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bg7 / BG7

bacterial genome annotation system
bg7.ohnosequences.com
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run BG7 locally #39

Open haruosuz opened 11 years ago

haruosuz commented 11 years ago

Dear BG7 Team:

I was wondering if there is any documentation about how to run BG7 locally. I could not find any example syntax/scripts to run the program from the command-line at http://bg7.ohnosequences.com and https://github.com/bg7/bg7/wiki. I would appreciate any feedback you can give.

Thank you, paruo

rtobes commented 11 years ago

There is not significant differences between run BG7 locally or in the cloud.

You can find some information about how to run BG7 here: http://bg7.ohnosequences.com/faq/#hardware-reqs

haruosuz commented 11 years ago

Thank you for your reply. I downloaded the 'BG7-master' directory by clicking [Download ZIP] at https://github.com/bg7/BG7. Could you provide me with the expected output file names when running bg7 in bg7_example_input_files?

I typed the following commands. cd BG7-master/bg7_example_input_files ../bin/bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta \ --proteins EHEC_ReferenceProteins_17_08_2012.fasta \ --rnas EHEC_Reference_RNAs.frn \ --genetic_code genetic_code.txt \ --genbank_data GenBankExternalData.xml

This generated the following output files, bg7project.genome.db.log bg7project.genome.db.nhr bg7project.genome.db.nin bg7project.genome.db.nsq bg7project_proteins_tBLASTn.xml bg7project_ReferenceProteins.fasta bg7project_RNA_blastn.xml bg7project.rnas.db.log bg7project.rnas.db.nhr bg7project.rnas.db.nin bg7project.rnas.db.nsq bg7project_sequences.fna params.log

and printed the following message. cp: snip/BG7-master/bg7_example_input_files/genetic_code.txt' and snip/BG7-master/bg7_example_input_files/genetic_code.txt' are the same file

Running bg7 with --project_name and --out options printed the following message. cp: cannot stat `/jar/bg7.jar': No such file or directory

krittima2525 commented 10 years ago

Dear paruo,

I tried to run them like your command but it was not showed any output files. Could you suggest me about this error? My command is

~/Documents/BG7/bin/bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta \

--proteins EHEC_ReferenceProteins_17_08_2012.fasta \ --rnas EHEC_Reference_RNAs.frn \ --genetic_code genetic_code.txt \ --genbank_data GenBankExternalData.xml Error message : -bash: /Users/linamac/Documents/BG7/bin/bg7: Permission denied

So I changed command to run by BG7.jar as following command; java -jar BG7.jar bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta --proteins EHEC_ReferenceProteins_17_08_2012.fasta --rnas EHEC_Reference_RNAs.frn --genetics_code genetic_code.txt --genbank_data GenBankExternalData.xml

The output was showed as following; Aug 20, 2014 9:28:14 PM com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile main SEVERE: null java.io.FileNotFoundException: executions.xml (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:131) at java.io.FileReader.(FileReader.java:72) at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:37) at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)

So I don't know why it was occurred. Thank you in advance for your suggestion.

Krittima

haruosuz commented 10 years ago

Alternatively, you can use Prokka for prokaryotic genome annotation. http://www.vicbioinformatics.com/software.prokka.shtml http://www.ncbi.nlm.nih.gov/pubmed/24642063

On Aug 20, 2014, at 8:33, krittima2525 notifications@github.com wrote:

Dear paruo,

I tried to run them like your command but it was not showed any output files. Could you suggest me about this error? My command is ~/Documents/BG7/bin/bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta \

--proteins EHEC_ReferenceProteins_17_08_2012.fasta \ --rnas EHEC_Reference_RNAs.frn \ --genetic_code genetic_code.txt \ --genbank_data GenBankExternalData.xml Error message : -bash: /Users/linamac/Documents/BG7/bin/bg7: Permission denied

So I changed command to run by BG7.jar as following command; java -jar BG7.jar bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta --proteins EHEC_ReferenceProteins_17_08_2012.fasta --rnas EHEC_Reference_RNAs.frn --genetics_code genetic_code.txt --genbank_data GenBankExternalData.xml

The output was showed as following; Aug 20, 2014 9:28:14 PM com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile main SEVERE: null java.io.FileNotFoundException: executions.xml (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:131) at java.io.FileReader.(FileReader.java:72) at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:37) at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)

So I don't know why it was occurred. Thank you in advance for your suggestion.

Krittima

— Reply to this email directly or view it on GitHub.

krittima2525 commented 10 years ago

Dear Paruo,

Thank you for your kindness.

Best regards, Krittima

2014-08-20 23:24 GMT+07:00 paruo notifications@github.com:

Alternatively, you can use Prokka for prokaryotic genome annotation. http://www.vicbioinformatics.com/software.prokka.shtml http://www.ncbi.nlm.nih.gov/pubmed/24642063

On Aug 20, 2014, at 8:33, krittima2525 notifications@github.com wrote:

Dear paruo,

I tried to run them like your command but it was not showed any output files. Could you suggest me about this error? My command is ~/Documents/BG7/bin/bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta \

--proteins EHEC_ReferenceProteins_17_08_2012.fasta \ --rnas EHEC_Reference_RNAs.frn \ --genetic_code genetic_code.txt \ --genbank_data GenBankExternalData.xml Error message : -bash: /Users/linamac/Documents/BG7/bin/bg7: Permission denied

So I changed command to run by BG7.jar as following command; java -jar BG7.jar bg7 --genome escherichia_coli_o104_h4_str._ty-2482_1_supercontigs.fasta --proteins EHEC_ReferenceProteins_17_08_2012.fasta --rnas EHEC_Reference_RNAs.frn --genetics_code genetic_code.txt --genbank_data GenBankExternalData.xml

The output was showed as following; Aug 20, 2014 9:28:14 PM com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile main SEVERE: null java.io.FileNotFoundException: executions.xml (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(FileInputStream.java:131) at java.io.FileReader.(FileReader.java:72) at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:37)

at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)

So I don't know why it was occurred. Thank you in advance for your suggestion.

Krittima

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/bg7/BG7/issues/39#issuecomment-52803060.

Krittima Anekthanakul Aquatic animal Researcher and Biostatician Veterinary Medical Aquatic animal Research Center (VMARC) Faculty of Veterinary Science, Chulalongkorn University, Henri-Dunant Rd., Pathumwan, Bangkok 10330, Thailand Tel (66) 2251 8887 Fax (66) 2251 8887 Mobile (668) 4078 8300