This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Samtools sort error

Hello,

I've got a SAM file that was aligned using HISAT2, I've converted it into a BAM file using samtools view, I then wanted to sort it using samtools sort and this output comes out and just keeps going and going so I stop it.

G{�q�[�p�Π�������3FqB��m6�p�0���ꜘ-â��&�S��]��qn�Շ��67^�Q<GK?��=c<�>d�9�.�!�.���� 0�_�f*:�h?��'�4��닱�؍7Kp•�}�
              <�}�q۵��"�<���W�(�N��v�Zf��YTW�P�:�����v23l��2�
�q��@��
       /�6D&������]�ש���
�Dtc+q�ʔ)�}���zX��g�=;ήT�D��9��B�)�|��J��   N<e���֐٘3����e>��D�R"@�E9bꁞJ���H��r�0F`���n�{�aW��(���AIu�����\xq�o��A������\{�;�u9�W%����/ٍ%��o8
                                                     ��Z(�j[�EV=����@�A�Fsf�W9�-�t4�;���b�!���
��'6�����m�$v�f�e&���������u�Ni�5sZ�Dq���s&������s�y@Lʑas{�qM��S����1��95|^>��w�9�¢52��1k��|r���z�gC�bV�]�7���B,F��{��'�f1Ƶв�XH%�
                                            �'lzů��
X8���`ʁL�  
                k^{{�h���L�IS���?���v�ե0����H���f��hأ)<kI���~   �˟���4hQ�"�j*�tN�fltT��)�>�J��PVՄ������cbT�ډ�5��b�2xg�!���).����cS����c7���jS�pq

The ultimate goal is that I want to convert my sam file into a bam file and then index it to help with viewing. Would anyone know of a way around this or how to fix this?

samtools rnaseq
• 4,057 views • link
written by V V

samtools has very convenient help information on the command line. Just type samtools or samtools sort to get usage information. In addition, which version are you using?

• 0 views • link
written by WouterDeCoster WouterDeCoster

I almost feel sorry for the Biostars syntax highlighter :(

Write this stuff out to a file with "> sorted.bam"

• 0 views • link
written by John John

I am pleased that the site did not blow up to pieces when a BAM file is posted - though the RSS feed did.

As for the answer, what you have there is a binary, BAM file that is being output to your screen. Redirect it or use the manual to see how to save that into a file rather than a screen.

• 0 views • link
written by Istvan Albert Istvan Albert

Yes yes lets all troll the ubuntu newbie :) Thanks! Got it to work.

• 0 views • link
written by V V

We promise not to .. only if use ADD REPLY/ADD COMMENT when responding to existing posts next time :) This helps keep threads logically organized.

• 0 views • link
written by GenoMax GenoMax

Sorry...growing pains!

• 0 views • link
written by V V

2 answers

Try rereading the samtools sort documentation (see man samtools, or here for the current version) and checking that you are giving the sort options and arguments correctly.

• 0 views • link
written by John Marshall John Marshall

Don't worry! This is how a bam file should look like:) It is a binary version of the "human readable" sam file. If I look at the first few lines of one of my own bam files with "head mysample.bam", what I see looks very similar to your output. If you want to see the "human readable" format again, use samtools: "samtools view mysample.bam | head" should show you the first lines of your bam file as you had it in the original sam file. As John suggested, write the output to a file and not to the screen.

• 0 views • link
written by Johanna Schott Johanna Schott

Log in to answer this question.

More posts like this