar Chaudhari posted a comment on ticket #9
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.
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WANG created ticket #9
Error about "Illegal modulus zero" and can't be fixed after relaunching BPGA
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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...
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Results
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Ran AJ created ticket #8
List of core genes
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All outputs removed
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You are welcome.
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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
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They are moved to Results folder and other files are moved to sequence folder or Supporting_files folder created inside bin.
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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
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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.
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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.
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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.
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All outputs removed
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Idowu Olawoye posted a comment on ticket #6
Please Help with the above
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Then, close BPGA. Relaunch it and then directly run to step 2.
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Input Clustering Error
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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.
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I am having the same error and restarting step 2 doesnt solve it. What can I do?
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Functional Analysis
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Please refer to closed ticket #2 Linux Illegal modulus zero
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Linux Illegal modulus zero
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A few issues on Linux and PC
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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...
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jacastillo created ticket #5
MLST based core phylogeny
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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
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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.
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Functional Analysis
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Codie posted a comment on ticket #2
I was receiving the same error. I followed Narendrakumar's advice and it worked for me!!
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Pablo Cruz Morales created ticket #3
Illegal modulus zero at /BPGA/lib/std/cavaexecscript/BPGA-Version-1.3.pl line 2193, <DATA> line 1.
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Results
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FAQs
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Results
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Description 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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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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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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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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General Instructions
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Interpretation of Results
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BPGA released /BPGA-1.3-mswin-x86-0-0-0.zip
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Boahemaa Adu-Oppong posted a comment on ticket #2
Thank you for the response. I'll go ahead and try that. Thank you.
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Check if Input_all.seq is not empty. If all are files generated during peparation, relaunch BPGA and start from step 2.
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Check if Input_all.seq is not empty. if all files generated during peparation relaunch BPGA and start from step 2.
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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
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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
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Linux Illegal modulus zero
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Ben Vezina posted a comment on ticket #1
Thanks!
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Hi Narendrakumar, Thanks for the response. I'll give that a go then
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Ben, If you select any fasta option we must ignore your headers because it may not...
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Sorry, @Ben Vezina, We did not get any notification about your post. Check out the...
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Sorry don't know how to edit original post, but another feature that is missing is...
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Sorry don't know how to edit original post, but another featuer that is missing is...
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A few issues on Linux and PC
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