<p>I am a beginner and trying to read a bam file in Python.</p>
<p>The lines below throw the error</p>
<pre><code>OSError: [Errno 8] could not open alignment file `mybam.bam`: Exec format error
</code></pre>
<p>What could be the possible solution?</p>
<pre><code>user@server:~/Documents$ python3
Python 3.8.10 (default, Jun  2 2021, 10:49:15)
[GCC 9.4.0] on linux
Type &quot;help&quot;, &quot;copyright&quot;, &quot;credits&quot; or &quot;license&quot; for more information.

&gt;&gt;&gt; import pysam
&gt;&gt;&gt; samfile = pysam.AlignmentFile(&quot;mybam.bam&quot;, &quot;rb&quot;)

[E::hts_hopen] Failed to open file mybam.bam
[E::hts_open_format] Failed to open file &quot;mybam.bam&quot; : Exec format error
Traceback (most recent call last):
  File &quot;&lt;stdin&gt;&quot;, line 1, in &lt;module&gt;
  File &quot;pysam/libcalignmentfile.pyx&quot;, line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File &quot;pysam/libcalignmentfile.pyx&quot;, line 941, in pysam.libcalignmentfile.AlignmentFile._open
OSError: [Errno 8] could not open alignment file `mybam.bam`: Exec format error
</code></pre>

CC BY-SA 4.0
2021-10-15T18:25:31.143Z
this is something related to the file not with python. Check the file with the linux command `file mybam.bam` just to know that you have a bam instead of a sam, text format. If you have a compressed file in bam format, check the head with `samtools view mybam.bam | head -100`, if this fails check the mapping software again where you got the alignment from.
zorbax
CC BY-SA 4.0
2021-10-15T22:02:53.320Z
https://www.biostars.org/p/284417/
Maximilian Press
CC BY-SA 4.0
2021-10-16T09:54:17.300Z
Thank you for the help. samtools view mybam.bam | head -100
outputed a hundred lines, which have no index. As there is no index, I was able to retrieve the content with:
for read in samfile.fetch(until_eof=True):
    print(read)
monade
<python><phylogenetics><sam><file-formats><pysam>
pysam "Exec format" error
# pysam "Exec format" error

(Asked by: username_0 on 2021-10-15)

I am a beginner and trying to read a bam file in Python.
The lines below throw the error
OSError: [Errno 8] could not open alignment file `mybam.bam`: Exec format error

What could be the possible solution?
user@server:~/Documents$ python3
Python 3.8.10 (default, Jun  2 2021, 10:49:15)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

>>> import pysam
>>> samfile = pysam.AlignmentFile("mybam.bam", "rb")

[E::hts_hopen] Failed to open file mybam.bam
[E::hts_open_format] Failed to open file "mybam.bam" : Exec format error
Traceback (most recent call last):
  File "", line 1, in 
  File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.__cinit__
  File "pysam/libcalignmentfile.pyx", line 941, in pysam.libcalignmentfile.AlignmentFile._open
OSError: [Errno 8] could not open alignment file `mybam.bam`: Exec format error

**Tags:** python, phylogenetics, sam, file-formats, pysam
> **Comments:**
> **username_1**: this is something related to the file not with python. Check the file with the linux command `file mybam.bam` just to know that you have a bam instead of a sam, text format. If you have a compressed file in bam format, check the head with `samtools view mybam.bam | head -100`, if this fails check the mapping software again where you got the alignment from.  
> **username_2**: https://www.biostars.org/p/284417/  
> **username_0**: Thank you for the help. samtools view mybam.bam | head -100 outputed a hundred lines, which have no index. As there is no index, I was able to retrieve the content with: for read in samfile.fetch(until_eof=True):     print(read)  

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## 0 answers

