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  • shrujan
    replied
    hmmm thanks a lot.

    I am right now learning NGS, in starting stage. Just completed QC(Quality control for reads) by using NGSQCTOOL_KIT. I need your valuable guidelines so that i can learn NGS in a step by step process.

    Thank you-
    Shrujan

    Leave a comment:


  • sklages
    replied
    Code:
    man apt-cache

    Leave a comment:


  • shrujan
    replied
    Thank you so much it worked. Where did you get that from ??

    Leave a comment:


  • sklages
    replied
    Originally posted by shrujan View Post
    shrujan@ubuntu:~$ sudo apt-get install String::Approx
    [sudo] password for shrujan:
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    E: Unable to locate package String::Approx
    Code:
    apt-cache search String::Approx
    libstring-approx-perl - Perl extension for approximate matching (fuzzy matching)
    
    sudo apt-get install libstring-approx-perl

    Leave a comment:


  • shrujan
    replied
    shrujan@ubuntu:~$ sudo apt-get install String::Approx
    [sudo] password for shrujan:
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    E: Unable to locate package String::Approx

    Leave a comment:


  • sklages
    replied
    Originally posted by shrujan View Post
    cpan[2]> install String::Approx
    Running install for module 'String::Approx'
    Running make for J/JH/JHI/String-Approx-3.27.tar.gz
    Has already been unwrapped into directory /home/shrujan/.cpan/build/String-Approx-3.27-wjqVH7
    Has already been made
    Running make test
    Has already been tested successfully
    Running make install
    Already tried without success
    hmm, you have installed the module as a normal user. Where is it installed? In your home dir? It is probably better to install this module as root. But why don't you simply use synaptic for installation (or apt-get)?

    Leave a comment:


  • shrujan
    replied
    cpan[2]> install String::Approx
    Running install for module 'String::Approx'
    Running make for J/JH/JHI/String-Approx-3.27.tar.gz
    Has already been unwrapped into directory /home/shrujan/.cpan/build/String-Approx-3.27-wjqVH7
    Has already been made
    Running make test
    Has already been tested successfully
    Running make install
    Already tried without success

    Leave a comment:


  • shrujan
    replied
    Ya, i have reinstalled everything. I have reinstalled all perl modules.

    Leave a comment:


  • GenoMax
    replied
    Have you reinstalled String::Approx after you reinstalled the OS 64-bit OS?

    Leave a comment:


  • shrujan
    replied
    Ya now i got it. thank you.

    Do you have any idea regarding NGS QC Toolkit ??

    If so i had a problem with that i.e.,

    I was trying to run NGS QC Toolkit in Ubuntu 12.04 LTS 64 bit version, but after executing the command error shows that cannot find module 'String::Approx' and needs to be installed even though i have installed it successfully.

    here is the command which i gave:

    shrujan@ubuntu:~$ perl ~/Programs/NGSQCToolkit_v2.3/QC/IlluQC_PRLL.pl -c 2 -pe /home/shrujan/Desktop/NGS_Shrujan/SRR072111_1.fastq /home/shrujan/Desktop/NGS_Shrujan/SRR072111_2.fastq 2 A Error: Can not find module 'String::Approx' Install it and try again

    So please guide me in resolving this issue.

    Thank you- Shrujan

    Leave a comment:


  • GenoMax
    replied
    I think sklages has almost got shrujan to the finish line. If not:

    What does the following command produce?

    Code:
    file ./fastq-dump

    Leave a comment:


  • sklages
    replied
    Originally posted by shrujan View Post
    shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
    bash: ./fastq-dump: No such file or directory
    The directory containing the binaries is

    Code:
    ~/Programs/sratoolkit.2.3.2[U]-4-ubuntu64[/U]/bin
    But you are trying to execute fastq-dump in

    Code:
    ~/Programs/sratoolkit.2.3.2/bin
    Please change to ~/Programs/sratoolkit.2.3.2-4-ubuntu64/bin and then try again to execute fastq-dump.

    Leave a comment:


  • shrujan
    replied
    shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
    bash: ./fastq-dump: No such file or directory

    Leave a comment:


  • sklages
    replied
    and now, when you type

    Code:
    ./fastq-dump
    What do you get?

    And please add CODE tags around your command outputs

    Code:
    This is easier to read for code and directory listings
    Last edited by sklages; 04-18-2013, 01:42 PM.

    Leave a comment:


  • shrujan
    replied
    shrujan@ubuntu:~/Programs/sratoolkit.2.3.2-4-ubuntu64/bin$ ls -l
    total 1484456
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 abi-dump -> abi-dump.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 abi-dump.2 -> abi-dump.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2717488 Apr 6 00:46 abi-dump.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 abi-load -> abi-load.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 abi-load.2 -> abi-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 4170728 Apr 6 00:46 abi-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 align-info -> align-info.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 align-info.2 -> align-info.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2618001 Apr 6 02:01 align-info.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 bam-load -> bam-load.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 bam-load.2 -> bam-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2829495 Apr 6 00:46 bam-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 9 Apr 12 01:44 cg-load -> cg-load.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 cg-load.2 -> cg-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2804084 Apr 6 00:47 cg-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 32562 Apr 12 01:49 configuration-assistant.perl
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 fastq-dump -> fastq-dump.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 fastq-dump.2 -> fastq-dump.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2737162 Apr 6 00:46 fastq-dump.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 fastq-load -> fastq-load.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 fastq-load.2 -> fastq-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 4186701 Apr 6 00:46 fastq-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 helicos-load -> helicos-load.2
    lrwxrwxrwx 1 shrujan shrujan 18 Apr 12 01:44 helicos-load.2 -> helicos-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 4160670 Apr 6 00:46 helicos-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 15 Apr 12 01:44 illumina-dump -> illumina-dump.2
    lrwxrwxrwx 1 shrujan shrujan 19 Apr 12 01:44 illumina-dump.2 -> illumina-dump.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2712697 Apr 6 00:46 illumina-dump.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 15 Apr 12 01:44 illumina-load -> illumina-load.2
    lrwxrwxrwx 1 shrujan shrujan 19 Apr 12 01:44 illumina-load.2 -> illumina-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 4174936 Apr 6 00:46 illumina-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 5 Apr 12 01:44 kar -> kar.2
    lrwxrwxrwx 1 shrujan shrujan 9 Apr 12 01:44 kar.2 -> kar.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1437696 Apr 6 00:46 kar.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 9 Apr 12 01:44 kdbmeta -> kdbmeta.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 kdbmeta.2 -> kdbmeta.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1602945 Apr 6 00:46 kdbmeta.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 libcurl.so -> libcurl.so.4.3.0
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 libcurl.so.4 -> libcurl.so.4.3.0
    -rw-rw-r-- 1 shrujan shrujan 341280 Feb 14 03:46 libcurl.so.4.3.0
    -rwxrwxr-x 1 shrujan shrujan 2592016 Apr 6 02:25 libvdb_jni.so
    drwxrwxr-x 2 shrujan shrujan 4096 Apr 6 03:23 ncbi
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 nenctool -> nenctool.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 nenctool.2 -> nenctool.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1426395 Apr 6 00:47 nenctool.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 pacbio-load -> pacbio-load.2
    lrwxrwxrwx 1 shrujan shrujan 17 Apr 12 01:44 pacbio-load.2 -> pacbio-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 5583242 Apr 6 00:47 pacbio-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 prefetch -> prefetch.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 prefetch.2 -> prefetch.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2516867 Apr 6 00:47 prefetch.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 11 Apr 12 01:44 rcexplain -> rcexplain.2
    lrwxrwxrwx 1 shrujan shrujan 15 Apr 12 01:44 rcexplain.2 -> rcexplain.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1413939 Apr 6 00:46 rcexplain.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 refseq-load -> refseq-load.2
    lrwxrwxrwx 1 shrujan shrujan 17 Apr 12 01:44 refseq-load.2 -> refseq-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2816329 Apr 6 00:47 refseq-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 sam-dump -> sam-dump.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 sam-dump.2 -> sam-dump.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2747904 Apr 6 00:46 sam-dump.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 sff-dump -> sff-dump.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 sff-dump.2 -> sff-dump.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2708291 Apr 6 00:46 sff-dump.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 sff-load -> sff-load.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 sff-load.2 -> sff-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 4173303 Apr 6 00:46 sff-load.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 sra-dbcc -> sra-dbcc.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 sra-dbcc.2 -> sra-dbcc.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2655280 Apr 6 00:46 sra-dbcc.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 9 Apr 12 01:44 sra-kar -> sra-kar.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 sra-kar.2 -> sra-kar.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2098004 Apr 6 00:46 sra-kar.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 9 Apr 12 01:44 srapath -> srapath.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 srapath.2 -> srapath.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1424129 Apr 6 00:46 srapath.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 sra-pileup -> sra-pileup.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 sra-pileup.2 -> sra-pileup.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2641343 Apr 6 00:46 sra-pileup.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 sra-sort -> sra-sort.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 sra-sort.2 -> sra-sort.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2948557 Apr 6 00:47 sra-sort.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 sra-stat -> sra-stat.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 sra-stat.2 -> sra-stat.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2677134 Apr 6 00:46 sra-stat.2.3.2
    -rw-rw-r-- 1 shrujan shrujan 492893 Apr 6 02:25 sratoolkit.jar
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 srf-load -> srf-load.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 srf-load.2 -> srf-load.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 4220765 Apr 6 00:46 srf-load.2.3.2
    -rw-rw-r-- 1 shrujan shrujan 723002874 Apr 19 01:43 SRR072111_1.fastq
    -rw-rw-r-- 1 shrujan shrujan 492653650 Apr 19 01:43 SRR072111_2.fastq
    -rw-r--r-- 1 shrujan shrujan 201584037 Apr 15 22:56 SRR072111.sra
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 test-sra -> test-sra.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 test-sra.2 -> test-sra.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2650565 Apr 6 00:46 test-sra.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 vdb-config -> vdb-config.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 vdb-config.2 -> vdb-config.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1971277 Apr 6 00:46 vdb-config.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 vdb-copy -> vdb-copy.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 vdb-copy.2 -> vdb-copy.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2832455 Apr 6 00:46 vdb-copy.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 vdb-decrypt -> vdb-decrypt.2
    lrwxrwxrwx 1 shrujan shrujan 17 Apr 12 01:44 vdb-decrypt.2 -> vdb-decrypt.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1435569 Apr 6 00:47 vdb-decrypt.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 vdb-dump -> vdb-dump.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 vdb-dump.2 -> vdb-dump.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2670935 Apr 6 00:46 vdb-dump.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 13 Apr 12 01:44 vdb-encrypt -> vdb-encrypt.2
    lrwxrwxrwx 1 shrujan shrujan 17 Apr 12 01:44 vdb-encrypt.2 -> vdb-encrypt.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1435111 Apr 6 00:47 vdb-encrypt.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 10 Apr 12 01:44 vdb-lock -> vdb-lock.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 vdb-lock.2 -> vdb-lock.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2000910 Apr 6 00:46 vdb-lock.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 vdb-passwd -> vdb-passwd.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 vdb-passwd.2 -> vdb-passwd.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 1416801 Apr 6 00:46 vdb-passwd.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 12 Apr 12 01:44 vdb-unlock -> vdb-unlock.2
    lrwxrwxrwx 1 shrujan shrujan 16 Apr 12 01:44 vdb-unlock.2 -> vdb-unlock.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2000912 Apr 6 00:46 vdb-unlock.2.3.2
    lrwxrwxrwx 1 shrujan shrujan 14 Apr 12 01:44 vdb-validate -> vdb-validate.2
    lrwxrwxrwx 1 shrujan shrujan 18 Apr 12 01:44 vdb-validate.2 -> vdb-validate.2.3.2
    -rwxrwxr-x 1 shrujan shrujan 2658917 Apr 6 00:47 vdb-validate.2.3.2


    x86_64

    Leave a comment:

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