How to run Queue for the first time

Geraldine_VdAuwera

Objective

Run a basic analysis command on example data, parallelized with Queue.

Prerequisites

• Successfully completed "How to test your Queue installation" and "How to run GATK for the first time"
• GATK resource bundle downloaded

Steps

1. Set up a dry run of Queue
2. Run the analysis for real
3. Running on a computing farm

---

1. Set up a dry run of Queue

One very cool feature of Queue is that you can test your script by doing a "dry run". That means Queue will prepare the analysis and build the scatter commands, but not actually run them. This makes it easier to check the sanity of your script and command.

Here we're going to set up a dry run of a CountReads analysis. You should be familiar with the CountReads walker and the example files from the bundles, as used in the basic "GATK for the first time" tutorial. In addition, we're going to use the example QScript called ExampleCountReads.scala provided in the Queue package download.

Action

Type the following command:

java -Djava.io.tmpdir=tmp -jar Queue.jar -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam

where -S ExampleCountReads.scala specifies which QScript we want to run, -R exampleFASTA.fasta specifies the reference sequence, and -I exampleBAM.bam specifies the file of aligned reads we want to analyze.

Expected Result

After a few seconds you should see output that looks nearly identical to this:

INFO  00:30:45,527 QScriptManager - Compiling 1 QScript 
INFO  00:30:52,869 QScriptManager - Compilation complete 
INFO  00:30:53,284 HelpFormatter - ---------------------------------------------------------------------- 
INFO  00:30:53,284 HelpFormatter - Queue v2.0-36-gf5c1c1a, Compiled 2012/08/08 20:18:21 
INFO  00:30:53,284 HelpFormatter - Copyright (c) 2012 The Broad Institute 
INFO  00:30:53,284 HelpFormatter - Fro support and documentation go to http://www.broadinstitute.org/gatk 
INFO  00:30:53,285 HelpFormatter - Program Args: -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam 
INFO  00:30:53,285 HelpFormatter - Date/Time: 2012/08/09 00:30:53 
INFO  00:30:53,285 HelpFormatter - ---------------------------------------------------------------------- 
INFO  00:30:53,285 HelpFormatter - ---------------------------------------------------------------------- 
INFO  00:30:53,290 QCommandLine - Scripting ExampleCountReads 
INFO  00:30:53,364 QCommandLine - Added 1 functions 
INFO  00:30:53,364 QGraph - Generating graph. 
INFO  00:30:53,388 QGraph - ------- 
INFO  00:30:53,402 QGraph - Pending:  'java'  '-Xmx1024m'  '-Djava.io.tmpdir=/Users/vdauwera/sandbox/Q2/resources/tmp'  '-cp' '/Users/vdauwera/sandbox/Q2/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/Users/vdauwera/sandbox/Q2/resources/exampleBAM.bam'  '-R' '/Users/vdauwera/sandbox/Q2/resources/exampleFASTA.fasta'  
INFO  00:30:53,403 QGraph - Log:     /Users/vdauwera/sandbox/Q2/resources/ExampleCountReads-1.out 
INFO  00:30:53,403 QGraph - Dry run completed successfully! 
INFO  00:30:53,404 QGraph - Re-run with "-run" to execute the functions. 
INFO  00:30:53,409 QCommandLine - Script completed successfully with 1 total jobs 
INFO  00:30:53,410 QCommandLine - Writing JobLogging GATKReport to file /Users/vdauwera/sandbox/Q2/resources/ExampleCountReads.jobreport.txt 

If you don't see this, check your spelling (GATK commands are case-sensitive), check that the files are in your working directory, and if necessary, re-check that the GATK and Queue are properly installed.

If you do see this output, congratulations! You just successfully ran you first Queue dry run!

2. Run the analysis for real

Once you have verified that the Queue functions have been generated successfully, you can execute the pipeline by appending -run to the command line.

Action

Instead of this command, which we used earlier:

java -Djava.io.tmpdir=tmp -jar Queue.jar -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam

this time you type this:

java -Djava.io.tmpdir=tmp -jar Queue.jar -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run

See the difference?

Result

You should see output that looks nearly identical to this:

INFO  00:56:33,688 QScriptManager - Compiling 1 QScript 
INFO  00:56:39,327 QScriptManager - Compilation complete 
INFO  00:56:39,487 HelpFormatter - ---------------------------------------------------------------------- 
INFO  00:56:39,487 HelpFormatter - Queue v2.0-36-gf5c1c1a, Compiled 2012/08/08 20:18:21 
INFO  00:56:39,488 HelpFormatter - Copyright (c) 2012 The Broad Institute 
INFO  00:56:39,488 HelpFormatter - Fro support and documentation go to http://www.broadinstitute.org/gatk 
INFO  00:56:39,489 HelpFormatter - Program Args: -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run 
INFO  00:56:39,490 HelpFormatter - Date/Time: 2012/08/09 00:56:39 
INFO  00:56:39,490 HelpFormatter - ---------------------------------------------------------------------- 
INFO  00:56:39,491 HelpFormatter - ---------------------------------------------------------------------- 
INFO  00:56:39,498 QCommandLine - Scripting ExampleCountReads 
INFO  00:56:39,569 QCommandLine - Added 1 functions 
INFO  00:56:39,569 QGraph - Generating graph. 
INFO  00:56:39,589 QGraph - Running jobs. 
INFO  00:56:39,623 FunctionEdge - Starting:  'java'  '-Xmx1024m'  '-Djava.io.tmpdir=/Users/vdauwera/sandbox/Q2/resources/tmp'  '-cp' '/Users/vdauwera/sandbox/Q2/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/Users/vdauwera/sandbox/Q2/resources/exampleBAM.bam'  '-R' '/Users/vdauwera/sandbox/Q2/resources/exampleFASTA.fasta'  
INFO  00:56:39,623 FunctionEdge - Output written to /Users/GG/codespace/GATK/Q2/resources/ExampleCountReads-1.out 
INFO  00:56:50,301 QGraph - 0 Pend, 1 Run, 0 Fail, 0 Done 
INFO  00:57:09,827 FunctionEdge - Done:  'java'  '-Xmx1024m'  '-Djava.io.tmpdir=/Users/vdauwera/sandbox/Q2/resources/tmp'  '-cp' '/Users/vdauwera/sandbox/Q2/resources/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/Users/vdauwera/sandbox/Q2/resources/exampleBAM.bam'  '-R' '/Users/vdauwera/sandbox/Q2/resources/exampleFASTA.fasta'  
INFO  00:57:09,828 QGraph - 0 Pend, 0 Run, 0 Fail, 1 Done 
INFO  00:57:09,835 QCommandLine - Script completed successfully with 1 total jobs 
INFO  00:57:09,835 QCommandLine - Writing JobLogging GATKReport to file /Users/vdauwera/sandbox/Q2/resources/ExampleCountReads.jobreport.txt 
INFO  00:57:10,107 QCommandLine - Plotting JobLogging GATKReport to file /Users/vdauwera/sandbox/Q2/resources/ExampleCountReads.jobreport.pdf 
WARN  00:57:18,597 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. 

Great! It works!

The results of the traversal will be written to a file in the current directory. The name of the file will be printed in the output, ExampleCountReads.out in this example.

If for some reason the run was interrupted, in most cases you can resume by just launching the command. Queue will pick up where it left off without redoing the parts that ran successfully.

3. Running on a computing farm

Run with -bsub to run on LSF, or for early Grid Engine support see Queue with Grid Engine.

See also QFunction and Command Line Options for more info on Queue options.

oriol_senan

The link "how to use GATK for the first time" is not working

Geraldine_VdAuwera

Prerequisites links are fixed, thanks for reporting this.

lucdh

I looks like some more links need fixing:

• on this page the 3 links under paragraph 3. Running on a computing farm
• on http://gatkforums.broadinstitute.org/discussion/1285/parallelism-with-the-gatk: the GATK-Queue link

Geraldine_VdAuwera

Thanks for reporting, we'll fix these asap.

omedvedeva

I can't perform a first dry run on Windows 7 with Queue 2.2.5. The installation seems to be correct since --help option works. It looks like it can't find the tmp directory that it creates at the correct location. The same problem occurs with QueueLite too. What am I missing? In the stack trace below fasta, bam and scala files were in the working directory:

C:\GATK\Queue-2.2-5-g3bf5e3f>java -Djava.io.tmpdir=tmp -jar Queue.jar -S Example CountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam ERROR 10:17:34,493 QScriptManager - \GATK\Queue-2.2-5-g3bf5e3f\tmp\Q-Classes-80 75780960630530304 does not exist or is not a directory INFO 10:17:35,965 QScriptManager - Compiling 1 QScript INFO 10:17:40,538 QScriptManager - Compilation complete

...

ERROR stack trace

org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with name 'R' isn't defined. at org.broadinstitute.sting.commandline.ParsingEngine.validate(ParsingEn gine.java:303) at org.broadinstitute.sting.commandline.ParsingEngine.validate(ParsingEn gine.java:276) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:204) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:146) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala: 62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

##### ERROR --------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 2.2-5-g3bf5e3f):

...

ERROR MESSAGE: Argument with name 'R' isn't defined.

ERROR --------------------------------------------------------------------

Thank you, Olga.

Geraldine_VdAuwera

I'm sorry Olga, we can't provide support for running GATK or Queue on Windows. There are differences in I/O management that cause problems with filepaths, and we can't shoulder the support burden of helping you figure that out. You should post this question in the Ask the Community section; perhaps others will be able to advise you on this point.

elisa1507

Hi, So I'm trying to run this tutorial and the first script runs fine and looks exactly like step 1. Once I put -run at the end of it, I'm getting an error that looks like this :

ERROR 15:07:45,844 FunctionEdge - Error:  'java'  '-Xmx1024m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/Users/jones/bin/Queue/tmp'  '-cp' '/Users/jones/bin/Queue/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/Users/jones/bin/Queue/resources/exampleBAM.bam'  '-R' '/Users/jones/bin/Queue/resources/exampleFASTA.fasta'  
ERROR 15:07:45,851 FunctionEdge - Contents of /Users/jones/bin/Queue/ExampleCountReads-1.out:
Conflicting collector combinations in option list; please refer to the release notes for the combinations allowed
Could not create the Java virtual machine. 
INFO  15:07:45,852 QGraph - Writing incremental jobs reports... 
INFO  15:07:45,853 QJobsReporter - Writing JobLogging GATKReport to file /Users/jones/bin/Queue/ExampleCountReads.jobreport.txt 
INFO  15:07:45,884 QGraph - 0 Pend, 0 Run, 1 Fail, 0 Done 
INFO  15:07:45,886 QCommandLine - Script failed with 1 total jobs 
INFO  15:07:45,889 QCommandLine - Writing final jobs report... 
INFO  15:07:45,889 QJobsReporter - Writing JobLogging GATKReport to file /Users/jones/bin/Queue/ExampleCountReads.jobreport.txt 
INFO  15:07:45,893 QJobsReporter - Plotting JobLogging GATKReport to file /Users/jones/bin/Queue/ExampleCountReads.jobreport.pdf 
WARN  15:07:46,693 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. 
INFO  15:07:46,695 QCommandLine - Done with errors 
INFO  15:07:46,697 QGraph - ------- 
INFO  15:07:46,699 QGraph - Failed:   'java'  '-Xmx1024m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/Users/jones/bin/Queue/tmp'  '-cp' '/Users/jones/bin/Queue/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/Users/jones/bin/Queue/resources/exampleBAM.bam'  '-R' '/Users/jones/bin/Queue/resources/exampleFASTA.fasta'  
INFO  15:07:46,700 QGraph - Log:     /Users/jones/bin/Queue/ExampleCountReads-1.out 

Do you know why this could be please? I'm new to this!

Thanks!

grumblr

The QFunction and Command Line Options links point to this same page....

See also QFunction and Command Line Options for more info on Queue options.

Geraldine_VdAuwera

Hi @grumblr, sorry about the dead links, I'll fix them asap. The articles they refer to should be in the Developer Zone.

Geraldine_VdAuwera

Hi @elisa1507, I just realized I never answered your question. Sorry about that, it must have slipped through my net. Did you find the solution to your problem or do you still need help with that?

chukhman

Hi all, I ran the above tutorial and received the specified output but I'm not sure how to interpret it. The ExampleCountReads-1.out file seems error free but the ExampleCountReads.jobreport.txt file only contains the line "#:GATKReport.v1.1:0" and nothing else. Also, the ExampleCountReads.jobreport.pdf file is unreadable. The warning "RScriptExecutor - RScript exited with 1" bothers me and upon rerunning with -l DEBUG, it shows several issues with R packages having functions masked (not sure what that means) and the exit status 1 seems to be caused by some "argument 1 is not a vector". Is this all the correct behavior or are these issues really problems that I need to worry about? Thanks for your help!

Morris Chukhman, MS UIC Bioinformatics

Geraldine_VdAuwera

Hi Morris,

It sounds like your analysis run went fine but it's the peripheral reporting that screwed up. Can you post the contents of the ExampleCountReads-1.out file to be sure? Also, do you know if you have gsalib installed?

chukhman

Thanks Geraldine for you reply!

Here is the contents of ExampleCountReads-1.out:

INFO 15:24:31,080 GenomeAnalysisEngine - Strictness is SILENT INFO 15:24:31,083 ReferenceDataSource - Dict file /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleFASTA.dict does not exist. Trying to create it now. [Tue Feb 05 15:24:31 CST 2013] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleFASTA.fasta OUTPUT=/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/dict3620772975149938405.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Feb 05 15:24:31 CST 2013] Executing as pkanabar@nike.structure.uic.edu on Linux 2.6.32-279.1.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_17-b04; Picard version: null [Tue Feb 05 15:24:31 CST 2013] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=244187136 INFO 15:24:31,406 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 15:24:31,415 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 15:24:31,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 15:24:31,461 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 15:24:31,461 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 15:24:31,517 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 15:24:31,521 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 15:24:31,540 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 15:24:31,549 Walker - [REDUCE RESULT] Traversal result is: 33 INFO 15:24:31,551 ProgressMeter - done 3.30e+01 0.1 s 44.9 m 97.3% 0.1 s 0.0 s INFO 15:24:31,552 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours INFO 15:24:31,669 MicroScheduler - 0 reads were filtered out during traversal out of 33 total (0.00%) INFO 15:24:32,547 GATKRunReport - Uploaded run statistics report to AWS S3 ~

It seems to be working properly since that is exactly what the sample output in the GATK tutorial looks like.

Here is the output when I run the whole Queue.jar job and the command that I used:

java -Djava.io.tmpdir=tmp -jar /data1/rhel60/gatk_git20130205/dist/Queue.jar -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run -l DEBUG

INFO  11:06:34,442 QScriptManager - Compiling 1 QScript
DEBUG 11:06:34,446 QScriptManager - Compilation directory: /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/tmp/Q-Classes-5894914949320226077
INFO  11:06:38,335 QScriptManager - Compilation complete
INFO  11:06:38,578 HelpFormatter - ----------------------------------------------------------------------
INFO  11:06:38,578 HelpFormatter - Queue vexported, Compiled 2013/02/06 15:30:41
INFO  11:06:38,578 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO  11:06:38,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
DEBUG 11:06:38,578 HelpFormatter - Current directory: /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk
INFO  11:06:38,579 HelpFormatter - Program Args: -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run -l DEBUG
INFO  11:06:38,579 HelpFormatter - Date/Time: 2013/02/11 11:06:38
INFO  11:06:38,579 HelpFormatter - ----------------------------------------------------------------------
INFO  11:06:38,579 HelpFormatter - ----------------------------------------------------------------------
INFO  11:06:38,587 QCommandLine - Scripting ExampleCountReads
DEBUG 11:06:38,635 QGraph - adding QNode: 0
INFO  11:06:38,644 QCommandLine - Added 1 functions
INFO  11:06:38,645 QGraph - Generating graph.
INFO  11:06:38,659 QGraph - Running jobs.
INFO  11:06:38,663 QGraph - -------
INFO  11:06:38,676 QGraph - Done:     'java'  '-Xmx1024m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/tmp'  '-cp' '/data1/rhel60/gatk_git20130205/dist/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleBAM.bam'  '-R' '/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleFASTA.fasta'
DEBUG 11:06:38,676 QGraph - Inputs:  List(/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleBAM.bai, /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleBAM.bam, /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleBAM.bam.bai, /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/exampleFASTA.fasta)
DEBUG 11:06:38,676 QGraph - Outputs: List(/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads-1.out)
DEBUG 11:06:38,677 QGraph - Done+:   List(/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/.ExampleCountReads-1.out.done)
DEBUG 11:06:38,677 QGraph - Done-:   List()
DEBUG 11:06:38,677 QGraph - CmdDir:  /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk
DEBUG 11:06:38,677 QGraph - Temp?:   false
DEBUG 11:06:38,678 QGraph - Prev:    none (reset = false)
INFO  11:06:38,678 QGraph - Log:     /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads-1.out
INFO  11:06:38,685 QGraph - 0 Pend, 0 Run, 0 Fail, 1 Done
INFO  11:06:38,687 QCommandLine - Script failed with 1 total jobs
INFO  11:06:38,687 QCommandLine - Writing final jobs report...
INFO  11:06:38,687 QJobsReporter - Writing JobLogging GATKReport to file /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads.jobreport.txt
INFO  11:06:38,698 QJobsReporter - Plotting JobLogging GATKReport to file /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads.jobreport.pdf
DEBUG 11:06:38,709 RScriptExecutor - Executing:
DEBUG 11:06:38,709 RScriptExecutor -   Rscript
DEBUG 11:06:38,709 RScriptExecutor -   -e
DEBUG 11:06:38,709 RScriptExecutor -   tempLibDir = '/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/tmp/Rlib.4673101731368374405';install.packages(pkgs=c('/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/tmp/gsalib.tar.6822779882938808174.gz'), lib=tempLibDir, repos=NULL, type='source', INSTALL_opts=c('--no-libs', '--no-data', '--no-help', '--no-demo', '--no-exec'));library('gsalib', lib.loc=tempLibDir);source('/mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/tmp/queueJobReport.6906968465526462577.R');
DEBUG 11:06:38,710 RScriptExecutor -   /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads.jobreport.txt
DEBUG 11:06:38,710 RScriptExecutor -   /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads.jobreport.pdf
* installing *source* package âgsalibâ ...
** Creating default NAMESPACE file
** R
** preparing package for lazy loading
** building package indices
** testing if installed package can be loaded

* DONE (gsalib)
Loading required package: methods
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: âgdataâ

The following object(s) are masked from âpackage:statsâ:

    nobs

The following object(s) are masked from âpackage:utilsâ:

    object.size

Loading required package: caTools
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: MASS

Attaching package: âgplotsâ

The following object(s) are masked from âpackage:statsâ:

    lowess

Loading required package: plyr

Attaching package: âreshapeâ

The following object(s) are masked from âpackage:plyrâ:

    rename, round_any

[1] "Report"
[1] "Project          : /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/ExampleCountReads.jobreport.txt"
Error in order(allJobs$analysisName, allJobs$startTime, decreasing = T) :
  argument 1 is not a vector
Calls: source ... withVisible -> eval -> eval -> plotJobsGantt -> order
Execution halted
DEBUG 11:06:42,668 RScriptExecutor - Result: 1
WARN  11:06:42,668 RScriptExecutor - RScript exited with 1
DEBUG 11:06:42,674 IOUtils - Deleted /mnt/pinal/pinal/sgreen/genotype_11_samples/dry_run_gatk/tmp/Q-Classes-5894914949320226077

It doesn't seem to be complaining about 'gsalib' in particular but the objects masked from the packages seem a bit odd. The failure seems to be in plotJobsGantt but I'm not sure if its the app itself or something upstream that is causing the failure.

Thanks so much for helping us debug this!

Cheers!

Morris

chukhman

Thanks Geraldine for you reply!

Here is the contents of ExampleCountReads-1.out:

INFO 15:24:31,080 GenomeAnalysisEngine - Strictness is SILENT INFO 15:24:31,083 ReferenceDataSource - Dict file /dry_run_gatk/exampleFASTA.dict does not exist. Trying to create it now. [Tue Feb 05 15:24:31 CST 2013] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/dry_run_gatk/exampleFASTA.fasta OUTPUT=/dry_run_gatk/dict3620772975149938405.tmp TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Tue Feb 05 15:24:31 CST 2013] Executing as pkanabar@nike.structure.uic.edu on Linux 2.6.32-279.1.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.6.0_17-b04; Picard version: null [Tue Feb 05 15:24:31 CST 2013] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=244187136 INFO 15:24:31,406 GenomeAnalysisEngine - Downsampling Settings: No downsampling INFO 15:24:31,415 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 15:24:31,428 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01 INFO 15:24:31,461 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 15:24:31,461 ProgressMeter - Location processed.reads runtime per.1M.reads completed total.runtime remaining INFO 15:24:31,517 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 15:24:31,521 ReadShardBalancer$1 - Done loading BAM index data for next contig INFO 15:24:31,540 ReadShardBalancer$1 - Loading BAM index data for next contig INFO 15:24:31,549 Walker - [REDUCE RESULT] Traversal result is: 33 INFO 15:24:31,551 ProgressMeter - done 3.30e+01 0.1 s 44.9 m 97.3% 0.1 s 0.0 s INFO 15:24:31,552 ProgressMeter - Total runtime 0.09 secs, 0.00 min, 0.00 hours INFO 15:24:31,669 MicroScheduler - 0 reads were filtered out during traversal out of 33 total (0.00%) INFO 15:24:32,547 GATKRunReport - Uploaded run statistics report to AWS S3 ~

It seems to be working properly since that is exactly what the sample output in the GATK tutorial looks like.

Here is the output when I run the whole Queue.jar job and the command that I used:

java -Djava.io.tmpdir=tmp -jar /data1/rhel60/gatk_git20130205/dist/Queue.jar -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run -l DEBUG

INFO  11:06:34,442 QScriptManager - Compiling 1 QScript
DEBUG 11:06:34,446 QScriptManager - Compilation directory: /dry_run_gatk/tmp/Q-Classes-5894914949320226077
INFO  11:06:38,335 QScriptManager - Compilation complete
INFO  11:06:38,578 HelpFormatter - ----------------------------------------------------------------------
INFO  11:06:38,578 HelpFormatter - Queue vexported, Compiled 2013/02/06 15:30:41
INFO  11:06:38,578 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO  11:06:38,578 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
DEBUG 11:06:38,578 HelpFormatter - Current directory: /dry_run_gatk
INFO  11:06:38,579 HelpFormatter - Program Args: -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run -l DEBUG
INFO  11:06:38,579 HelpFormatter - Date/Time: 2013/02/11 11:06:38
INFO  11:06:38,579 HelpFormatter - ----------------------------------------------------------------------
INFO  11:06:38,579 HelpFormatter - ----------------------------------------------------------------------
INFO  11:06:38,587 QCommandLine - Scripting ExampleCountReads
DEBUG 11:06:38,635 QGraph - adding QNode: 0
INFO  11:06:38,644 QCommandLine - Added 1 functions
INFO  11:06:38,645 QGraph - Generating graph.
INFO  11:06:38,659 QGraph - Running jobs.
INFO  11:06:38,663 QGraph - -------
INFO  11:06:38,676 QGraph - Done:     'java'  '-Xmx1024m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/dry_run_gatk/tmp'  '-cp' '/data1/rhel60/gatk_git20130205/dist/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/dry_run_gatk/exampleBAM.bam'  '-R' '/dry_run_gatk/exampleFASTA.fasta'
DEBUG 11:06:38,676 QGraph - Inputs:  List(/dry_run_gatk/exampleBAM.bai, /dry_run_gatk/exampleBAM.bam, /dry_run_gatk/exampleBAM.bam.bai, /dry_run_gatk/exampleFASTA.fasta)
DEBUG 11:06:38,676 QGraph - Outputs: List(/dry_run_gatk/ExampleCountReads-1.out)
DEBUG 11:06:38,677 QGraph - Done+:   List(/dry_run_gatk/.ExampleCountReads-1.out.done)
DEBUG 11:06:38,677 QGraph - Done-:   List()
DEBUG 11:06:38,677 QGraph - CmdDir:  /dry_run_gatk
DEBUG 11:06:38,677 QGraph - Temp?:   false
DEBUG 11:06:38,678 QGraph - Prev:    none (reset = false)
INFO  11:06:38,678 QGraph - Log:     /dry_run_gatk/ExampleCountReads-1.out
INFO  11:06:38,685 QGraph - 0 Pend, 0 Run, 0 Fail, 1 Done
INFO  11:06:38,687 QCommandLine - Script failed with 1 total jobs
INFO  11:06:38,687 QCommandLine - Writing final jobs report...
INFO  11:06:38,687 QJobsReporter - Writing JobLogging GATKReport to file /dry_run_gatk/ExampleCountReads.jobreport.txt
INFO  11:06:38,698 QJobsReporter - Plotting JobLogging GATKReport to file /dry_run_gatk/ExampleCountReads.jobreport.pdf
DEBUG 11:06:38,709 RScriptExecutor - Executing:
DEBUG 11:06:38,709 RScriptExecutor -   Rscript
DEBUG 11:06:38,709 RScriptExecutor -   -e
DEBUG 11:06:38,709 RScriptExecutor -   tempLibDir = '/dry_run_gatk/tmp/Rlib.4673101731368374405';install.packages(pkgs=c('/dry_run_gatk/tmp/gsalib.tar.6822779882938808174.gz'), lib=tempLibDir, repos=NULL, type='source', INSTALL_opts=c('--no-libs', '--no-data', '--no-help', '--no-demo', '--no-exec'));library('gsalib', lib.loc=tempLibDir);source('/dry_run_gatk/tmp/queueJobReport.6906968465526462577.R');
DEBUG 11:06:38,710 RScriptExecutor -   /dry_run_gatk/ExampleCountReads.jobreport.txt
DEBUG 11:06:38,710 RScriptExecutor -   /dry_run_gatk/ExampleCountReads.jobreport.pdf
* installing *source* package âgsalibâ ...
** Creating default NAMESPACE file
** R
** preparing package for lazy loading
** building package indices
** testing if installed package can be loaded

* DONE (gsalib)
Loading required package: methods
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: âgdataâ

The following object(s) are masked from âpackage:statsâ:

    nobs

The following object(s) are masked from âpackage:utilsâ:

    object.size

Loading required package: caTools
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: MASS

Attaching package: âgplotsâ

The following object(s) are masked from âpackage:statsâ:

    lowess

Loading required package: plyr

Attaching package: âreshapeâ

The following object(s) are masked from âpackage:plyrâ:

    rename, round_any

[1] "Report"
[1] "Project          : /dry_run_gatk/ExampleCountReads.jobreport.txt"
Error in order(allJobs$analysisName, allJobs$startTime, decreasing = T) :
  argument 1 is not a vector
Calls: source ... withVisible -> eval -> eval -> plotJobsGantt -> order
Execution halted
DEBUG 11:06:42,668 RScriptExecutor - Result: 1
WARN  11:06:42,668 RScriptExecutor - RScript exited with 1
DEBUG 11:06:42,674 IOUtils - Deleted /dry_run_gatk/tmp/Q-Classes-5894914949320226077

It doesn't seem to be complaining about 'gsalib' in particular but the objects masked from the packages seem a bit odd. The failure seems to be in plotJobsGantt but I'm not sure if its the app itself or something upstream that is causing the failure.

Thanks so much for helping us debug this!

Cheers!

Morris

Geraldine_VdAuwera

Hi Morris,

OK, your analysis job definitely executed correctly. What is screwing up is just Queue's reporting about the job(s) that it ran, which is annoying but not of real importance. I think the failure may be linked to a bug in the reporting system which we've fixed in our development version. You can safely ignore this error for now; if it persists in the next version (2.4, estimated for release next week) let us know in this thread.

chukhman

The same error occurs both with the 2.3.9 tarball as well as the version on github. Is the dev version different thatn the github version?

Geraldine_VdAuwera

That's correct, the dev version is different and is currently not available to the public. The github version is the last stable version we released, and is the same thing as the tarball. We're in the process of changing our release workflow and may in the near future start providing nightly builds of the dev source; but right now that's just not possible, sorry.

chukhman

Has 2.4 been released yet? The downloads page still links to 2.3.9.

Geraldine_VdAuwera

Not yet -- we're planning on releasing it Monday if all goes well.

Alessandro

Hi Geraldine, I have a problem running of the "dry run" pre-analysis that you suggest. I've read the comments above, but none seemed to help my case, so I post the command line that I've used and the error...thanks in advance!!!

java -Xmx10g -jar /path/directory/2.4-9/Queue.jar --temp_directory /path/directory/tmp_processes/ -S ExampleCountReads.scala -R /path/directory/reference_sorted_normalized.fasta -I input.bam

INFO 11:41:27,268 QScriptManager - Compiling 1 QScript ERROR 11:41:27,274 QScriptManager - IO error while decoding ExampleCountReads.scala with UTF-8 Please try specifying another one using the -encoding option ERROR 11:41:27,275 QScriptManager - one error found

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

org.broadinstitute.sting.queue.QException: Compile of ExampleCountReads.scala failed with 1 error at org.broadinstitute.sting.queue.QScriptManager.loadScripts(QScriptManager.scala:71) at org.broadinstitute.sting.queue.QCommandLine.org$broadinstitute$sting$queue$QCommandLine$$qScriptPluginManager(QCommandLine.scala:95) at org.broadinstitute.sting.queue.QCommandLine.getArgumentSources(QCommandLine.scala:227) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:202) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala:62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 2.4-9-g532efad):

ERROR

ERROR Please visit the wiki to see if this is a known problem

ERROR If not, please post the error, with stack trace, to the GATK forum

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Compile of ExampleCountReads.scala failed with 1 error

ERROR ------------------------------------------------------------------------------------------

INFO 11:41:27,348 QCommandLine - Shutting down jobs. Please wait...

Geraldine_VdAuwera

Hi Alessandro, this is actually just telling you that it didn't find the scala script you specified. Unlike the regular GATK commands where you just give the tool name, with Queue scripts you need to provide the full path to the script relative to your working directory.

Alessandro

Fantastic, dry run successfully executed! Thank you so much!

blueskypy

hi, I'm getting the following error. Could someone help me? Thanks a lot!

[usnee1-lph001-n066 42] ~ $ ls
R  script  seqs  test
[14:04 0.04]
[usnee1-lph001-n066 43] ~ $   java -Djava.io.tmpdir=tmp -jar $queue_jar -S ./seqs/softwares/Queue-2.5-2/resources/ExampleCountReads.scala -R /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleFASTA.fasta -I /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleBAM.bam -l DEBUG -run
INFO  14:05:29,297 QScriptManager - Compiling 1 QScript
DEBUG 14:05:29,298 QScriptManager - Compilation directory: /site/ne/home/cuiji01/tmp/Q-Classes-568453805836268123
INFO  14:05:32,089 QScriptManager - Compilation complete
INFO  14:05:32,193 HelpFormatter - ----------------------------------------------------------------------
INFO  14:05:32,193 HelpFormatter - Queue v2.5-2-gf57256b, Compiled 2013/05/01 09:29:04
INFO  14:05:32,193 HelpFormatter - Copyright (c) 2012 The Broad Institute
INFO  14:05:32,193 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
DEBUG 14:05:32,194 HelpFormatter - Current directory: /site/ne/home/cuiji01
INFO  14:05:32,194 HelpFormatter - Program Args: -S ./seqs/softwares/Queue-2.5-2/resources/ExampleCountReads.scala -R /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleFASTA.fasta -I /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleBAM.bam -l DEBUG -run
INFO  14:05:32,194 HelpFormatter - Date/Time: 2013/05/06 14:05:32
INFO  14:05:32,194 HelpFormatter - ----------------------------------------------------------------------
INFO  14:05:32,194 HelpFormatter - ----------------------------------------------------------------------
INFO  14:05:32,202 QCommandLine - Scripting ExampleCountReads
DEBUG 14:05:32,259 QGraph - adding QNode: 0
INFO  14:05:32,268 QCommandLine - Added 1 functions
INFO  14:05:32,269 QGraph - Generating graph.
INFO  14:05:32,279 QGraph - Running jobs.
INFO  14:05:32,281 QGraph - -------
INFO  14:05:32,289 QGraph - Done:     'java'  '-Xmx1024m'  '-XX:+UseParallelOldGC'  '-XX:ParallelGCThreads=4'  '-XX:GCTimeLimit=50'  '-XX:GCHeapFreeLimit=10'  '-Djava.io.tmpdir=/site/ne/home/cuiji01/tmp'  '-cp' '/site/ne/home/cuiji01/seqs/softwares/Queue-2.5-2/Queue.jar'  'org.broadinstitute.sting.gatk.CommandLineGATK'  '-T' 'CountReads'  '-I' '/site/ne/app/x86_64/gatk/v2.4.9/resources/exampleBAM.bam'  '-R' '/site/ne/app/x86_64/gatk/v2.4.9/resources/exampleFASTA.fasta'
DEBUG 14:05:32,289 QGraph - Inputs:  List(/site/ne/app/x86_64/gatk/v2.4.9/resources/exampleBAM.bai, /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleBAM.bam, /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleBAM.bam.bai, /site/ne/app/x86_64/gatk/v2.4.9/resources/exampleFASTA.fasta)
DEBUG 14:05:32,289 QGraph - Outputs: List(/site/ne/home/cuiji01/ExampleCountReads-1.out)
DEBUG 14:05:32,290 QGraph - Done+:   List(/site/ne/home/cuiji01/.ExampleCountReads-1.out.done)
DEBUG 14:05:32,290 QGraph - Done-:   List()
DEBUG 14:05:32,290 QGraph - CmdDir:  /site/ne/home/cuiji01
DEBUG 14:05:32,290 QGraph - Temp?:   false
DEBUG 14:05:32,290 QGraph - Prev:    none (reset = false)
INFO  14:05:32,290 QGraph - Log:     /site/ne/home/cuiji01/ExampleCountReads-1.out
INFO  14:05:32,295 QGraph - 0 Pend, 0 Run, 0 Fail, 1 Done
INFO  14:05:32,296 QCommandLine - Writing final jobs report...
INFO  14:05:32,296 QJobsReporter - Writing JobLogging GATKReport to file /site/ne/home/cuiji01/ExampleCountReads.jobreport.txt
INFO  14:05:32,310 QJobsReporter - Plotting JobLogging GATKReport to file /site/ne/home/cuiji01/ExampleCountReads.jobreport.pdf
DEBUG 14:05:32,344 RScriptExecutor - Executing:
DEBUG 14:05:32,345 RScriptExecutor -   Rscript
DEBUG 14:05:32,345 RScriptExecutor -   -e
DEBUG 14:05:32,345 RScriptExecutor -   tempLibDir = '/site/ne/home/cuiji01/tmp/Rlib.8304889352133617132';install.packages(pkgs=c('/site/ne/home/cuiji01/tmp/RlibSources.3490673511527363174/gsalib'), lib=tempLibDir, repos=NULL, type='source', INSTALL_opts=c('--no-libs', '--no-data', '--no-help', '--no-demo', '--no-exec'));library('gsalib', lib.loc=tempLibDir);source('/site/ne/home/cuiji01/tmp/queueJobReport.2164983308823639078.R');
DEBUG 14:05:32,345 RScriptExecutor -   /site/ne/home/cuiji01/ExampleCountReads.jobreport.txt
DEBUG 14:05:32,345 RScriptExecutor -   /site/ne/home/cuiji01/ExampleCountReads.jobreport.pdf
* installing *source* package âgsalibâ ...
** Creating default NAMESPACE file
** R
** preparing package for lazy loading
** building package indices ...
** testing if installed package can be loaded

* DONE (gsalib)
Loading required package: methods
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: âgdataâ

The following object(s) are masked from âpackage:statsâ:

    nobs

The following object(s) are masked from âpackage:utilsâ:

    object.size

Loading required package: caTools
Loading required package: bitops
Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: âgplotsâ

The following object(s) are masked from âpackage:statsâ:

    lowess

Loading required package: plyr

Attaching package: âreshapeâ

The following object(s) are masked from âpackage:plyrâ:

    rename, round_any

[1] "Report"
[1] "Project          : /site/ne/home/cuiji01/ExampleCountReads.jobreport.txt"
Error in order(allJobs$analysisName, allJobs$startTime, decreasing = T) :
  argument 1 is not a vector
Calls: source ... eval.with.vis -> eval.with.vis -> plotJobsGantt -> order
Execution halted
DEBUG 14:05:39,893 RScriptExecutor - Result: 1
WARN  14:05:39,894 RScriptExecutor - RScript exited with 1
INFO  14:05:39,930 QCommandLine - Script completed successfully with 1 total jobs
DEBUG 14:05:39,953 IOUtils - Deleted /site/ne/home/cuiji01/tmp/Q-Classes-568453805836268123
[14:05 0.32]
[usnee1-lph001-n066 44] ~ $ ls
ExampleCountReads.jobreport.pdf  ExampleCountReads.jobreport.txt  R  script  seqs  test  tmp

Geraldine_VdAuwera

Hi @blueskypy,

We've seen this error from another user recently -- it looks like there's a software version issue that is affecting the generation of the job report plots. Unfortunately we don't have the resources to track down the exact issue right now, sorry. On the bright side you can ignore the rscript error, since it's not an issue with the Queue run, it's just the plot that summarizes the run info.

blueskypy

hi, Geraldine, Thanks for the help! At another thread, a user suggested the error was caused by outdated version of ggplot2. So I updated ggplot2, but still get the error. The file ExampleCountReads-1.out was not produced either, could you help me to find the reason?

Thanks a lot!

Geraldine_VdAuwera

Hi @blueskypy,

Based on the output you posted earlier, the file should be there : /site/ne/home/cuiji01/ExampleCountReads-1.out. Is it not the case? Do you get a different "Outputs" line in your second run than in your first? Any error messages?

blueskypy

before I run the Queue:

[usnee1-lph001-n066 42] ~ $ ls

R script seqs test

After

[usnee1-lph001-n066 44] ~ $ ls

ExampleCountReads.jobreport.pdf ExampleCountReads.jobreport.txt R script seqs test tmp

Geraldine_VdAuwera

Can you list hidden files to see if there is a .ExampleCountReads-1.out.done file there?

blueskypy

that's right! it's there but it's empty!

blueskypy

the ExampleCountReads.jobreport.pdf cannot be opened either, the error says there is no page. Also very little content in the 3rd file:

[usnee1-lph001-n066 74] ~ $ more ExampleCountReads.jobreport.txt

#:GATKReport.v1.1:0

Geraldine_VdAuwera

That file tells Queue that the job has already been successfully completed, and it doesn't need to do it again. This is useful for bigger jobs, to be able to resume after a failure without redoing all the work that has already successfully completed. You can either delete the .done file, or add -startFromScratch to the Queue command line to override it.

blueskypy

hi, Geraldine, Good news! I deleted the .ExampleCountReads-1.out.done and re-run the Queue. And this time everything works fine and the output looks correct as well.

So I think the error maybe indeed was due to outdated ggplot2. But in my previous runs, even if I updated ggplot2, I didn't delete the old 'done' file so the Queue didn't really run and I still got the same error msg. Is my understanding right?

Geraldine_VdAuwera

Great, I'm glad to hear that! Good to know about the ggplot2 version, thanks for reporting your solution.

Yes, I believe that's correct -- the "failure" of your second run was due to the leftover .done file telling Queue not to do anything. This generated an empty table in the job report (since nothing was done) so you got the same error (rscript couldn't run) for a slightly different reason.

blueskypy

Thanks Geraldine for your help! You may want to provide the solution to this thread: http://gatk.vanillaforums.com/discussion/2467/install-gsalib

I was going to post the suggestion but somehow have a problem to login using google on that page.

Geraldine_VdAuwera

Done, thanks for pointing it out! FYI the problem you encountered on that page is that it uses an older URL format for the forum, which affects some of our older articles; you should be able to access it normally by changing "https" to "http" in the link.

blueskypy

hi, Geraldine, I wonder if I can ask another question. Is the '-jobRunner GridEngine' option same as using the following?

bsub java -Djava.io.tmpdir=tmp -jar Queue.jar -S ExampleCountReads.scala -R exampleFASTA.fasta -I exampleBAM.bam -run

Geraldine_VdAuwera

Hi @blueskypy,

That option is used to specify which job runner your cluster/server uses for job management. I can't tell you the details of the syntax used with GridEngine as that's not what we use in-house, but we do have other users around who use it -- hopefully they will jump in to contribute their experience.