bg7/BG7 — Issue #22: Current master has issues
Author: mscook
Created: 2012-01-13 07:56:43+00:00
State: open

Hi Guys -

In bin/bg7 -

# MJSC - Typo here. /jars/ not jar
# MJSC - Typo - Should be BG7.jar
# ugly hack, executions.xml should be a param
cp $BG7_HOME/jars/BG7.jar $output_folder/
# run bg7!
# I will add memory conf through the script later on, no time for this now
echo "running bg7 now!"
java -d64 -Xmx6G -Xms1G -jar $output_folder/BG7.jar
# clean up
rm -f $output_folder/BG7.jar

After fixing those I get this (std.err and std.out are piped separately, sorry) -

java.io.FileNotFoundException: Annotation_test_PredictedGenes.xml (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileReader.(FileReader.java:72)
at com.era7.bioinfo.annotation.RemoveDuplicatedGenes.main(RemoveDuplicatedGenes.java:88)
at com.era7.bioinfo.annotation.RemoveDuplicatedGenes.execute(RemoveDuplicatedGenes.java:47)
at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)
at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)
java.io.FileNotFoundException: Annotation_test_NoDuplicates.xml (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileReader.(FileReader.java:72)
at com.era7.bioinfo.annotation.SolveOverlappings.main(SolveOverlappings.java:90)
at com.era7.bioinfo.annotation.SolveOverlappings.execute(SolveOverlappings.java:49)
at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)
at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)
Jan 13, 2012 5:36:30 PM com.era7.bioinfo.annotation.GenerateFastaFiles main
SEVERE: null
java.io.FileNotFoundException: Annotation_test_SolvedOverlaps.xml (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileReader.(FileReader.java:72)
at com.era7.bioinfo.annotation.GenerateFastaFiles.main(GenerateFastaFiles.java:86)
at com.era7.bioinfo.annotation.GenerateFastaFiles.execute(GenerateFastaFiles.java:58)
at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)
at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)

java.io.FileNotFoundException: Annotation_test_SolvedOverlaps.xml (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileReader.(FileReader.java:72)
at com.era7.bioinfo.annotation.FillDataFromUniprot.main(FillDataFromUniprot.java:67)
at com.era7.bioinfo.annotation.FillDataFromUniprot.execute(FillDataFromUniprot.java:48)
at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)
at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)

logging your params to /home/uqmstan1/bg7_test/bg7_example_input_files/out/params.log
it looks like this machine has 16 cores, will use that for blast settings
creating RNAs blast db
RNA blast db created: /home/uqmstan1/bg7_test/bg7_example_input_files/out/Annotation_test.rnas.db
if you want, you can check makeblastdb log: /home/uqmstan1/bg7_test/bg7_example_input_files/out/Annotation_test.rnas.db.log
running blastn: RNAs vs genome sequence
done! will do a basic results check now
checking if blast xml output file looks ok...
done! everything looks ok
creating blast db with genome sequences
genome blast db created: /home/uqmstan1/bg7_test/bg7_example_input_files/out/Annotation_test.genome.db
you can check makeblastdb log: /home/uqmstan1/bg7_test/bg7_example_input_files/out/Annotation_test.genome.db.log
running tblastn: proteins vs genome sequence
done! will do a basic results check now
checking if blast xml output file looks ok...
done! everything looks ok
Now I will create the executions.xml file that will drive bg7 execution
you can take a look at it, if you want: /home/uqmstan1/bg7_test/bg7_example_input_files/out/executions.xml
running bg7 now!
This program expects six parameters:
1. BlastOutput XML filename
2. Contigs FNA filename
3. Output results XML filename
4. Maximum gene length (integer)
5. Flag (boolean) indicating if this genome corresponds to a virus (true/false)
6. Dif span (integer)

Contents of my output directory -

Annotation_test_GenBankExternalData.xml
Annotation_test.genome.db.log
Annotation_test.genome.db.nhr
Annotation_test.genome.db.nin
Annotation_test.genome.db.nsq
Annotation_test_proteins_tBLASTn.xml
Annotation_test_ReferenceProteins.fasta
Annotation_test_RNA_blastn.xml
Annotation_test.rnas.db.log
Annotation_test.rnas.db.nhr
Annotation_test.rnas.db.nin
Annotation_test.rnas.db.nsq
Annotation_test_sequences.fna
BG7.jar
consoleSolapamientos.txt
console.txt
executions.xml
genetic_code.txt
params.log

Any ideas?

Cheers

Mitch