[maivantan]

Dear GenoMax
I tried bellow commands, i think it worked.

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | ~/tan_analysis/samtools-0.1.19/bcftools/bcftools view -bvcg - > eg2.raw.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
[afs] 0:4254.406 1:3.562 2:113.032
USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ ~/tan_analysis/samtools-0.1.19/bcftools/bcftools view eg2.raw.bcf
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT eg2.sorted.bam
gi|9626243|ref|NC_001416.1| 2 . GGCG GGCGCGGGGGCG 5.08 . INDEL;IS=1,0.500000;DP=2;AF1=1;AC1=2;DP4=0,0,1,0;MQ=42;FQ=-37.5 GT:PL:GQ 1/1:41,3,0:3
gi|9626243|ref|NC_001416.1| 244 . CA C 30.6 . INDEL;IS=1,0.028571;DP=35;VDB=1.039505e-01;AF1=1;AC1=2;DP4=0,0,4,2;MQ=37;FQ=-52.5 GT:PL:GQ 1/1:71,18,0:33
gi|9626243|ref|NC_001416.1| 245 . ATT AT 194 . INDEL;IS=33,0.942857;DP=34;VDB=2.115336e-01;AF1=1;AC1=2;DP4=0,0,13,12;MQ=37;FQ=-110 GT:PL:GQ 1/1:235,75,0:99
gi|

is it correct? can you check it?

Thank you very much

[GenoMax]

As you can see the "bcftools" binary file is present in the /User/user/tan_analysis/samtools-0.1.19/bcftools/ directory. It also has execute permissions that are needed to "run" a program.

[maivantan]

Here the results

total 2096
-rw-r-----@ 1 user staff 1232 3 19 2013 Makefile
-rw-r----- 1 user staff 1966 3 19 2013 README
-rw-r-----@ 1 user staff 10569 3 19 2013 bcf.c
-rw-r-----@ 1 user staff 7223 3 19 2013 bcf.h
-rw-r-----@ 1 user staff 7226 3 19 2013 bcf.h~
-rw-r--r-- 1 user staff 40332 10 28 20:57 bcf.o
-rw-r-----@ 1 user staff 4217 3 19 2013 bcf.tex
-rw-r-----@ 1 user staff 3028 3 19 2013 bcf2qcall.c
-rw-r--r-- 1 user staff 7468 10 28 20:57 bcf2qcall.o
-rwxr-xr-x 1 user staff 166644 10 28 20:57 bcftools
-rw-r-----@ 1 user staff 13251 3 19 2013 bcfutils.c
-rw-r--r-- 1 user staff 42172 10 28 20:57 bcfutils.o
-rw-r-----@ 1 user staff 26288 3 19 2013 call1.c
-rw-r--r-- 1 user staff 60648 10 28 20:57 call1.o
-rw-r-----@ 1 user staff 8985 3 19 2013 em.c
-rw-r--r-- 1 user staff 21156 10 28 20:57 em.o
-rw-r-----@ 1 user staff 3122 3 19 2013 fet.c
-rw-r--r-- 1 user staff 8120 10 28 20:57 fet.o
-rw-r-----@ 1 user staff 8256 3 19 2013 index.c
-rw-r--r-- 1 user staff 25444 10 28 20:57 index.o
-rw-r-----@ 1 user staff 4960 3 19 2013 kfunc.c
-rw-r--r-- 1 user staff 18228 10 28 20:57 kfunc.o
-rw-r-----@ 1 user staff 7269 3 19 2013 kmin.c
-rw-r-----@ 1 user staff 1619 3 19 2013 kmin.h
-rw-r--r-- 1 user staff 11968 10 28 20:57 kmin.o
-rw-r--r-- 1 user staff 293456 10 28 20:57 libbcf.a
-rw-r-----@ 1 user staff 5184 3 19 2013 main.c
-rw-r--r-- 1 user staff 17652 10 28 20:57 main.o
-rw-r-----@ 1 user staff 3816 3 19 2013 mut.c
-rw-r--r-- 1 user staff 11060 10 28 20:57 mut.o
-rw-r-----@ 1 user staff 33429 3 19 2013 prob1.c
-rw-r-----@ 1 user staff 1457 3 19 2013 prob1.h
-rw-r--r-- 1 user staff 77440 10 28 20:57 prob1.o
-rw-r-----@ 1 user staff 7040 3 19 2013 vcf.c
-rw-r--r-- 1 user staff 27272 10 28 20:57 vcf.o
-rwxr-x---@ 1 user staff 15707 3 19 2013 vcfutils.pl

[GenoMax]

Can you verify that the "bcftools" executable is present (based on the error you are getting it appears to have not been "made" when you compiled samtools).

Post the listing of this directory:

$ ls -l /User/user/tan_analysis/samtools-0.1.19/bcftools/

[maivantan]

It was stil not working

SER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | /User/user/tan_analysis/samtools-0.1.19/bcftools/bcftools view -bvcg - > eg2.raw.bcf
-bash: /User/user/tan_analysis/samtools-0.1.19/bcftools/bcftools: No such file or directory
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

[GenoMax]

Likely missing parts highlighted in red. Try the command below:

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | [COLOR="Red"]/[/COLOR]User/user/tan_analysis/samtools-0.1.19/bcftools[COLOR="Red"]/bcftools[/COLOR] view -bvcg - > eg2.raw.bcf

[maivantan]

i provided full path of bcftools as bellowing

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | User/user/tan_analysis/samtools-0.1.19/bcftools view -bvcg - > eg2.raw.bcf
-bash: User/user/tan_analysis/samtools-0.1.19/bcftools: No such file or directory
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

but the same problem i got.
Please give suggestion
Thank you

[GenoMax]

If you built samtools on this computer then "bcftools" program is generally present in its own directory (also called "bcftools" btw). You can either add these directories to your $PATH or provide the full path to the bcftools executable in your command line.

[maivantan]

Any one can suggest me about below problem

USER-no-MacBook-Pro-4:bowtie2-2.1.0 user$ samtools mpileup -uf example/reference/lambda_virus.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
[fai_load] build FASTA index.
-bash: bcftools: command not found
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000

Thank you very much

[jlc_1020]

I installed samtools in a folder on the desktop and then put my files in the home folder so I wouldn't have to specify a path to them (since terminal is automatically in the home folder when it opens). To run, I used:

desktop/samtools/samtools view myfile.bam

[adamdeluca]

quick tip for mac users, if you drag a file into a terminal window the full path will appear.

It does not matter where you install samtools, you just need to provide the correct path to the executable, and the input files.

[raiseal]

using samtools with mac

could you post the directory that you installed samtools into in order to get it to work? I have this problem too.

[jlc_1020]

I figured it out. It was a problem with the directory where my files were located. I moved them to a new directory and it worked fine.

[lparsons]

From the samtools directory, try:

./samtools view my.bam

[jlc_1020]

Umm.. try:

$ /Users/jlc/desktop/samtools/samtools view /Users/jlc/desktop/samtools/my.bam

And get a Unix book

Same error message:

open: No such file or directory
[main_samview] fail to open file for reading.

Thanks though