[GenoMax]

From where I can get the "bcftools" files?

You have to download and compile bcftools from here: http://sourceforge.net/projects/samt...r.bz2/download

[zillur]

Thank you very much. I am working on this. Meanwhile I have another problem.

Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.fa lambdaout.rev.1.bt2
eg2.sam lambda_virus.rev.1.bt2 lambdaout.rev.2.bt2
egl.sam lambda_virus.rev.2.bt2 nohup.out
lambda_virus.1.bt2 lambdaout.1.bt2 out
lambda_virus.2.bt2 lambdaout.2.bt2 out.sam
lambda_virus.3.bt2 lambdaout.3.bt2
lambda_virus.4.bt2 lambdaout.4.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools view -bS eg2.sam > eg2.bam
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.4.bt2 lambdaout.4.bt2
eg2.bam lambda_virus.fa lambdaout.rev.1.bt2
eg2.sam lambda_virus.rev.1.bt2 lambdaout.rev.2.bt2
egl.sam lambda_virus.rev.2.bt2 nohup.out
lambda_virus.1.bt2 lambdaout.1.bt2 out
lambda_virus.2.bt2 lambdaout.2.bt2 out.sam
lambda_virus.3.bt2 lambdaout.3.bt2
Mds-MacBook-Pro:reference ZILLURRAHMAN$ more eg2.bam
"eg2.bam" may be a binary file. See it anyway?
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools sort eg2.bam eg2.sorted
Mds-MacBook-Pro:reference ZILLURRAHMAN$ ls
commands lambda_virus.3.bt2 lambdaout.3.bt2
eg2.bam lambda_virus.4.bt2 lambdaout.4.bt2
eg2.sam lambda_virus.fa lambdaout.rev.1.bt2
eg2.sorted.bam lambda_virus.rev.1.bt2 lambdaout.rev.2.bt2
egl.sam lambda_virus.rev.2.bt2 nohup.out
lambda_virus.1.bt2 lambdaout.1.bt2 out
lambda_virus.2.bt2 lambdaout.2.bt2 out.sam
Mds-MacBook-Pro:reference ZILLURRAHMAN$ more eg2.sorted.bam
"eg2.sorted.bam" may be a binary file. See it anyway?
Mds-MacBook-Pro:reference ZILLURRAHMAN$ samtools mpileup -uf /example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
[fai_load] build FASTA index.
[fai_build] fail to open the FASTA file /example/reference/lambda_virus.fa
[fai_load] fail to open FASTA index.
-bash: bcftools: command not found
Mds-MacBook-Pro:reference ZILLURRAHMAN$

From where I can get the "bcftools" files?

[GenoMax]

This is a simple work around.

Since you are having trouble editing .bash_profile file put the PATH command in a text file (let us call the file "set_path_file") using an editor. Then when you open a new terminal do the following

$ source set_path_file

That should set the PATH variable correctly for that terminal session. You will need to do this for each new terminal you open.

[zillur]

Thank you very much. Its really great to find some people like you. Now I am able to create paths for programs that I need.

Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ pwd
/Users/ZILLURRAHMAN/desktop/bioinformatics/samtools/samtools-1.1
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/samtools/samtools-1.1/:$PATH"
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ type samtools.1
samtools.1 is /Users/ZILLURRAHMAN/Desktop/Bioinformatics/samtools/samtools-1.1/samtools.1
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ type bowtie2
bowtie2 is /Users/ZILLURRAHMAN/Desktop/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$

But another problem, every time I close the terminal it loses all the newly created paths. Even if I open a new tab on the same terminal window it can't find the newly created paths.

Last login: Sun Nov 2 17:00:11 on ttys000
-bash: $: command not found
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ type bowtie2
-bash: type: bowtie2: not found
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$ type samtools.1
-bash: type: samtools.1: not found
Mds-MacBook-Pro:samtools-1.1 ZILLURRAHMAN$

What should I do now? I just don't want to create path every time I am opening a new shell.

Best Regards
Zillur

[GenoMax]

It is safe to work in the terminal. Adding the path modifier to profile file is a convenience so you don't have to do it in the terminal each time. You can use the same method to add path for samtools (and any additional programs you need).

[zillur]

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?

[GenoMax]

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.

[zillur]

Thank you very much. So I should just need to type it in the command line. Don't I need any vi editor?

[GenoMax]

export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/[COLOR="Red"]b[/COLOR]ow-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.

[zillur]

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

[GenoMax]

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.

[GenomExpert]

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

[GenoMax]

@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.

[zillur]

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?

[GenomExpert]

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...