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samtools sort error

I am having a problem with samtools.

It looks like I successfully created a .bam file. When I enter: 

samtools view Y13.bam | head

I get a file that is formatted like this: 

TCTGGCGCAGTATGTCACACCTGCATTGGACAGAGCTTGTTTTCATGGCAGACAAAC   AAFAFJFAJJFJJ<JJJJAJJJJF7F7FJJJJJ<FJJJJFJ-FJFJ<<JFJJJF-7JFJ-7FJ-F-AF7FF---<7<-7FFF--77F-F-A-777F<F<JF<---77FF-7A7A<-AA7--A<F-7FJ<77A7<--7-7--A-777F<-F  YT:Z:UP
E00558:452:H3WH2CCX2:1:1101:21572:5739  141 *   0   0   *   *   0   0

But when I run: 

samtools sort Y13.bam -o Y13.sorted.bam

the output printed in terminal looks like this: 

     W�����x��O�U�e�$ytL��S�#�_ɧN���Ie��ifz����!��nW���c�f54���HE���m^O��u;\���m���&8VTZ>���X0�I�#�X�
             g��}��J��y�e�����ܲ4� 7`�I��Iݼ�ʉLOՏ����!^H�=��d< Oj/��5ȩ"�܉�g��~����So4�mY�dd�z��|��WD��k9���ɵ�̎@<�t�pG��^O4d����S�(d"{ߗ���#��1�%��aA�x  �nt��

Also, there is no Y13.sorted.bam file being created.

Any suggestions as to what might be going on here?

snp alignment
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updated by Ram Ram • written by JC • JC

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

• 0 views • link
written by Ram Ram

JC : Please upgrade your samtools to the latest version, which is now 1.9. Version you are using is really ancient.

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written by GenoMax GenoMax

it is working with v.1.9. Thanks!

• 0 views • link
written by JC • JC

1 answer

What version of samtools are you running? It looks like an older version that wants a ">" instead of "-o" to redirect output to a file instead of the terminal.

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written by swbarnes2 swbarnes2

Version: 0.1.19-44428cd

it looks like -o is the option for this version based on the options available:

$ samtools sort

Usage:   samtools sort [options] <in.bam> <out.prefix>

Options: -n        sort by read name
         -f        use <out.prefix> as full file name instead of prefix
         -o        final output to stdout
         -l INT    compression level, from 0 to 9 [-1]
         -@ INT    number of sorting and compression threads [1]
         -m INT    max memory per thread; suffix K/M/G recognized [768M]
• 0 views • link
updated by GenoMax GenoMax • written by JC • JC

-o final output to stdout looks like exactly what is happening. I used that ancient version for a long time, I'm pretty sure I used > sorted.bam

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written by swbarnes2 swbarnes2

It looks like it was a version issue. I have this step working now with the new version. Thanks!

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written by JC • JC

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