Difference between revisions of "Tips Shim"
From Crop Genomics Lab.
Sangrea Shim (Talk | contribs) |
Sangrea Shim (Talk | contribs) |
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+ | '''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''' | '''about PiCard and GATK pipe for bam created by bwa aln pipe''' | ||
Revision as of 05:34, 17 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 in 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!!
This function is now available on both servers