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
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Originally posted by shrujan View Postshrujan@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::ApproxCode:apt-cache search String::Approx libstring-approx-perl - Perl extension for approximate matching (fuzzy matching) sudo apt-get install libstring-approx-perl
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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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Originally posted by shrujan View Postcpan[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
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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
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Ya, i have reinstalled everything. I have reinstalled all perl modules.
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Have you reinstalled String::Approx after you reinstalled the OS 64-bit OS?
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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
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I think sklages has almost got shrujan to the finish line. If not:
What does the following command produce?
Code:file ./fastq-dump
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Originally posted by shrujan View Postshrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
bash: ./fastq-dump: No such file or directory
Code:~/Programs/sratoolkit.2.3.2[U]-4-ubuntu64[/U]/bin
Code:~/Programs/sratoolkit.2.3.2/bin
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shrujan@ubuntu:~/Programs/sratoolkit.2.3.2/bin$ ./fastq-dump
bash: ./fastq-dump: No such file or directory
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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
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