Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.
Comment: Update memory usage

...

  • We have created a special queue for BLAST2GO: -q lTb2g.q
  • You must also request the resource "b2g": -l b2g
  • Job time limits are the same  as as other 'long' queues. Memory is limited to 6GB.24GB

Command line

  • Use the module bioinformatics/blast2go to load the dependencies for BLAST2GO
  • This will create an alias runblast2go which incorporates the java options needed for the program.
  • A java maxheapsize of 1024m 2048m for JAVA is used by default. This can be overridden by setting the environmental variable BLAST2GO_HEAP_SIZE
  • The -tempfolder (where logs and temporary files are put) is set to the current working directory. This can be changed with the environmental variable BLAST2GO_TEMP

Code Block
# /bin/sh
# ----------------Parameters---------------------- #
#$ -S /bin/sh
#$ -q lTb2g.q
#$ -l b2g,mres=6G24G,h_data=6G24G,h_vmem=6G24G
#$ -cwd -j y -N b2g-test -o b2g-test.log
#
# ----------------Modules------------------------- #
#
module load bioinformatics/blast2go
#
# ----------------Your Commands------------------- #
#
echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
#
#

# Make local copy of cli.prop
# (this overwrites any existing cli.prop file in the current directory and only needs to be done once):
hydracliprop

# Run example dataset:
runblast2go \
  -properties cli.prop \
  -loadfasta example_data/1000_plant.fasta \
  -loadblast example_data/1000_plant_blastResult.xml \
  -mapping \
  -annotation \
  -saveb2g example.b2g \
  -savereport example.pdf

#
echo = `date` job $JOB_NAME done

Anchor
db
db
cli.prop and Local Database Access

The file cli.prop gives the settings for the execution of the program. A template configured with the database access information for running BLAST2GO on the Hydra cluster can be copied to your current directory with the command hydracliprop after you load the BLAST2GO module.

Anchor
dbpolicy
dbpolicy
Local Database Policy

The local database is large and system constraints limit us from keeping old versions. When the database is updated, the old version will no longer be available.

Anchor
stats
stats
Outputting Graphs and Statistics

The command line version of BLAST2GO can produce many types of graphs as well as a summary report. The option -statistics all will produce all available statistics as png images, csv and .b2g files. Start BLAST2GO with -statistics (committing any options) to see a list of available charts. The option --savereport <name> creates a PDF with common summary statistics. Creating a combined graph can only be done with the GUI based BLAST2GO Basic which has a free license. This program can also be used to work with the .b2g files created by the command line version.


14  MPK