[zillur]

Thank you very much for your kind reply. May be I am annoying. But what is the base name means?

Best Regards
Zillur

Zillur-Rahman:bowtie2index ZILLURRAHMAN$ bowtie2 -x saccharomyces -1 ../chromosomes/ch_1.fa -2 ../chromosomes/ch_2.fa -S eg2.sam
Could not locate a Bowtie index corresponding to basename "saccharomyces"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 ../chromosomes/ch_1.fa -2 ../chromosomes/ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:bowtie2index ZILLURRAHMAN$ pwd
/Users/ZILLURRAHMAN/desktop/phd/saccharomyces/saccharomyces_cerevisiae_ensembl_r64-1-1/saccharomyces_cerevisiae/ensembl/r64-1-1/sequence/bowtie2index
Zillur-Rahman:bowtie2index ZILLURRAHMAN$

[GenoMax]

You are in (using) the wrong folder (you are is plain sequence folder = WholeGenomeFasta). You want to use the index files in the Bowtie2Index folder.

[zillur]

Hi,
Thank you very much for your kind reply. I am trying this following ways. but.... May be I am missing something..........

Zillur-Rahman:wholegenomefasta ZILLURRAHMAN$ ls
GenomeSize.xml genome.dict genome.fa genome.fa.fai
Zillur-Rahman:wholegenomefasta ZILLURRAHMAN$ bowtie2 -x saccharomyces -1 genome.fa -2 genome.fa.fai -S eg2.sam
Could not locate a Bowtie index corresponding to basename "saccharomyces"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 genome.fa -2 genome.fa.fai
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:wholegenomefasta ZILLURRAHMAN$ cd ..
Zillur-Rahman:sequence ZILLURRAHMAN$ ls
AbundantSequences Bowtie2Index Chromosomes
BWAIndex BowtieIndex WholeGenomeFasta
Zillur-Rahman:sequence ZILLURRAHMAN$ cd chromosomes
Zillur-Rahman:chromosomes ZILLURRAHMAN$ ls
I.fa III.fa IX.fa V.fa VII.fa X.fa XII.fa XIV.fa XVI.fa
II.fa IV.fa MT.fa VI.fa VIII.fa XI.fa XIII.fa XV.fa
Zillur-Rahman:chromosomes ZILLURRAHMAN$ ls
IV.fa MT.fa VI.fa VIII.fa XI.fa XIII.fa XV.fa ch_1.fa ch_3.fa
IX.fa V.fa VII.fa X.fa XII.fa XIV.fa XVI.fa ch_2.fa
Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x saccharomyces ch_1.fa -2 ch_2.fa -3 ch_3.fa -S eg2.sam
Error: 1 mate files/sequences were specified with -1, but 0
mate files/sequences were specified with -2. The same number of mate files/
sequences must be specified with -1 and -2.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -3 ch_3.fa -S eg2.sam -1 -2 ch_1.fa ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x saccharomyces ch_1.fa -2 ch_2.fa -S eg2.sam
Error: 1 mate files/sequences were specified with -1, but 0
mate files/sequences were specified with -2. The same number of mate files/
sequences must be specified with -1 and -2.
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 -2 ch_1.fa ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x saccharomyces -1 ch_1.fa -2 ch_2.fa -S eg2.sam
Could not locate a Bowtie index corresponding to basename "saccharomyces"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x saccharomyces -S eg2.sam -1 ch_1.fa -2 ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x chromosomes -1 ch_1.fa -2 ch_2.fa -S eg2.sam
Could not locate a Bowtie index corresponding to basename "chromosomes"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x chromosomes -S eg2.sam -1 ch_1.fa -2 ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x genome -1 ch_1.fa -2 ch_2.fa -S eg2.sam
Could not locate a Bowtie index corresponding to basename "genome"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x genome -S eg2.sam -1 ch_1.fa -2 ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:chromosomes ZILLURRAHMAN$ bowtie2 -x ..genome -1 ch_1.fa -2 ch_2.fa -S eg2.sam
Could not locate a Bowtie index corresponding to basename "..genome"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /Users/ZILLURRAHMAN/Desktop/1st_semester/Bioinformatics/bow-tie/bowtie2-2.2.3/bowtie2-align-s --wrapper basic-0 -x ..genome -S eg2.sam -1 ch_1.fa -2 ch_2.fa
(ERR): bowtie2-align exited with value 1
Zillur-Rahman:chromosomes ZILLURRAHMAN$ pwd
/Users/ZILLURRAHMAN/desktop/phd/saccharomyces/saccharomyces_cerevisiae_ensembl_r64-1-1/saccharomyces_cerevisiae/ensembl/r64-1-1/sequence/chromosomes
Zillur-Rahman:chromosomes ZILLURRAHMAN$

[GenoMax]

Zillur: Save yourself trouble and download one of the genome bundles (NCBI, Ensembl take your pick) from Illumina's iGenomes page. This bundle includes all kinds of indexes (bowtie is one of them) and annotations etc.

http://support.illumina.com/sequencing/sequencing_software/igenome.html

[zillur]

Hi,
Sorry for the inconvenience. I have found the solution. I just had to add a folder in my path. Now everything is working.

But can you help me about this matter?
I have to map yeast genome and then find SNP. For this from where I can download genome.

http://www.ebi.ac.uk/ena/data/search?query=yeast

http://downloads.yeastgenome.org/seq...nome_releases/

http://www.yeastgenome.org/download-data/sequence

http://www.yeastgenome.org/strain/S288C/overview

Where I can find reference genome?

Best Regards
Zillur

[zillur]

Hi,
Thank you very much. I am facing now an old problem. Again my bowtie, samtools, bcftools commands are not working even after "source" command. What should I do now?

Best Regards
Zillur

Zillur-Rahman:~ ZILLURRAHMAN$ source desktop/1st_semester/bioinformatics/pathcommand_mod.txt
Zillur-Rahman:~ ZILLURRAHMAN$ type bowtie2
-bash: type: bowtie2: not found
Zillur-Rahman:~ ZILLURRAHMAN$ cd desktop/1st_semester/bioinformatics/
Zillur-Rahman:bioinformatics ZILLURRAHMAN$ ls
2nd_exam
An A-Z Index of the Bash command line for Linux | Bash | SS64.com.webarchive
AtoZCommands.pdf
Bioinfo
Books
Bow-tie
Canadian_bioinformatics
Lectures
NCBI_BLASTexercises.pdf
Papers
Project
SamTools
Workshop (11-13 Nov, 14)
bcftools-1.1
bioinformaticprojectbabesiamicrotipapers
e_coli
nohup.out
path_set
pathcommand.txt
pathcommand_mod.txt
perldoc
s_cerevisiae_c-2
Zillur-Rahman:bioinformatics ZILLURRAHMAN$ head pathcommand_mod.txt
export PATH="/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bow-tie/bowtie2-2.2.3:/Users/ZILLURRAHMAN/Desktop/Bioinformatics/samtools/samtools-1.1:/Users/ZILLURRAHMAN/Desktop/Bioinformatics/bcftools-1.1:$PATH"
Zillur-Rahman:bioinformatics ZILLURRAHMAN$ source pathcommand_mod.txt
Zillur-Rahman:bioinformatics ZILLURRAHMAN$ type bowtie2
-bash: type: bowtie2: not found
Zillur-Rahman:bioinformatics ZILLURRAHMAN$

[GenoMax]

Yes! that worked, thankyou so much! Do you know why that had to be done? will i have to do that whenever i install other softwares too?

In case the execute permissions are not set on a binary you would need to do that in future for other software.

[lonesome_forager]

Make is a utility that compiles/links/makes executables from source code. Assuming that you did not encounter any errors during "make" you should have the binaries available. You may need to add execute permissions to the files before you can use them.

$ chmod u+x bowtie2*

then try

$ ./bowtie2

Yes! that worked, thankyou so much! Do you know why that had to be done? will i have to do that whenever i install other softwares too?

[GenoMax]

Hello,

I'm also having trouble installing bowtie2 and its undoubtedly due to my own incompetence!

I'm using a mac and have downloaded the bowtie2 source file and used the make command to unpack it.

now here's where my issue is, i have tried to set the PATH as described in this thread but i still get 'command not found' when i try to run bowtie. I am new to command line and reading around there seems to be suggestions of changing either bash_profile or bashrc, but neither seem to make a difference.

If i navigate to the bowtie2 folder that was populated following the make command, and list the contents, i can see the full list of files and executables including bowtie2. if i type bowtie2 (or .bowtie2) from this folder, i still get the same error 'command not found'.

I presume its something trivial that ive done wrong. Does anyone have any ideas?

My mac is not a vanilla setup and was previously used by someone who's then removed all of their programs and files, is it possible something was removed that i need to reinstall?

Make is a utility that compiles/links/makes executables from source code. Assuming that you did not encounter any errors during "make" you should have the binaries available. You may need to add execute permissions to the files before you can use them.

$ chmod u+x bowtie2*

then try

$ ./bowtie2

[lonesome_forager]

Bowtie2

Hello,

I'm also having trouble installing bowtie2 and its undoubtedly due to my own incompetence!

I'm using a mac and have downloaded the bowtie2 source file and used the make command to unpack it.

now here's where my issue is, i have tried to set the PATH as described in this thread but i still get 'command not found' when i try to run bowtie. I am new to command line and reading around there seems to be suggestions of changing either bash_profile or bashrc, but neither seem to make a difference.

If i navigate to the bowtie2 folder that was populated following the make command, and list the contents, i can see the full list of files and executables including bowtie2. if i type bowtie2 (or .bowtie2) from this folder, i still get the same error 'command not found'.

I presume its something trivial that ive done wrong. Does anyone have any ideas?

My mac is not a vanilla setup and was previously used by someone who's then removed all of their programs and files, is it possible something was removed that i need to reinstall?

[GenoMax]

Now I have to measure the quality of the data that we generated as vcc format. Would you please to give me some suggestions by which I can measure the quality of the data.

Best Regards
Zillur

Since this question is no longer associated with the subject of this thread you should post it as a separate question (after due diligence of searching SeqAnswers.com for prior postings).

To start a new thread: http://seqanswers.com/forums/showpos...69&postcount=9

[zillur]

Now I have to measure the quality of the data that we generated as vcc format. Would you please to give me some suggestions by which I can measure the quality of the data.

Best Regards
Zillur

[zillur]

Thank you very much. I am working on it. I will inform you about my progresses. Thank you again.

Best Regards
Zillur

[GenoMax]

That file is in VCF v.4.2 format. You can find the details about the format here: http://samtools.github.io/hts-specs/VCFv4.2.pdf

[zillur]

Thank you very much. Its working now.
another issue, using $ bcftools view eg2.raw.bcf I have got a large data containing like these:

gi|9626243|ref|NC_001416.1| 48496 . G <X> 0 . DP=2;I16=0,2,0,0,65,2125,0,0,45,1773,0,0,28,634,0,0;QS=1,0;MQ0F=0 PL 0,6,37
gi|9626243|ref|NC_001416.1| 48497 . G <X> 0 . DP=2;I16=0,1,0,0,27,729,0,0,3,9,0,0,25,625,0,0;QS=1,0;MQ0F=0 PL 0,3,4
gi|9626243|ref|NC_001416.1| 48498 . T <X> 0 . DP=2;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0
gi|9626243|ref|NC_001416.1| 48499 . T <X> 0 . DP=2;I16=0,1,0,0,33,1089,0,0,42,1764,0,0,0,0,0,0;QS=1,0;MQ0F=0 PL 0,3,33
gi|9626243|ref|NC_001416.1| 48500 . A <X> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0
gi|9626243|ref|NC_001416.1| 48501 . C <X> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0
gi|9626243|ref|NC_001416.1| 48502 . G <X> 0 . DP=1;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0 PL 0,0,0

so many of this. How can I interpret this data?

Best Regards
Zillur