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  • Cannot use SRA data access in HISAT2

    everytime I try to run this command, i got this error :
    Code:
    $ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran --sra-acc ERR188245 –S ERR188245_chrX.sam
    hisat2-align-s: unrecognized option '--sra-acc'
    so that I follow this instruction and download ngs-sdk.1.3.0-linux.tar.gz
    Code:
    "For the support of SRA data access in HISAT2, please download and install the NCBI-NGS toolkit."
    HTML Code:
    http://ftp-trace.ncbi.nlm.nih.gov/sra/ngs/1.3.0/ngs-sdk.1.3.0-linux.tar.gz
    After extract and follow the instruction of this ngs-sdk.1.3.0-linux.tar.gz, I got this message :
    Code:
    ~/RNAseq/tools/ngs-sdk.1.3.0-linux$ cd share
    ~/RNAseq/tools/ngs-sdk.1.3.0-linux/share$ make
    make: uname: Command not found
    make: true: Command not found
    /home/atonidas/RNAseq/tools/ngs-sdk.1.3.0-linux/share/Makefile.config:53: recipe for target 'ncbi-headers' failed
    make: *** [ncbi-headers] Error 127
    Did I make something wrong? please advice, thank you so much
    Last edited by atonidas; 05-24-2017, 10:03 PM.

  • #2
    Are you doing this in MingW? If so use real linux since you installed it.

    Comment


    • #3
      Originally posted by GenoMax View Post
      Are you doing this in MingW? If so use real linux since you installed it.
      nope, I did not do that in MinW, I did that in terminal of Linux.

      Comment


      • #4
        Then why are common unix commands like "uname" not found?

        Can you look in /bin to see if the uname and true commands are there? Also make sure /bin is in your $PATH.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Then why are common unix commands like "uname" not found?

          Can you look in /bin to see if the uname and true commands are there? Also make sure /bin is in your $PATH.
          I set /home/atonidas/bin as my $PATH and I did installed all of my tools in there but there is no uname and true commands in that folder.

          I have just installed ubuntu for 2 days and this is the first time of my life using this OS so that I really have no idea why common unix commands like "uname" are not there.

          Comment


          • #6
            I am referring to /bin (which is the system bin not the one in your home directory). Can you check that directory?

            Comment


            • #7
              I just checked the computer/bin directory, and there are uname and true command in here. it's here.

              Comment


              • #8
                So is that /bin directory in your $PATH. It normally should be (unless you changed the $PATH drastically). Put that directly back in there, if it is not present.
                Code:
                 export PATH=$PATH:\bin

                Comment


                • #9
                  Originally posted by GenoMax View Post
                  So is that /bin directory in your $PATH. It normally should be (unless you changed the $PATH drastically). Put that directly back in there, if it is not present.
                  Code:
                   export PATH=$PATH:\bin
                  I am following your advice and I put everything back in there. Then I start compiling the "ngs-sdk.1.3.0-linux" again following the instruction and I got this message :

                  Code:
                  atonidas@atonidas:~/tool/ngs-sdk.1.3.0-linux/share$ make
                  c++   -g -o AlignSliceTest AlignSliceTest.cpp -L/usr/local/ngs/ngs-sdk/lib64/ -L/usr/local/ngs/ngs-sdk/lib64 -lncbi-ngs-c++ -lngs-c++ -lngs-bam-c++ -lncbi-ngs-c++ -lncbi-vdb-static -lngs-adapt-c++ -lpthread -ldl -lm 
                  AlignSliceTest.cpp:28:31: fatal error: ngs-bam/ngs-bam.hpp: No such file or directory
                  compilation terminated.
                  Makefile:84: recipe for target 'AlignSliceTest' failed
                  make: *** [AlignSliceTest] Error 1
                  I already add library directory to my LD_LIBRARY_PATH as instructed, but I still got the same message. I am not sure what happen

                  Comment


                  • #10
                    Perhaps you have a corrupted/incomplete download of the software. Can you re-download and try again?

                    Comment

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