You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Whilst attempting to use your software, I found a number of problems which I fixed manually. Perhaps it may be of some help.
The first problem I encountered was in the bin/bg7 shell script on the blastn and tblastn validation lines. My ncbi-blast install is version 2.2.28+ and i found that the generated .xml output files all had a blank line at the bottom. Therefore, the validation lines:
Line 241: rnaBlastOk=$(tail -n 1 ${rnasVsContigsOutputPath} | grep -c '')
Line 279: proteinBlastOk=tail -n 1 ${proteinsVsContigsOutPath} | grep -c '</BlastOutput>'
Had to be changed to:
Line 241: rnaBlastOk=$(tail -n 2 ${rnasVsContigsOutputPath} | grep -c '')
Line 279: proteinBlastOk=tail -n 2 ${proteinsVsContigsOutPath} | grep -c '</BlastOutput>'
The -n argument of the "tail" program had to change from 1 to 2 to skip that newline at the end.
The second problem I found is within the directory structure of BG7. The BG7 jar file is jars/BG7.jar. However, the bg7 shell script looks for it as "jar/bg7.jar". I had to change this:
To correct for the jar directory name mismatch and the jar's case.
Finally, the template execution file for the PredictGenes task was lacking a parameter, which I added as the default DIF_SPAN value (indicated as 30 in the PredictGenes.java file). To do this, I changed in the bg7 script the following lines:
So now it takes in account the last argument when invoking the BG7.jar in the last part of the script. I also changed the "executionsTemplate.xml" file that comes with in the BG7 directory to add the same parameter line on the same place. So this:
Hi mcoimbra, I came across the same problems with BG7 you had 11 months ago. Thank you very much for this post. It saved me a lot of time. :)
Did you also encounter ArrayIndexOUtOfBounds in PredictGenes?
Dear developers,
Whilst attempting to use your software, I found a number of problems which I fixed manually. Perhaps it may be of some help.
The first problem I encountered was in the bin/bg7 shell script on the blastn and tblastn validation lines. My ncbi-blast install is version 2.2.28+ and i found that the generated .xml output files all had a blank line at the bottom. Therefore, the validation lines:
Line 241: rnaBlastOk=$(tail -n 1 ${rnasVsContigsOutputPath} | grep -c '')
Line 279: proteinBlastOk=
tail -n 1 ${proteinsVsContigsOutPath} | grep -c '</BlastOutput>'
Had to be changed to:
Line 241: rnaBlastOk=$(tail -n 2 ${rnasVsContigsOutputPath} | grep -c '')
Line 279: proteinBlastOk=
tail -n 2 ${proteinsVsContigsOutPath} | grep -c '</BlastOutput>'
The -n argument of the "tail" program had to change from 1 to 2 to skip that newline at the end.
The second problem I found is within the directory structure of BG7. The BG7 jar file is jars/BG7.jar. However, the bg7 shell script looks for it as "jar/bg7.jar". I had to change this:
cp $BG7_HOME/jar/bg7.jar $output_folder/
echo "running bg7 now!"
java -d64 -Xmx6G -Xms1G -jar $output_folder/bg7.jar
rm -f $output_folder/bg7.jar
To this:
cp $BG7_HOME/jars/BG7.jar $output_folder/
echo "running bg7 now!"
java -d64 -Xmx6G -Xms1G -jar $output_folder/BG7.jar
rm -f $output_folder/BG7.jar
To correct for the jar directory name mismatch and the jar's case.
Finally, the template execution file for the PredictGenes task was lacking a parameter, which I added as the default DIF_SPAN value (indicated as 30 in the PredictGenes.java file). To do this, I changed in the bg7 script the following lines:
To:
So now it takes in account the last argument when invoking the BG7.jar in the last part of the script. I also changed the "executionsTemplate.xml" file that comes with in the BG7 directory to add the same parameter line on the same place. So this:
Changed to this:
Finally, after doing all of the above, I managed to get bg7 working properly. I hope this is of some help to the team.
Out of curiosity, how long do you estimate for a release with these fixes, so that BG7 comes "working out of the box"?
Thanks for your time!
The text was updated successfully, but these errors were encountered: