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  1. [jcervantes@mazorka log]$ qstat -f 1437
  2. Job Id: 1437.mazorka
  3.     Job_Name = BioScope_Mapping_1.2
  4.     Job_Owner = jcervantes@mazorka
  5.     job_state = Q
  6.     queue = twin
  7.     server = mazorka
  8.     Checkpoint = u
  9.     ctime = Tue May 18 14:30:55 2010
  10.     Error_Path = mazorka:/home/bioscope-1.2/results/examples/demos/mapping/Bio
  11.     Scope_Mapping_1.2.e1437
  12.     Hold_Types = n
  13.     Join_Path = oe
  14.     Keep_Files = n
  15.     Mail_Points = a
  16.     mtime = Tue May 18 14:30:56 2010
  17.     Output_Path = mazorka:/home/bioscope-1.2/results/examples/demos/mapping/lo
  18.     g/TORQUE/Mapping-1.2.temp.01.20100518193055665.log
  19.     Priority = 0
  20.     qtime = Tue May 18 14:30:56 2010
  21.     Rerunable = True
  22.     Resource_List.mem = 16gb
  23.     Resource_List.nodect = 1
  24.     Resource_List.nodes = 1:ppn=8
  25.     Resource_List.walltime = 120:00:00
  26.     User_List = jcervantes
  27.     Variable_List = PBS_O_HOME=/home/jcervantes,PBS_O_LANG=en_US.UTF-8,
  28.     PBS_O_LOGNAME=jcervantes,
  29.     PBS_O_PATH=/usr/kerberos/bin:/home/bioscope-1.2/deps/jdk1.6.0_20/bin:
  30.     /opt/intel/ictce/3.2.0.020/bin:/opt/intel/impi/3.2.0.011/bin64:/opt/in
  31.     tel/itac/7.2.0.011/bin:/opt/intel/fc/11.0.074/bin/intel64:/opt/intel/c
  32.     c/11.0.074/bin/intel64:/home/bioscope-1.2/bioscope/bin:/usr/local/bin:
  33.     /bin:/usr/bin:/home/genome/bin:/home/emboss/bin:/home/clustal:/home/bl
  34.     ast64/bin:/home/CAP3:/home/net/cbc/bin:/home/R/bin:/home/MUMmer3.18:/o
  35.     pt/454/bin:/data/storage/software/libsvm-2.9:/data/storage/software/li
  36.     bsvm-2.9/tools:/home/gustavo/software/TEclass:/data/storage/software/m
  37.     mtsb_toolset/bin:/data/storage/software/mmtsb_toolset/perl:/data/stora
  38.     ge/software/hmmer:/home/bioscope-1.2/deps/jdk1.6.0_20/bin:/data/storag
  39.     e/software/wgs-6.1/Linux-amd64/bin:/opt/454/bin:/home/jcervantes/bin,
  40.     PBS_O_MAIL=/var/spool/mail/jcervantes,PBS_O_SHELL=/bin/bash,
  41.     PBS_SERVER=mazorka,PBS_O_HOST=mazorka,
  42.     PBS_O_WORKDIR=/home/bioscope-1.2/results/examples/demos/mapping,
  43.     MKLROOT=/opt/intel/mkl/10.1.0.015,
  44.     MANPATH=/opt/intel/mkl/10.1.0.015/man:/opt/intel/itac/7.2.0.011/man:/
  45.     opt/intel/fc/11.0.074/man:/opt/intel/cc/11.0.074/man:/usr/local/share/
  46.     man:/usr/share/man/en:/usr/share/man:/home/bioscope-1.2/deps/jdk1.6.0_
  47.     20/man:/usr/local/man:/usr/X11R6/man,
  48.     BIOSCOPEROOT=/home/bioscope-1.2/bioscope,HOSTNAME=mazorka,
  49.     VT_MPI=impi3,
  50.     INTEL_LICENSE_FILE=/opt/intel/licenses:/opt/intel/fc/11.0.074/license
  51.     s:/opt/intel/licenses:/home/jcervantes/intel/licenses:/opt/intel/cc/11
  52.     .0.074/licenses:/opt/intel/licenses:/home/jcervantes/intel/licenses,
  53.     SHELL=/bin/bash,TERM=xterm,HISTSIZE=1000,
  54.     SSH_CLIENT=10.10.120.188 51401 22,
  55.     PERL5LIB=/home/bioscope-1.2/bioscope/lib/perl,
  56.     LIBRARY_PATH=/opt/intel/mkl/10.1.0.015/lib/em64t,
  57.     MMTSBDIR=/data/storage/software/mmtsb_toolset,
  58.     FPATH=/opt/intel/mkl/10.1.0.015/include,SSH_TTY=/dev/pts/1,
  59.     USER=jcervantes,PHRED_PARAMETER_FILE=/home/genome/lib/phredpar.dat,
  60.     PSIPREDDIR=/data/storage/software/psipred,
  61.     LD_LIBRARY_PATH=/home/bioscope-1.2/deps/jdk1.6.0_20/jre/lib/amd64/ser
  62.     ver:/home/bioscope-1.2/deps/jdk1.6.0_20/jre/lib/amd64:/home/bioscope-1
  63.     .2/deps/jdk1.6.0_20/jre/../lib/amd64:/opt/intel/impi/3.2.0.011/lib64:/
  64.     opt/intel/mkl/10.1.0.015/lib/em64t:/opt/intel/itac/7.2.0.011/itac/slib
  65.     _impi3:/opt/intel/fc/11.0.074/lib/intel64:/opt/intel/cc/11.0.074/lib/i
  66.     ntel64:/home/bioscope-1.2/bioscope/lib/local:,
  67.     LS_COLORS=no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01
  68.     :cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:*.cmd=00;32:*.exe=
  69.     00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar
  70.     =00;31:*.tgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.z
  71.     =00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.bz=00;31:*.tz=00;31:*.rpm=00
  72.     ;31:*.cpio=00;31:*.jpg=00;35:*.gif=00;35:*.bmp=00;35:*.xbm=00;35:*.xpm
  73.     =00;35:*.png=00;35:*.tif=00;35:,
  74.     CPATH=/opt/intel/mkl/10.1.0.015/include,RIGDIR=/opt/454/bin,
  75.     NLSPATH=/opt/intel/mkl/10.1.0.015/lib/em64t/locale/%l_%t/%N:/opt/inte
  76.     l/fc/11.0.074/lib/intel64/locale/%l_%t/%N:/opt/intel/cc/11.0.074/idb/i
  77.     ntel64/locale/%l_%t/%N:/opt/intel/cc/11.0.074/lib/intel64/locale/%l_%t
  78.     /%N:/usr/dt/lib/nls/msg/%L/%N.cat,
  79.     PATH=/usr/kerberos/bin:/home/bioscope-1.2/deps/jdk1.6.0_20/bin:/opt/i
  80.     ntel/ictce/3.2.0.020/bin:/opt/intel/impi/3.2.0.011/bin64:/opt/intel/it
  81.     ac/7.2.0.011/bin:/opt/intel/fc/11.0.074/bin/intel64:/opt/intel/cc/11.0
  82.     .074/bin/intel64:/home/bioscope-1.2/bioscope/bin:/usr/local/bin:/bin:/
  83.     usr/bin:/home/genome/bin:/home/emboss/bin:/home/clustal:/home/blast64/
  84.     bin:/home/CAP3:/home/net/cbc/bin:/home/R/bin:/home/MUMmer3.18:/opt/454
  85.     /bin:/data/storage/software/libsvm-2.9:/data/storage/software/libsvm-2
  86.     .9/tools:/home/gustavo/software/TEclass:/data/storage/software/mmtsb_t
  87.     oolset/bin:/data/storage/software/mmtsb_toolset/perl:/data/storage/sof
  88.     tware/hmmer:/home/bioscope-1.2/deps/jdk1.6.0_20/bin:/data/storage/soft
  89.     ware/wgs-6.1/Linux-amd64/bin:/opt/454/bin:/home/jcervantes/bin,
  90.     MAIL=/var/spool/mail/jcervantes,
  91.     VT_ADD_LIBS=-ldwarf -lelf -lvtunwind -lnsl -lm -ldl -lpthread,
  92.     _=/usr/local/bin/qsub,
  93.     PWD=/home/bioscope-1.2/results/examples/demos/mapping,
  94.     INPUTRC=/etc/inputrc,JAVA_HOME=/home/bioscope-1.2/deps/jdk1.6.0_20,
  95.     IDB_HOME=/opt/intel/cc/11.0.074/bin/intel64,LANG=en_US.UTF-8,
  96.     VT_LIB_DIR=/opt/intel/itac/7.2.0.011/itac/lib_impi3,
  97.     XFILESEARCHPATH=/usr/dt/app-defaults/%L/Dt,
  98.     VT_ROOT=/opt/intel/itac/7.2.0.011,
  99.     SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass,
  100.     HOME=/home/jcervantes,SHLVL=6,CONSED_HOME=/home/genome,
  101.     EMBOSS_DATA=/home/emboss/share/EMBOSS/data/TRANSFAC:/home/emboss/shar
  102.     e/EMBOSS/data:/home/emboss/share/EMBOSS/data/PROSITE,
  103.     VT_SLIB_DIR=/opt/intel/itac/7.2.0.011/itac/slib_impi3,
  104.     LOGNAME=jcervantes,CVS_RSH=ssh,
  105.     SSH_CONNECTION=10.10.120.188 51401 10.10.10.240 22,
  106.     CLASSPATH=/home/bioscope-1.2/bioscope/lib/java/plugins:/home/bioscope
  107.     -1.2/bioscope/lib/java/shared:/home/bioscope-1.2/bioscope/etc/analysis
  108.     :/home/bioscope-1.2/bioscope/lib/java/plugins/WholeTranscriptome.jar:/
  109.     home/bioscope-1.2/bioscope/lib/java/plugins/com.apldbio.aga.saetplugin
  110.     .jar:/home/bioscope-1.2/bioscope/lib/java/plugins/com.lifetechnologies
  111.     .indelcommon.jar:/home/bioscope-1.2/bioscope/lib/java/plugins/com.life
  112.     technologies.small-indel-frag-plugins.jar:/home/bioscope-1.2/bioscope/
  113.     lib/java/plugins/com.apldbio.aga.mapping_stats.jar:/home/bioscope-1.2/
  114.     bioscope/lib/java/plugins/com.apldbio.aga.wt-plugins.jar:/home/bioscop
  115.     e-1.2/bioscope/lib/java/plugins/com.lifetechnologies.small-indel-plugi
  116.     ns.jar:/home/bioscope-1.2/bioscope/lib/java/plugins/com.apldbio.aga.in
  117.     version.jar:/home/bioscope-1.2/bioscope/lib/java/plugins/com.apldbio.a
  118.     ga.wt_single_reads_plugin.jar:/home/bioscope-1.2/bioscope/lib/java/plu
  119.     gins/com.apldbio.aga.pairing.jar:/home/bioscope-1.2/bioscope/lib/java/
  120.     plugins/com.apldbio.aga.reports.jar:/home/bioscope-1.2/bioscope/lib/ja
  121.     va/plugins/com.apldbio.aga.cnv.jar:/home/bioscope-1.2/bioscope/lib/jav
  122.     a/plugins/com.lifetechnologies.ma-to-bam-plugins.jar:/home/bioscope-1.
  123.     2/bioscope/lib/java/plugins/com.apldbio.aga.dibayes.jar:/home/bioscope
  124.     -1.2/bioscope/lib/java/plugins/com.apldbio.aga.mapping.jar:/home/biosc
  125.     ope-1.2/bioscope/lib/java/plugins/com.apldbio.aga.position.errors.jar:
  126.     /home/bioscope-1.2/bioscope/lib/java/plugins/com.lifetechnologies.larg
  127.     e-indel-plugins.jar::/home/bioscope-1.2/bioscope/lib/java/moap/seconda
  128.     ry.jar::/home/bioscope-1.2/bioscope/lib/java/shared/xstream-1.2.2.jar:
  129.     /home/bioscope-1.2/bioscope/lib/java/shared/jfreechart-1.0.13.jar:/hom
  130.     e/bioscope-1.2/bioscope/lib/java/shared/commons-io-1.4.jar:/home/biosc
  131.     ope-1.2/bioscope/lib/java/shared/com.apldbio.aga.common.jar:/home/bios
  132.     cope-1.2/bioscope/lib/java/shared/freemarker.jar:/home/bioscope-1.2/bi
  133.     oscope/lib/java/shared/activemq/activemq-protobuf-1.0.jar:/home/biosco
  134.     pe-1.2/bioscope/lib/java/shared/activemq/activemq-web-5.3.0.jar:/home/
  135.     bioscope-1.2/bioscope/lib/java/shared/activemq/activation-1.1.jar:/hom
  136.     e/bioscope-1.2/bioscope/lib/java/shared/activemq/geronimo-jta_1.0.1B_s
  137.     pec-1.0.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/jax
  138.     b-impl-2.1.6.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/
  139.     kahadb-5.3.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/
  140.     jaxb-api-2.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/
  141.     web/rome-0.8.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/
  142.     web/ant-1.7.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq
  143.     /web/jdom-1.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq
  144.     /web/jetty-xbean-6.1.9.jar:/home/bioscope-1.2/bioscope/lib/java/shared
  145.     /activemq/web/geronimo-servlet_2.5_spec-1.2.jar:/home/bioscope-1.2/bio
  146.     scope/lib/java/shared/activemq/web/jsp-api-2.1-6.1.9.jar:/home/bioscop
  147.     e-1.2/bioscope/lib/java/shared/activemq/web/jetty-util-6.1.9.jar:/home
  148.     /bioscope-1.2/bioscope/lib/java/shared/activemq/web/spring-webmvc-2.5.
  149.     6.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/web/slf4j-j
  150.     cl-1.5.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/web/
  151.     sitemesh-2.2.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activem
  152.     q/web/jsp-2.1-6.1.9.jar:/home/bioscope-1.2/bioscope/lib/java/shared/ac
  153.     tivemq/web/spring-web-2.5.6.jar:/home/bioscope-1.2/bioscope/lib/java/s
  154.     hared/activemq/web/core-3.1.1.jar:/home/bioscope-1.2/bioscope/lib/java
  155.     /shared/activemq/web/slf4j-api-1.5.0.jar:/home/bioscope-1.2/bioscope/l
  156.     ib/java/shared/activemq/web/jetty-6.1.9.jar:/home/bioscope-1.2/bioscop
  157.     e/lib/java/shared/activemq/camel-spring-2.0.0.jar:/home/bioscope-1.2/b
  158.     ioscope/lib/java/shared/activemq/geronimo-jms_1.1_spec-1.1.1.jar:/home
  159.     /bioscope-1.2/bioscope/lib/java/shared/activemq/stax-1.2.0.jar:/home/b
  160.     ioscope-1.2/bioscope/lib/java/shared/activemq/geronimo-j2ee-management
  161.     _1.0_spec-1.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq
  162.     /activemq-core-5.3.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/a
  163.     ctivemq/activemq-camel-5.3.0.jar:/home/bioscope-1.2/bioscope/lib/java/
  164.     shared/activemq/commons-logging-1.1.jar:/home/bioscope-1.2/bioscope/li
  165.     b/java/shared/activemq/camel-jms-2.0.0.jar:/home/bioscope-1.2/bioscope
  166.     /lib/java/shared/activemq/activemq-jaas-5.3.0.jar:/home/bioscope-1.2/b
  167.     ioscope/lib/java/shared/activemq/camel-core-2.0.0.jar:/home/bioscope-1
  168.     .2/bioscope/lib/java/shared/activemq/stax-api-1.0.1.jar:/home/bioscope
  169.     -1.2/bioscope/lib/java/shared/activemq/optional/spring-beans-2.5.6.jar
  170.     :/home/bioscope-1.2/bioscope/lib/java/shared/activemq/optional/log4j-1
  171.     .2.14.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/optiona
  172.     l/spring-aop-2.5.6.jar:/home/bioscope-1.2/bioscope/lib/java/shared/act
  173.     ivemq/optional/commons-codec-1.2.jar:/home/bioscope-1.2/bioscope/lib/j
  174.     ava/shared/activemq/optional/activemq-pool-5.3.0.jar:/home/bioscope-1.
  175.     2/bioscope/lib/java/shared/activemq/optional/spring-oxm-tiger-1.5.8.ja
  176.     r:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/optional/spring
  177.     -core-2.5.6.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/o
  178.     ptional/commons-collections-3.2.1.jar:/home/bioscope-1.2/bioscope/lib/
  179.     java/shared/activemq/optional/commons-net-2.0.jar:/home/bioscope-1.2/b
  180.     ioscope/lib/java/shared/activemq/optional/commons-pool-1.4.jar:/home/b
  181.     ioscope-1.2/bioscope/lib/java/shared/activemq/optional/commons-httpcli
  182.     ent-3.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/optio
  183.     nal/spring-tx-2.5.6.jar:/home/bioscope-1.2/bioscope/lib/java/shared/ac
  184.     tivemq/optional/activemq-xmpp-5.3.0.jar:/home/bioscope-1.2/bioscope/li
  185.     b/java/shared/activemq/optional/xmlpull-1.1.3.4d_b4_min.jar:/home/bios
  186.     cope-1.2/bioscope/lib/java/shared/activemq/optional/activemq-jmdns_1.0
  187.     -5.3.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/option
  188.     al/spring-context-2.5.6.jar:/home/bioscope-1.2/bioscope/lib/java/share
  189.     d/activemq/optional/xstream-1.3.1.jar:/home/bioscope-1.2/bioscope/lib/
  190.     java/shared/activemq/optional/geronimo-j2ee-connector_1.5_spec-2.0.0.j
  191.     ar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/optional/wstx-
  192.     asl-3.0.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/opt
  193.     ional/jettison-1.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/act
  194.     ivemq/optional/activeio-core-3.1.2.jar:/home/bioscope-1.2/bioscope/lib
  195.     /java/shared/activemq/optional/xbean-spring-3.6.jar:/home/bioscope-1.2
  196.     /bioscope/lib/java/shared/activemq/optional/commons-dbcp-1.2.2.jar:/ho
  197.     me/bioscope-1.2/bioscope/lib/java/shared/activemq/optional/activemq-op
  198.     tional-5.3.0.jar:/home/bioscope-1.2/bioscope/lib/java/shared/activemq/
  199.     optional/spring-jms-2.5.6.jar:/home/bioscope-1.2/bioscope/lib/java/sha
  200.     red/activemq/optional/commons-beanutils-1.6.1.jar:/home/bioscope-1.2/b
  201.     ioscope/lib/java/shared/activemq/camel-jetty-2.0.0.jar:/home/bioscope-
  202.     1.2/bioscope/lib/java/shared/activemq/activemq-console-5.3.0.jar:/home
  203.     /bioscope-1.2/bioscope/lib/java/shared/commons-math-1.2.jar:/home/bios
  204.     cope-1.2/bioscope/lib/java/shared/pipelinecommon.jar:/home/bioscope-1.
  205.     2/bioscope/lib/java/shared/iText-2.1.5.jar:/home/bioscope-1.2/bioscope
  206.     /lib/java/shared/commons-cli-1.2.jar:/home/bioscope-1.2/bioscope/lib/j
  207.     ava/shared/xpp3_min-1.1.3.4.O.jar:/home/bioscope-1.2/bioscope/lib/java
  208.     /shared/bam-api.jar:/home/bioscope-1.2/bioscope/lib/java/shared/com.ap
  209.     ldbio.aga.common.test.jar:/home/bioscope-1.2/bioscope/lib/java/shared/
  210.     log4j-1.2.15.jar:/home/bioscope-1.2/bioscope/lib/java/shared/commons-l
  211.     ogging-1.1.jar:/home/bioscope-1.2/bioscope/lib/java/shared/commons-lan
  212.     g-2.2.jar:/home/bioscope-1.2/bioscope/lib/java/shared/junit-4.5.jar:/h
  213.     ome/bioscope-1.2/bioscope/lib/java/shared/jcommon-1.0.16.jar,
  214.     LESSOPEN=|/usr/bin/lesspipe.sh %s,BLASTMAT=/home/blast64/data,
  215.     CROSS_MATCH_VECTOR=/home/genome/lib/screenLibs/vector.seq,
  216.     INCLUDE=/opt/intel/mkl/10.1.0.015/include,G_BROKEN_FILENAMES=1,
  217.     I_MPI_ROOT=/opt/intel/impi/3.2.0.011,PBS_O_QUEUE=twin
  218.     etime = Tue May 18 14:30:56 2010
  219.     umask = 2
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