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Old 10-19-2014, 07:06 AM   #61
zillur
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Thank you very much. Now I can open the vi editor with /usr/bin/vi a window open containing : ~
~ VIM - Vi IMproved
~
~ version 7.3
~ by Bram Moolenaar et al.
~ Vim is open source and freely distributable
~
~ Help poor children in Uganda!
~ type :help iccf<Enter> for information
~
~ type :q<Enter> to exit
~ type :help<Enter> or <F1> for on-line help
~ type :help version7<Enter> for version info
~
Then I was setting path :
export PATH=“/Users/ZILLURRAHMAN/Desktop/Bioinformatics/Bow-tie/bowtie2-2.2.3/:$PATH” and this was my previously setted path. But still it is not working. I think somehow I replaced this path by
“users/ZILLURRAHMAN/desktop/bioinformatics/bow-tie/bowtie2-2.2.3/BT2_HOME:??
As I am very new in command line I am making mistakes. Sorry guys I am giving you too much pain.

I can't use http://www.tech-recipes.com/rx/2618/...with_textedit/ this link cause my open command also not working.

[6]+ Stopped /usr/bin/vim
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ /usr/bin/vim

[7]+ Stopped /usr/bin/vim
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ ls
-bash: ls: command not found
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ /usr/bin/vim

[8]+ Stopped /usr/bin/vim
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ open .profile
-bash: open: command not found
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ open -a TextEdit .profile
-bash: open: command not found
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ cd
Mds-MacBook-Pro:~ ZILLURRAHMAN$ /usr/bin/vim

[9]+ Stopped /usr/bin/vim
Mds-MacBook-Pro:~ ZILLURRAHMAN$ /usr/bin/vim

[10]+ Stopped /usr/bin/vim
Mds-MacBook-Pro:~ ZILLURRAHMAN$ echo $PATH
“users/ZILLURRAHMAN/desktop/bioinformatics/bow-tie/bowtie2-2.2.3/BT2_HOME:??

May be I am missing something very fundamental line...........
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Old 10-19-2014, 09:03 AM   #62
GenoMax
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Can you create a new user account with administrative privileges and see if you are able to get around the problems you are facing with this account? That would also verify that you don't have some other fundamental problem with your OS.

If the new account works properly then we can copy the programs/data over to the new account.
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Old 10-19-2014, 09:21 AM   #63
zillur
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Thank you very much. I don't know how to create a new user account. Can give me instructions to create a new user account.
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Old 10-19-2014, 10:46 AM   #64
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Quote:
Originally Posted by zillur View Post
Thank you very much. I don't know how to create a new user account. Can give me instructions to create a new user account.
http://support.apple.com/kb/PH14411
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Old 10-19-2014, 11:47 AM   #65
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I don't think you know that you need to open a new Terminal window, or type
source ~/.bash_profile
for the changes to the .bash_profile file to take effect.

You simply edited the .bash_profile file.

As far as I can see, you didn't open a new Terminal window or source the .bash_profile file.

Once you do open a new Terminal window or source the .bash_profile file, the changes will take effect, and your PATH environment variable will be updated.
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Old 10-19-2014, 12:23 PM   #66
GenoMax
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@Zillur: Reboot your Mac before doing anything (e.g. adding an account). With a mac you may just be used to closing the lid and resuming your work. Opening a new terminal window (apple + t) may be enough as blancha mentions but just to be sure reboot (if you have indeed fixed your PATH variable).
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Old 10-19-2014, 03:24 PM   #67
zillur
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Thank you very much to you all for your helping hand.
Mds-MacBook-Pro:~ ZILLURRAHMAN$ source ~/.bash_profile
-bash: $: command not found

I added a new account and in this account everything is going fine. But I can't find any file from my previous account. I want to send all my files and folders from previous account to new account. Can you suggest me how can I do it?

Regards
Zillur
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Old 10-19-2014, 03:34 PM   #68
GenoMax
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Quote:
Originally Posted by zillur View Post

I added a new account and in this account everything is going fine. But I can't find any file from my previous account. I want to send all my files and folders from previous account to new account. Can you suggest me how can I do it?

Regards
Zillur
In the new account do the following (hopefully you have enough storage available to duplicate the data temporarily). This is only copying the "Bioinformatics" folder from /Users/ZILLURRAHMAN/Desktop/, repeat for anything else you need:

Code:
$ sudo cp -R /Users/ZILLURRAHMAN/Desktop/Bioinformatics /Users/Current_Acct_Name/Desktop
That hopefully should copy everything over to the desktop of the new account. You will need to adjust PATH etc to account for the new account, when you run the programs.

If you are not using "time machine" to keep a backup of your computer do yourself a favor and set this up first thing tomorrow. Get an external drive and get time machine backups going. That way you can roll back a mistake easily.
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Old 10-19-2014, 03:42 PM   #69
zillur
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Thank you very much for your kind reply. Here is the line with new user. But...

Mds-MacBook-Pro:desktop nemesisnemesis$ $ sudo cp -R /Users/ZILLURRAHMAN/Desktop/Bioinformatics /Users/nemesisnemesis/Desktop
-bash: $: command not found
Mds-MacBook-Pro:desktop nemesisnemesis$ cd
Mds-MacBook-Pro:~ nemesisnemesis$ $ sudo cp -R /Users/ZILLURRAHMAN/Desktop/Bioinformatics /Users/nemesisnemesis/Desktop
-bash: $: command not found
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Old 10-19-2014, 04:15 PM   #70
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That means things are not working right on your Mac for both (perhaps all accounts).

At this point you could check a couple more locations from this thread (last post in the thread): https://discussions.apple.com/thread...art=0&tstart=0 Those are /etc/profile and /etc/bashrc.

Note: I am still not sure how you managed to get your system into this state.

I do need to warn you that we are approaching areas of the system that may lead to irreparable damage, if you did something wrong. Perhaps it is time to call upon a friend/colleague who may be more knowledgeable about the command line and show them the problem and this thread.
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Old 10-22-2014, 03:49 AM   #71
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I'm also trying to install bowtie. What I did:

download bowtie2-2.1.0-mingW-win64.zip
unzip successfully..
now what to do next...
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Old 10-27-2014, 11:13 AM   #72
zillur
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Default Command lines.

Thank you all very much for your help and patience cause I was asking so many times about the same thing. I have upgrade my OS from OSX to X11 which gave me XQuartz with a new terminal Xterm and here everything is working fine. Like:
bash-3.2$ type more
more is /usr/bin/more
bash-3.2$ type less
less is /usr/bin/less
bash-3.2$ type cat
cat is /bin/cat
bash-3.2$ type head
head is /usr/bin/head
bash-3.2$ type ls
ls is hashed (/bin/ls)
bash-3.2$

What is the difference between hashed or without hashed?

But still my terminal doesn't work. Can I continue with the XQuartz? or i have to do anything else?
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Old 10-27-2014, 02:38 PM   #73
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@zillur: If you have no access to local help and if xterm in XQuartz is working then that is your only choice at this point.
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Old 10-28-2014, 06:37 AM   #74
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hiii,
i am trying to generate variant calls in VCF format using this command
samtools mpileup -uf $BT2_HOME/example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
but it generates the output like:
[mpileup] 1 sample in 1 input files
<mpileup>set max per-file depth to 8000
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs]0:0:000
plz help in solving this problem
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Old 10-28-2014, 06:59 AM   #75
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Quote:
Originally Posted by GenomExpert View Post
hiii,
i am trying to generate variant calls in VCF format using this command
samtools mpileup -uf $BT2_HOME/example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
but it generates the output like:
[mpileup] 1 sample in 1 input files
<mpileup>set max per-file depth to 8000
[bcf_sync] incorrect number of fields (0 != 5) at 0:0
[afs]0:0:000
plz help in solving this problem
GenomeExpert: Can you please create a new thread for this question (seqanswers.com --> Forums --> Select Appropriate forum --> New thread button on top left)? Please include information about the version of samtools/bcftools you are using.

It would be better since this question is not related to the original topic of this thread/would likely generate a response quicker.
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Old 11-01-2014, 08:16 PM   #76
zillur
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Thank you very much. I am a neophyte here and making mistakes in my every steps but you are always helping me. Its amazing for me. Thank you so much. However I have got my terminal back. I had to type
/bin/echo 'export PATH=${PATH}:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin' >> ~/.bash_profile then hit enter. Now its working
But now my bowtie2 command is not working. Should I create path using vi editor?
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ type ls
ls is hashed (/bin/ls)
Mds-MacBook-Pro:desktop ZILLURRAHMAN$ type bowtie2
-bash: type: bowtie2: not found
Mds-MacBook-Pro:desktop ZILLURRAHMAN$

Should I create path using vi editor?

Mds-MacBook-Pro:desktop ZILLURRAHMAN$ cd bioinformatics/bow-tie/bowtie2-2.2.3/
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ ls
AUTHORS bowtie2-align-l-debug bowtie2-inspect
LICENSE bowtie2-align-s bowtie2-inspect-l
MANUAL bowtie2-align-s-debug bowtie2-inspect-l-debug
MANUAL.markdown bowtie2-build bowtie2-inspect-s
NEWS bowtie2-build-l bowtie2-inspect-s-debug
TUTORIAL bowtie2-build-l-debug doc
VERSION bowtie2-build-s example
bowtie2 bowtie2-build-s-debug scripts
bowtie2-align-l bowtie2-buildc
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$ pwd
/Users/ZILLURRAHMAN/desktop/bioinformatics/bow-tie/bowtie2-2.2.3
Mds-MacBook-Pro:bowtie2-2.2.3 ZILLURRAHMAN$
Should I type:
export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/Bow-tie/bowtie2-2.2.3/:$PATH"
then save and quit the vi editor? I am asking you mentioning my details files and folders cause I don't another mess. Hope you understand my situation here.

Best Regards
Zillur
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Old 11-02-2014, 04:46 AM   #77
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Code:
export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bow-tie/bowtie2-2.2.3/:$PATH"
Make sure you use the correct case (you had a capital B in the line I copied above". Just do that on the command line before you go editing any files. OS should now be able to find bowtie2.
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Old 11-02-2014, 05:31 AM   #78
zillur
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Thank you very much. So I should just need to type it in the command line. Don't I need any vi editor?
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Old 11-02-2014, 05:53 AM   #79
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You can add that line to your .bash_profile using vi after you test it on the command line and confirm that it works. Then it would be automatically sourced when you log in next time since it will be there in the profile.
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Old 11-02-2014, 06:14 AM   #80
zillur
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Thank you very much. But I can't do it using vi editor. I don't know what is happening here. But I just typed the line in the terminal and its working now. But is it safe to work direct with terminal?
Mds-MacBook-Pro:~ ZILLURRAHMAN$ type bowtie2
bowtie2 is hashed (/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2)

Using same trick can I make path for samtools?
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