Difference between revisions of "Tips Shim"

Revision as of 06:51, 11 June 2015

/etc/fstab for mounting

    # /etc/fstab: static file system information.
    #
    # Use 'blkid -o value -s UUID' to print the universally unique identifier
    # for a device; this may be used with UUID= as a more robust way to name
    # devices that works even if disks are added and removed. See fstab(5).
    #
    # <file system> <mount point>   <type>  <options>       <dump>  <pass>
    proc            /proc           proc    nodev,noexec,nosuid 0       0
    # / was on /dev/sda3 during installation
    UUID=91289b82-f4a5-41af-83e1-4e6cf5c43362 /               ext4    errors=remount-ro,user_xattr 0       1
    # /boot was on /dev/sda1 during installation
    UUID=53c9f4d2-7252-45ac-a57a-c8f3d0134f4a /boot           ext4    defaults        0       2
    # swap was on /dev/sda2 during installation
    UUID=e265a866-50ad-479a-93ca-4956058594e1 none            swap    sw              0       0
    /dev/sdb1       /data   ext4    defaults        0 0
    /dev/sdc1       /data1  ext4    defaults        0 0
    /dev/sdd1       /data2  ext4    defaults        0 0

    UUID=2e2ac316-09f9-42dd-8a5b-05043edba397       /kev8305        xfs     defaults        0       0
    UUID=98ac9818-c21f-4821-8847-ea2f2ec5b661       /alima90        xfs     defaults        0       0
    UUID=5c8611a2-c1ba-4044-af00-847869370458       /hayasen        xfs     defaults        0       0
    UUID=36886f70-c9ca-42b4-b4fb-448ebcb1b38b       /NGS    xfs     defaults        0       0

    #sudo blkid
    #/dev/sdb: UUID="a5708fd6-ca09-4f9b-bc0f-172a0ab36fda" TYPE="ext4" 
    #/dev/sda1: UUID="53c9f4d2-7252-45ac-a57a-c8f3d0134f4a" TYPE="ext4" 
    #/dev/sda2: UUID="e265a866-50ad-479a-93ca-4956058594e1" TYPE="swap" 
    #/dev/sda3: UUID="91289b82-f4a5-41af-83e1-4e6cf5c43362" TYPE="ext4" 
    #/dev/sdd1: UUID="4daa4471-a2ca-4d1d-b197-b88c310a221e" TYPE="ext2" 
    #/dev/sde1: UUID="2e2ac316-09f9-42dd-8a5b-05043edba397" TYPE="xfs" 
    #/dev/sdc1: UUID="94372b8c-1834-4bf2-8d16-d3dafd9296f0" TYPE="ext2" 
    #/dev/sdf1: UUID="98ac9818-c21f-4821-8847-ea2f2ec5b661" TYPE="xfs" 
    #/dev/sdg1: UUID="5c8611a2-c1ba-4044-af00-847869370458" TYPE="xfs" 
    #/dev/sdh1: UUID="36886f70-c9ca-42b4-b4fb-448ebcb1b38b" TYPE="xfs"

    #/dev/sde1 /kev8305 xfs rw 0 0
    #/dev/sdf1 /alima90 xfs rw 0 0
    #/dev/sdg1 /hayasen xfs rw 0 0
    #/dev/sdh1 /NGS xfs rw 0 0

MAC address masking on Windows

   windows_key + x, shift + m (Device manager)
   Network adapter tab
   select adapter with right click, properties
   in advanced tab, click Network Address, input values without any special character like '-'.

MAC address masking on Ubuntu

   $ sudo ifconfig eth0 down
   $ sudo ifconfig eth0 hw ether ??:??:??:??:??:??
   $ sudo ifconfig eth0 up

fastx_barcode_splitter.pl

   $ zcat 4_NoIndex_L004_R1_001.fastq.gz | fastx_barcode_splitter.pl --bcfile barcode.3 --suffix ".fq" --prefix ./4_. --bol --exact ; cat fq_list.3 | parallel -j 2 '/data1/program/NGSQCToolkit_v2.3.3/Trimming/TrimmingReads.pl -l 6 -i {}' ; gzip *_trimmed

WGS assembler overlapInCore.C editing

  at the very first time script looks like this
  assert (8 * sizeof (uint64) > 2 * Kmer_Len);

  but it makes an error on overlap stage, so, I replaced the script like this
  assert (8 * sizeof (uint64) <= 2 * Kmer_Len);

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