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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: 5,838Administrator, 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
    ojects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_023_of_100/scatter
    .intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-
    sg/temp_024_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScat
    terGather/IntervalCovGG-1-sg/temp_025_of_100/scatter.intervals, /bit/data01/proj
    ects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_026_of_100/scatter.i
    ntervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg
    /temp_027_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatte
    rGather/IntervalCovGG-1-sg/temp_028_of_100/scatter.intervals, /bit/data01/projec
    ts/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_029_of_100/scatter.int
    ervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/t
    emp_030_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterG
    ather/IntervalCovGG-1-sg/temp_031_of_100/scatter.intervals, /bit/data01/projects
    /GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_032_of_100/scatter.inter
    vals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/tem
    p_033_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGat
    her/IntervalCovGG-1-sg/temp_034_of_100/scatter.intervals, /bit/data01/projects/G
    C_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_035_of_100/scatter.interva
    ls, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp

    036_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGathe
    r/IntervalCovGG-1-sg/temp_037_of_100/scatter.intervals, /bit/data01/projects/GC_
    coverage/queueScatterGather/IntervalCovGG-1-sg/temp_038_of_100/scatter.intervals
    , /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_03
    9_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/
    IntervalCovGG-1-sg/temp_040_of_100/scatter.intervals, /bit/data01/projects/GC_co
    verage/queueScatterGather/IntervalCovGG-1-sg/temp_041_of_100/scatter.intervals,
    /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_042_
    of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/In
    tervalCovGG-1-sg/temp_043_of_100/scatter.intervals, /bit/data01/projects/GC_cove
    rage/queueScatterGather/IntervalCovGG-1-sg/temp_044_of_100/scatter.intervals, /b
    it/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_045_of
    100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Inte
    rvalCovGG-1-sg/temp_046_of_100/scatter.intervals, /bit/data01/projects/GC_covera
    ge/queueScatterGather/IntervalCovGG-1-sg/temp_047_of_100/scatter.intervals, /bit
    /data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_048_of_1
    00/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interv
    alCovGG-1-sg/temp_049_of_100/scatter.intervals, /bit/data01/projects/GC_coverage
    /queueScatterGather/IntervalCovGG-1-sg/temp_050_of_100/scatter.intervals, /bit/d
    ata01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_051_of_100
    /scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Interval
    CovGG-1-sg/temp_052_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/q
    ueueScatterGather/IntervalCovGG-1-sg/temp_053_of_100/scatter.intervals, /bit/dat
    a01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_054_of_100/s
    catter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCo
    vGG-1-sg/temp_055_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/que
    ueScatterGather/IntervalCovGG-1-sg/temp_056_of_100/scatter.intervals, /bit/data0
    1/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_057_of_100/sca
    tter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovG
    G-1-sg/temp_058_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queue
    ScatterGather/IntervalCovGG-1-sg/temp_059_of_100/scatter.intervals, /bit/data01/
    projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_060_of_100/scatt
    er.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-
    1-sg/temp_061_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueSc
    atterGather/IntervalCovGG-1-sg/temp_062_of_100/scatter.intervals, /bit/data01/pr
    ojects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_063_of_100/scatter
    .intervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-
    sg/temp_064_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScat
    terGather/IntervalCovGG-1-sg/temp_065_of_100/scatter.intervals, /bit/data01/proj
    ects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_066_of_100/scatter.i
    ntervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg
    /temp_067_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatte
    rGather/IntervalCovGG-1-sg/temp_068_of_100/scatter.intervals, /bit/data01/projec
    ts/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_069_of_100/scatter.int
    ervals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/t
    emp_070_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterG
    ather/IntervalCovGG-1-sg/temp_071_of_100/scatter.intervals, /bit/data01/projects
    /GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_072_of_100/scatter.inter
    vals, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/tem
    p_073_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGat
    her/IntervalCovGG-1-sg/temp_074_of_100/scatter.intervals, /bit/data01/projects/G
    C_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_075_of_100/scatter.interva
    ls, /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp

    076_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGathe
    r/IntervalCovGG-1-sg/temp_077_of_100/scatter.intervals, /bit/data01/projects/GC_
    coverage/queueScatterGather/IntervalCovGG-1-sg/temp_078_of_100/scatter.intervals
    , /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_07
    9_of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/
    IntervalCovGG-1-sg/temp_080_of_100/scatter.intervals, /bit/data01/projects/GC_co
    verage/queueScatterGather/IntervalCovGG-1-sg/temp_081_of_100/scatter.intervals,
    /bit/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_082_
    of_100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/In
    tervalCovGG-1-sg/temp_083_of_100/scatter.intervals, /bit/data01/projects/GC_cove
    rage/queueScatterGather/IntervalCovGG-1-sg/temp_084_of_100/scatter.intervals, /b
    it/data01/projects/GC_coverage/queueScatterGather/IntervalCovGG-1-sg/temp_085_of
    _100/scatter.intervals, /bit/data01/projects/GC_coverage/queueScatterGather/Inte
    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: 5,838Administrator, 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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