Difference between revisions of "Tips Shim"

Revision as of 06:07, 26 November 2014

C++ compiler upgrade

  sudo apt-get update
  sudo apt-get install gcc-4.7 g++-4.7 gcc-4.7-base libstdc++6-4.7-dev gcc-4.7-base cpp-4.7 libgcc-4.7-dev
  sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.7 20
  sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.7 20
  sudo update-alternatives --config gcc
  sudo update-alternatives --config g++

about PiCard and GATK pipe for bam created by bwa aln pipe

  java -Djava.io.tmpdir=./temporary_dir/ -Xmx1g -jar /data/program/picard-tools-1.88/MarkDuplicates.jar\
  MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=1000 METRICS_FILE=out.metrics REMOVE_DUPLICATES=true\
  ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT\
  INPUT=??.sorted.bam OUTPUT=??.sorted.bam.dedup.bam

• in higher version of PiCard, following error will occur. "bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned"

• using LINIENT option for VALIDATION_STRINGENCY will report "MAPQ should be 0 for unmapped read"

  swbarnes2 had explained about this problem at SeqAnswers

• If you want to do InDel realign, you have to run AddOrReplaceReadGroups.jar

• missing "-Djava.io.tmpdir=./temporary_dir/" options, make critical error and stop running as Yang Jae Kang mentioned in Tips kang.

altered reference sequence

• See this page

soft link

    $ ln -s (obj_file) (dir_for_link)

• useful when using personal module

Running same works with different combinations of argvs using GNU parallel

    $ parallel command {1} {2} ::: argv[1] ::: argv[2]

this command is the most efficient method to schedule large amount of iterative jobs. if you set the maximum core limitation, work threads retained as you set. one job ended, then another job will start. and total number of working threads will retained as constatnt.

MPI library error while running ABySS

    error message: libopen-rte.so.7 is not found
    $ ldd /usr/local/bin/mpirun
    libopen-rte.so.7 => not found
    $ sudo apt-get install libcr-dev mpich2 mpich2-doc

Mailing at Terminal

    $ ssmtp recepient_email@domain.com
    $ To: recepient_email@domain.com
    $ From: sender_email@domain.com  >> asking Sangrea about configured email address
    $ Subject: JOB IS DONE
    ctrl+d

    $ ssmtp recepient_email@domain.com < mail.txt
    $ less mail.txt
    To: recepient_email@domain.com
    From: sender_email@domain.com
    Subject: JOB IS DONE
    calling SNP is done!! check your log file!!

Sending file attached E-mail at Terminal

    $ mpack -s subject attached_file recepient_email@domain.com

     This function is now available on both servers