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  • #16
    Can you post a listing of the bin directory?

    Code:
    ls -l

    Comment

    • #17
      Originally posted by shrujan View Post
      shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
      bash: ./fastq-dump: No such file or directory
      That is not the same error. As GenoMax wrote, post the content of your bin folder.

      Code:
      cd ~/Programs/sratoolkit.2.3.2/bin
ls -l

      Comment

      • #18
        shrujan@ubuntu:~/Programs/sratoolkit.2.3.2-4-ubuntu64/bin$ ls
        abi-dump ncbi sra-stat.2
        abi-dump.2 nenctool sra-stat.2.3.2
        abi-dump.2.3.2 nenctool.2 sratoolkit.jar
        abi-load nenctool.2.3.2 srf-load
        abi-load.2 pacbio-load srf-load.2
        abi-load.2.3.2 pacbio-load.2 srf-load.2.3.2
        align-info pacbio-load.2.3.2 SRR072111_1.fastq
        align-info.2 prefetch SRR072111_2.fastq
        align-info.2.3.2 prefetch.2 SRR072111.sra
        bam-load prefetch.2.3.2 test-sra
        bam-load.2 rcexplain test-sra.2
        bam-load.2.3.2 rcexplain.2 test-sra.2.3.2
        cg-load rcexplain.2.3.2 vdb-config
        cg-load.2 refseq-load vdb-config.2
        cg-load.2.3.2 refseq-load.2 vdb-config.2.3.2
        configuration-assistant.perl refseq-load.2.3.2 vdb-copy
        fastq-dump sam-dump vdb-copy.2
        fastq-dump.2 sam-dump.2 vdb-copy.2.3.2
        fastq-dump.2.3.2 sam-dump.2.3.2 vdb-decrypt
        fastq-load sff-dump vdb-decrypt.2
        fastq-load.2 sff-dump.2 vdb-decrypt.2.3.2
        fastq-load.2.3.2 sff-dump.2.3.2 vdb-dump
        helicos-load sff-load vdb-dump.2
        helicos-load.2 sff-load.2 vdb-dump.2.3.2
        helicos-load.2.3.2 sff-load.2.3.2 vdb-encrypt
        illumina-dump sra-dbcc vdb-encrypt.2
        illumina-dump.2 sra-dbcc.2 vdb-encrypt.2.3.2
        illumina-dump.2.3.2 sra-dbcc.2.3.2 vdb-lock
        illumina-load sra-kar vdb-lock.2
        illumina-load.2 sra-kar.2 vdb-lock.2.3.2
        illumina-load.2.3.2 sra-kar.2.3.2 vdb-passwd
        kar srapath vdb-passwd.2
        kar.2 srapath.2 vdb-passwd.2.3.2
        kar.2.3.2 srapath.2.3.2 vdb-unlock
        kdbmeta sra-pileup vdb-unlock.2
        kdbmeta.2 sra-pileup.2 vdb-unlock.2.3.2
        kdbmeta.2.3.2 sra-pileup.2.3.2 vdb-validate
        libcurl.so sra-sort vdb-validate.2
        libcurl.so.4 sra-sort.2 vdb-validate.2.3.2
        libcurl.so.4.3.0 sra-sort.2.3.2
        libvdb_jni.so sra-stat

        Comment

        • #19
          Please enter
          Code:
          ls -l
          hmm, and

          Code:
          uname -m

          Comment

          • #20
            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

            Comment

            • #21
              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.

              Comment

              • #22
                shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
                bash: ./fastq-dump: No such file or directory

                Comment

                • #23
                  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.

                  Comment

                  • #24
                    I think sklages has almost got shrujan to the finish line. If not:

                    What does the following command produce?

                    Code:
                    file ./fastq-dump

                    Comment

                    • #25
                      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

                      Comment

                      • #26
                        Have you reinstalled String::Approx after you reinstalled the OS 64-bit OS?

                        Comment

                        • #27
                          Ya, i have reinstalled everything. I have reinstalled all perl modules.

                          Comment

                          • #28
                            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

                            Comment

                            • #29
                              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)?

                              Comment

                              • #30
                                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

                                Comment

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