<p>Try re-indexing your bam file:</p>
<pre><code>samtools index input.bam
</code></pre>
<p>Or update the timestamp via <code>touch index.bam.bai</code> but I think re-indexing is safer. You might want to save any original index file first, e.g. via <code>mv input.bam.bai old_input.bam.bai</code> or similar</p>
<p>Also I think you meant <code>&gt; chr21.bam</code> instead of piping via <code>| chr21.bam</code> if you want to save the output file</p>

CC BY-SA 4.0
2022-02-28T19:09:53.387Z
Cool! I think the problem is because I use | chr21.bam.
Scott XU
CC BY-SA 4.0
2022-02-28T19:05:58.300Z
2022-02-28T19:05:58.300Z
Chris_Rands
<p>When I tried to use samtools to split a bam file based on different chromosomes, I used this command:</p>
<pre><code>samtools view input.bam -b chr21 | chr21.bam
</code></pre>
<p>However, I get error messages like this:</p>
<pre><code>-bash: chr21.bam: command not found
[W::hts_idx_load3] The index file is older than the data file: input.bam.bai
</code></pre>
<p>How could I solve this problem? Thanks in advance~~~</p>
<p>The version I am using is:</p>
<pre><code>Program: samtools (Tools for alignments in the SAM format)
Version: 1.10 (using htslib 1.10.2)
</code></pre>

<sam><samtools>
samtools view command not found error
# samtools view command not found error

(Asked by: username_0 on 2022-02-28)

When I tried to use samtools to split a bam file based on different chromosomes, I used this command:
samtools view input.bam -b chr21 | chr21.bam

However, I get error messages like this:
-bash: chr21.bam: command not found
[W::hts_idx_load3] The index file is older than the data file: input.bam.bai

How could I solve this problem? Thanks in advance~~~
The version I am using is:
Program: samtools (Tools for alignments in the SAM format)
Version: 1.10 (using htslib 1.10.2)

**Tags:** sam, samtools

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## 1 answers

### Answer by username_1 on 2022-02-28. Score: 5 | Accepted answer

Try re-indexing your bam file:
samtools index input.bam

Or update the timestamp via touch index.bam.bai but I think re-indexing is safer. You might want to save any original index file first, e.g. via mv input.bam.bai old_input.bam.bai or similar
Also I think you meant > chr21.bam instead of piping via | chr21.bam if you want to save the output file

> **Comments:**
> **username_0**: Cool! I think the problem is because I use | chr21.bam.  

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