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**GenoMax** · 04-18-2013, 11:22 AM

Can you post a listing of the bin directory?

Code:

ls -l

**sklages** · 04-18-2013, 12:40 PM

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

**shrujan** · 04-18-2013, 01:06 PM

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

**sklages** · 04-18-2013, 01:09 PM

Please enter

Code:

ls -l

hmm, and

Code:

uname -m

**shrujan** · 04-18-2013, 01:33 PM

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

**sklages** · 04-18-2013, 01:39 PM

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

**shrujan** · 04-18-2013, 01:41 PM

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

**sklages** · 04-18-2013, 01:54 PM

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.

**GenoMax** · 04-18-2013, 01:57 PM

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

What does the following command produce?

Code:

file ./fastq-dump

**shrujan** · 04-18-2013, 01:58 PM

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

**GenoMax** · 04-18-2013, 02:00 PM

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

**shrujan** · 04-18-2013, 02:03 PM

Ya, i have reinstalled everything. I have reinstalled all perl modules.

**shrujan** · 04-18-2013, 02:05 PM

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

**sklages** · 04-18-2013, 02:08 PM

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)?

**shrujan** · 04-18-2013, 02:13 PM

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

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