Current master has issues

[mscook]

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

It looks like BG7.jar should be given arguments, but the shell script (bg7 in bin/ does not provide them)

Any ideas?

Cheers

Mitch

[eparejatobes]

Hi Mitch,

sorry for the delay, I'd take a look into this ASAP.

[mscook]

Any updates on this?

Cheers

Mitch

[lf3045]

Any updates on this?

[larsius]

This is an old issue, still not solved? Got the same trouble, but got a step ahead.
The bg7 script creates executions.xml with advice for the next steps, here for
PredictGenes.jar there are 5 arguments listed, while the PredictGenes.jar needs indeed 6.
The "dif span" is missing, I did not find what it is actually and would really like to know.
As well the arguments for maximum gene length and virus flag are set arbitrarily (400 true),
not really best when annotating a bacterial genome. I changed all this and still got error with
PredictGenes.jar as well when running it separately after FixFastaHeaders and the bg7 script for BLAST.
Here is the error message:
Reading fna file...
java.lang.StringIndexOutOfBoundsExecption: String index out of range: 0
at java.lang.String.charAt(String.java:694)
at com.era7.bioinfo.annotation.PredictGenes.main(PredictGenes.java:147)

[larsius]

even with the test dataset of EHEC I got trouble, did FixFastaHeaders and script for BLASTing and corrected the
executions.xml for max gene length, virus flag and dif size (30) it still hangs in the PredictGenes part - heres the on-screen output.

java -d64 -Xmx6G -Xms1G -jar bg7.jar
Reading fna file...
Done!! :)
Calculating complementary inverted sequences....
Done!
Parsing blastoutput XML file
Done!
Iterations size: 146293
Iteration sp has 1hits
java.lang.ArrayIndexOutOfBoundsException: 1
at com.era7.bioinfo.annotation.PredictGenes.main(PredictGenes.java:208)
at com.era7.bioinfo.annotation.PredictGenes.execute(PredictGenes.java:46)
at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66)
at com.era7.bioinfo.annotation.BG7.main(BG7.java:32)
java.io.FileNotFoundException: ehec_PredictedGenes.xml (No such file or directory)
[...and going on with missing files errors in the next steps ]

[dnatag]

I got the same ArrayIndexOutOfBoundsException as @larsius

Any update?