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Unable to load library 'lsf': liblsf.so

qyuqyu Posts: 10Member
edited January 2013 in Ask the GATK team

I had no problem to run GATK two weeks ago. But today, when I run the following GATK command, I got error message. It seems it cannot load library " liblsf.so". Please see below. Is there any change recently on GATK library?

2:15pm qyu@vbronze /bit/data01/projects/GC_coverage $ java -Xmx4g -Djava.io.tmpdir=/broad/hptmp/vdauwera -jar /humgen/gsa-scr1/vdauwera/gatk/walker/dist/Queue.jar -S /bit/data01/projects/GC_coverage/src/IntervalCovGG.scala -i /humgen/gsa-hpprojects/GATK/data/genes_of_interest.exon_targets.interval_list -b /bit/data01/projects/GC_coverage/testGCcoverage/data/DEV-2129.list -o /bit/data01/projects/GC_coverage/testGCcoverage/DEV-2129.gatkreport -m 16 -sc 100 -bsub -jobQueue priority -startFromScratch -run

The error shows:

ERROR 14:13:06,238 QGraph - Uncaught error running jobs. 
java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot 
open shared object file: No such file or directory
        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
        at org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:9
0)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.<init>(Lsf
706JobRunner.scala:233)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.<clinit>(L
sf706JobRunner.scala)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.<init>(Lsf7
06JobRunner.scala:47)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf
706JobManager.scala:35)
        at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf
706JobManager.scala:33)
        at org.broadinstitute.sting.queue.engine.QGraph.newRunner(QGraph.scala:6
32)
        at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:408
)
        at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:131)
        at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scal
a:127)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command
LineProgram.java:236)
        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)
Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load librar
y 'lsf': liblsf.so: cannot open shared object file: No such file or directory
        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199)
        at org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.<clinit>(LibBat.java:9
.........

Thanks, Qing

Post edited by Geraldine_VdAuwera on
Tagged:

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,292Administrator, GATK Developer admin

    Hi Qing,

    Can you tell me at what point this error comes up when you run this command? I'm running your command right now (except with a different output directory) and it seems to be working fine (INFO 15:19:00,921 QGraph - 2 Pend, 84 Run, 0 Fail, 17 Done). I'll let it run to see if it fails later on, but right now I'm not seeing any problem. It might have been a transient system glitch.

    Geraldine Van der Auwera, PhD

  • qyuqyu Posts: 10Member

    Hi, Geraldine,

    Before I run the command, I set up environment as below. I used the same environment before.

    use R-2.15

    use Java-1.6

    use Scala-2.9

    use Perl-5.10

    The full output is as below. The last about 100 lines in the output shows 'Unable to load library 'lsf': liblsf.so:"

    INFO 14:10:04,720 QScriptManager - Compiling 1 QScript INFO 14:10:10,135 QScriptManager - Compilation complete

    INFO 14:10:10,288 HelpFormatter - ---------------------------------------------

    INFO 14:10:10,289 HelpFormatter - Queue v1.5-389-g45ff479, Compiled 2012/05/03 13:59:09 INFO 14:10:10,289 HelpFormatter - Copyright (c) 2012 The Broad Institute INFO 14:10:10,289 HelpFormatter - Please view our documentation at http://www.b roadinstitute.org/gsa/wiki INFO 14:10:10,290 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 14:10:10,291 HelpFormatter - Program Args: -S /bit/data01/projects/GC_cove rage/src/IntervalCovGG.scala -i /humgen/gsa-hpprojects/GATK/data/genes_of_intere st.exon_targets.interval_list -b /bit/data01/projects/GC_coverage/testGCcoverage /data/DEV-2129.list -o /bit/data01/projects/GC_coverage/testGCcoverage/data/byEx ons/DEV-2129.gatkreport -m 16 -sc 100 -bsub -jobQueue priority -startFromScratch -run INFO 14:10:10,291 HelpFormatter - Date/Time: 2013/01/15 14:10:10

    INFO 14:10:10,292 HelpFormatter - ---------------------------------------------

    INFO 14:10:10,292 HelpFormatter - ---------------------------------------------

    INFO 14:10:10,298 QCommandLine - Scripting IntervalCoverage INFO 14:10:10,390 QCommandLine - Added 1 functions INFO 14:10:10,391 QGraph - Generating graph. INFO 14:10:10,422 QGraph - Generating scatter gather jobs. INFO 14:10:10,978 QGraph - Removing original jobs. INFO 14:10:10,980 QGraph - Adding scatter gather jobs. INFO 14:10:11,393 QGraph - Regenerating graph. INFO 14:10:11,557 QGraph - Running jobs. INFO 14:10:11,559 QGraph - Removing outputs from previous runs. INFO 14:10:11,693 FunctionEdge - Starting: IntervalScatterFunction: List(/humge n/gsa-hpprojects/NA12878Collection/callsets/snps/CEUTrio.HiSeq.WGS.b37_decoy.rec alibrated.vcf, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/NA12878.va lidated.curated.polymorphic.indels.vcf.idx, /bit/data01/projects/GC_coverage/tes tGCcoverage/data/DEV-2129.list, /humgen/1kg/reference/human_g1k_v37_decoy.fasta, /humgen/gsa-hpprojects/NA12878Collection/callsets/snps/CEUTrio.HiSeq.WGS.b37_de coy.recalibrated.vcf.idx, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated /NA12878.validated.curated.polymorphic.indels.vcf) > List(/bit/data01/projects/G C_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_001_of_100/scatter.interva ls, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_ 002_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGathe r/IntervalCovGG-1-sg/temp_003_of_100/scatter.intervals, /bit/data01/projects/GC_ coverage/queueScatterGather/IntervalCovGG-1-sg/temp_004_of_100/scatter.intervals , /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_00 5_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/ IntervalCovGG-1-sg/temp_006_of_100/scatter.intervals, /bit/data01/projects/GC_co verage/queueScatterGather/IntervalCovGG-1-sg/temp_007_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_008_ of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/In tervalCovGG-1-sg/temp_009_of_100/scatter.intervals, /bit/data01/projects/GC_cove rage/queueScatterGather/IntervalCovGG-1-sg/temp_010_of_100/scatter.intervals, /b it/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_011_of 100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Inte rvalCovGG-1-sg/temp_012_of_100/scatter.intervals, /bit/data01/projects/GC_covera ge/queueScatterGather/IntervalCovGG-1-sg/temp_013_of_100/scatter.intervals, /bit /data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_014_of_1 00/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interv alCovGG-1-sg/temp_015_of_100/scatter.intervals, /bit/data01/projects/GC_coverage /queueScatterGather/IntervalCovGG-1-sg/temp_016_of_100/scatter.intervals, /bit/d ata01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_017_of_100 /scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interval CovGG-1-sg/temp_018_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/q ueueScatterGather/IntervalCovGG-1-sg/temp_019_of_100/scatter.intervals, /bit/dat a01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_020_of_100/s catter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_021_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/que ueScatterGather/IntervalCovGG-1-sg/temp_022_of_100/scatter.intervals, /bit/data0 1/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_023_of_100/sca tter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovG G-1-sg/temp_024_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queue ScatterGather/IntervalCovGG-1-sg/temp_025_of_100/scatter.intervals, /bit/data01/ projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_026_of_100/scatt er.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG- 1-sg/temp_027_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueSc atterGather/IntervalCovGG-1-sg/temp_028_of_100/scatter.intervals, /bit/data01/pr ojects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_029_of_100/scatter .intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1- sg/temp_030_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScat terGather/IntervalCovGG-1-sg/temp_031_of_100/scatter.intervals, /bit/data01/proj ects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_032_of_100/scatter.i ntervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg /temp_033_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatte rGather/IntervalCovGG-1-sg/temp_034_of_100/scatter.intervals, /bit/data01/projec ts/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_035_of_100/scatter.int ervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/t emp_036_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterG ather/IntervalCovGG-1-sg/temp_037_of_100/scatter.intervals, /bit/data01/projects /GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_038_of_100/scatter.inter vals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/tem p_039_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGat her/IntervalCovGG-1-sg/temp_040_of_100/scatter.intervals, /bit/data01/projects/G C_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_041_of_100/scatter.interva ls, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp 042_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGathe r/IntervalCovGG-1-sg/temp_043_of_100/scatter.intervals, /bit/data01/projects/GC_ coverage/queueScatterGather/IntervalCovGG-1-sg/temp_044_of_100/scatter.intervals , /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_04 5_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/ IntervalCovGG-1-sg/temp_046_of_100/scatter.intervals, /bit/data01/projects/GC_co verage/queueScatterGather/IntervalCovGG-1-sg/temp_047_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_048_ of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/In tervalCovGG-1-sg/temp_049_of_100/scatter.intervals, /bit/data01/projects/GC_cove rage/queueScatterGather/IntervalCovGG-1-sg/temp_050_of_100/scatter.intervals, /b it/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_051_of 100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Inte rvalCovGG-1-sg/temp_052_of_100/scatter.intervals, /bit/data01/projects/GC_covera ge/queueScatterGather/IntervalCovGG-1-sg/temp_053_of_100/scatter.intervals, /bit /data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_054_of_1 00/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interv alCovGG-1-sg/temp_055_of_100/scatter.intervals, /bit/data01/projects/GC_coverage /queueScatterGather/IntervalCovGG-1-sg/temp_056_of_100/scatter.intervals, /bit/d ata01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_057_of_100 /scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interval CovGG-1-sg/temp_058_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/q ueueScatterGather/IntervalCovGG-1-sg/temp_059_of_100/scatter.intervals, /bit/dat a01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_060_of_100/s catter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCo vGG-1-sg/temp_061_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/que ueScatterGather/IntervalCovGG-1-sg/temp_062_of_100/scatter.intervals, /bit/data0 1/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_063_of_100/sca tter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovG G-1-sg/temp_064_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queue ScatterGather/IntervalCovGG-1-sg/temp_065_of_100/scatter.intervals, /bit/data01/ projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_066_of_100/scatt er.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG- 1-sg/temp_067_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueSc atterGather/IntervalCovGG-1-sg/temp_068_of_100/scatter.intervals, /bit/data01/pr ojects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_069_of_100/scatter .intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1- sg/temp_070_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScat terGather/IntervalCovGG-1-sg/temp_071_of_100/scatter.intervals, /bit/data01/proj ects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_072_of_100/scatter.i ntervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg /temp_073_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_074_of_100/scatter.intervals, /bit/data01/projec ts/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_075_of_100/scatter.int ervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/t emp_076_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterG ather/IntervalCovGG-1-sg/temp_077_of_100/scatter.intervals, /bit/data01/projects /GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_078_of_100/scatter.inter vals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/tem p_079_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGat her/IntervalCovGG-1-sg/temp_080_of_100/scatter.intervals, /bit/data01/projects/G C_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_081_of_100/scatter.interva ls, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp 082_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGathe r/IntervalCovGG-1-sg/temp_083_of_100/scatter.intervals, /bit/data01/projects/GC_ coverage/queueScatterGather/IntervalCovGG-1-sg/temp_084_of_100/scatter.intervals , /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_08 5_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/ IntervalCovGG-1-sg/temp_086_of_100/scatter.intervals, /bit/data01/projects/GC_co verage/queueScatterGather/IntervalCovGG-1-sg/temp_087_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_088_ of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/In tervalCovGG-1-sg/temp_089_of_100/scatter.intervals, /bit/data01/projects/GC_cove rage/queueScatterGather/IntervalCovGG-1-sg/temp_090_of_100/scatter.intervals, /b it/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_091_of 100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Inte rvalCovGG-1-sg/temp_092_of_100/scatter.intervals, /bit/data01/projects/GC_covera ge/queueScatterGather/IntervalCovGG-1-sg/temp_093_of_100/scatter.intervals, /bit /data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_094_of_1 00/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interv alCovGG-1-sg/temp_095_of_100/scatter.intervals, /bit/data01/projects/GC_coverage /queueScatterGather/IntervalCovGG-1-sg/temp_096_of_100/scatter.intervals, /bit/d ata01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_097_of_100 /scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interval CovGG-1-sg/temp_098_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/q ueueScatterGather/IntervalCovGG-1-sg/temp_099_of_100/scatter.intervals, /bit/dat a01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_100_of_100/scatter.intervals) INFO 14:10:11,696 FunctionEdge - Output written to /bit/data01/projects/GC_cove rage/queueScatterGather/IntervalCovGG-1-sg/scatter/scatter.out INFO 14:10:12,976 QGraph - 102 Pend, 1 Run, 0 Fail, 0 Done INFO 14:10:41,857 FunctionEdge - Done: IntervalScatterFunction: List(/humgen/gs a-hpprojects/NA12878Collection/callsets/snps/CEUTrio.HiSeq.WGS.b37_decoy.recalib rated.vcf, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/NA12878.valida ted.curated.polymorphic.indels.vcf.idx, /bit/data01/projects/GC_coverage/testGCc overage/data/DEV-2129.list, /humgen/1kg/reference/human_g1k_v37_decoy.fasta, /hu mgen/gsa-hpprojects/NA12878Collection/callsets/snps/CEUTrio.HiSeq.WGS.b37_decoy. recalibrated.vcf.idx, /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/NA1 2878.validated.curated.polymorphic.indels.vcf) > List(/bit/data01/projects/GC_co verage/queueScatterGather/IntervalCovGG-1-sg/temp_001_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_002 of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/In tervalCovGG-1-sg/temp_003_of_100/scatter.intervals, /bit/data01/projects/GC_cove rage/queueScatterGather/IntervalCovGG-1-sg/temp_004_of_100/scatter.intervals, /b it/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_005_of 100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Inte rvalCovGG-1-sg/temp_006_of_100/scatter.intervals, /bit/data01/projects/GC_covera ge/queueScatterGather/IntervalCovGG-1-sg/temp_007_of_100/scatter.intervals, /bit /data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_008_of_1 00/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interv alCovGG-1-sg/temp_009_of_100/scatter.intervals, /bit/data01/projects/GC_coverage /queueScatterGather/IntervalCovGG-1-sg/temp_010_of_100/scatter.intervals, /bit/d ata01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_011_of_100 /scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interval CovGG-1-sg/temp_012_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/q ueueScatterGather/IntervalCovGG-1-sg/temp_013_of_100/scatter.intervals, /bit/dat a01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_014_of_100/s catter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCo vGG-1-sg/temp_015_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/que ueScatterGather/IntervalCovGG-1-sg/temp_016_of_100/scatter.intervals, /bit/data0 1/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_017_of_100/sca tter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovG G-1-sg/temp_018_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queue ScatterGather/IntervalCovGG-1-sg/temp_019_of_100/scatter.intervals, /bit/data01/ projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_020_of_100/scatt er.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG- 1-sg/temp_021_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueSc atterGather/IntervalCovGG-1-sg/temp_022_of_100/scatter.intervals, /bit/data01/pr 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rvalCovGG-1-sg/temp_086_of_100/scatter.intervals, /bit/data01/projects/GC_covera ge/queueScatterGather/IntervalCovGG-1-sg/temp_087_of_100/scatter.intervals, /bit /data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_088_of_1 00/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interv alCovGG-1-sg/temp_089_of_100/scatter.intervals, /bit/data01/projects/GC_coverage /queueScatterGather/IntervalCovGG-1-sg/temp_090_of_100/scatter.intervals, /bit/d ata01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_091_of_100 /scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interval CovGG-1-sg/temp_092_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/q ueueScatterGather/IntervalCovGG-1-sg/temp_093_of_100/scatter.intervals, /bit/dat a01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_094_of_100/s catter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCo vGG-1-sg/temp_095_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/que ueScatterGather/IntervalCovGG-1-sg/temp_096_of_100/scatter.intervals, /bit/data0 1/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_097_of_100/sca tter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovG G-1-sg/temp_098_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queue ScatterGather/IntervalCovGG-1-sg/temp_099_of_100/scatter.intervals, /bit/data01/ projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_100_of_100/scatt er.intervals) ERROR 14:10:42,012 QGraph - Uncaught error running jobs. java.lang.UnsatisfiedLinkError: Unable to load library 'lsf': liblsf.so: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.(LibBat.java:9 0) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.(Lsf 706JobRunner.scala:233) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.(L sf706JobRunner.scala) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.(Lsf7 06JobRunner.scala:47) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf 706JobManager.scala:35) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf 706JobManager.scala:33) at org.broadinstitute.sting.queue.engine.QGraph.newRunner(QGraph.scala:6 32) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:408 ) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:131) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scal a:127) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:146) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala: 62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) Exception in thread "main" java.lang.UnsatisfiedLinkError: Unable to load librar y 'lsf': liblsf.so: cannot open shared object file: No such file or directory at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:163) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:236) at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:199) at org.broadinstitute.sting.jna.lsf.v7_0_6.LibBat.(LibBat.java:9 0) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.(Lsf 706JobRunner.scala:233) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner$.(L sf706JobRunner.scala) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobRunner.(Lsf7 06JobRunner.scala:47) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf 706JobManager.scala:35) at org.broadinstitute.sting.queue.engine.lsf.Lsf706JobManager.create(Lsf 706JobManager.scala:33) at org.broadinstitute.sting.queue.engine.QGraph.newRunner(QGraph.scala:6 32) at org.broadinstitute.sting.queue.engine.QGraph.runJobs(QGraph.scala:408 ) at org.broadinstitute.sting.queue.engine.QGraph.run(QGraph.scala:131) at org.broadinstitute.sting.queue.QCommandLine.execute(QCommandLine.scal a:127) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:236) at org.broadinstitute.sting.commandline.CommandLineProgram.start(Command LineProgram.java:146) at org.broadinstitute.sting.queue.QCommandLine$.main(QCommandLine.scala: 62) at org.broadinstitute.sting.queue.QCommandLine.main(QCommandLine.scala) INFO 14:10:42,017 QCommandLine - Shutting down jobs. Please wait... 20.702u 1.001s 0:45.75 47.4% 0+0k 0+0io 1pf+0w

    Thanks, Qing

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,292Administrator, GATK Developer admin

    Hmm, I don't think your environment settings are the problem. I use the same and my run just completed successfully. It really does look like a system glitch. Have you tried running it again?

    Geraldine Van der Auwera, PhD

  • evolvedmicrobeevolvedmicrobe MGHPosts: 14Member

    You should try using the command

    use LSF

    before running things. For some reason it seems the LSF commands are no longer added by default on the Broad cluster (at least my experience this week). If that fails, try the following before running anything:

    setenv PATH /broad/lsf/7.0/linux2.6-glibc2.3-x86_64/lib:$PATH

  • qyuqyu Posts: 10Member

    You are right. It is problem system glitch in my virtual machine "vbronze". After I "use LSF" and "ish", and run the command is a computer node, The command works well and generates GATK report.

    Thanks a lot! Qing

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