<p>I download a BAM file from <a href="ftp://ftp-trace.ncbi.nlm.nih.gov//giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam" rel="nofollow noreferrer">ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam</a> (171G), and I am trying to view the comparison result of the BAM file using the following command:</p>
<pre><code>[yyn@localhost All]$ samtools flagstat NA12878_GRCh38.bam
</code></pre>
<p>The result shows that the file is truncated, the result as follows:</p>
<pre><code>[E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
[bam_flagstat_core] Truncated file? Continue anyway.
72639 + 0 in total (QC-passed reads + QC-failed reads)
896 + 0 secondary
0 + 0 supplementary
2529 + 0 duplicates
72639 + 0 mapped (100.00% : N/A)
71743 + 0 paired in sequencing
36865 + 0 read1
34878 + 0 read2
48600 + 0 properly paired (67.74% : N/A)
69949 + 0 with itself and mate mapped
1794 + 0 singletons (2.50% : N/A)
10233 + 0 with mate mapped to a different chr
2869 + 0 with mate mapped to a different chr (mapQ&gt;=5)
</code></pre>
<p>The total number of reads is only 72639, Obviously, this is the wrong result. And I checked the file again with the following command</p>
<pre><code>[yyn@localhost All]$ samtools quickcheck -qv NA12878_GRCh38.bam &amp;&amp; echo 'all ok' || echo 'failed check'
</code></pre>
<p>The result is:</p>
<pre><code>all ok
</code></pre>
<p>I checked the contents of the file again, and the result showed that there was no problem with the first 72620 lines in the file, but there was a problem with the first 72630 lines, so the file should be truncated in the 72620 to 72630 lines.</p>
<pre><code>[yyn@localhost All]$ samtools view NA12878_GRCh38.bam | head -n 72610 &gt;&gt; head72610.sam
</code></pre>
<p>That's ok.</p>
<pre><code>[yyn@localhost All]$ samtools view NA12878_GRCh38.bam | head -n 72620 &gt;&gt; head72620.sam
[E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
[main_samview] truncated file.
</code></pre>
<p><code>samtools sort</code> and <code>samtools index</code> are the same error results as above. Does anyone know what's going on? Thanks!</p>

CC BY-SA 4.0
2021-04-12T09:33:23.240Z
As you say, the file is truncated. Why are you investigating this instead of just downloading the entire file?
terdon
CC BY-SA 4.0
2021-04-12T23:58:31.503Z
I downloaded it three times using lftp, all of which are like this, and I can't restore it with bamUtil. But downloading with Aspera is slower than lftp.
yyn
<sam><samtools>
Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
# Inflate operation failed: progress temporarily not possible, or in() / out() returned an error

(Asked by: username_0 on 2021-04-12)

I download a BAM file from ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam (171G), and I am trying to view the comparison result of the BAM file using the following command:
[yyn@localhost All]$ samtools flagstat NA12878_GRCh38.bam

The result shows that the file is truncated, the result as follows:
[E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
[bam_flagstat_core] Truncated file? Continue anyway.
72639 + 0 in total (QC-passed reads + QC-failed reads)
896 + 0 secondary
0 + 0 supplementary
2529 + 0 duplicates
72639 + 0 mapped (100.00% : N/A)
71743 + 0 paired in sequencing
36865 + 0 read1
34878 + 0 read2
48600 + 0 properly paired (67.74% : N/A)
69949 + 0 with itself and mate mapped
1794 + 0 singletons (2.50% : N/A)
10233 + 0 with mate mapped to a different chr
2869 + 0 with mate mapped to a different chr (mapQ>=5)

The total number of reads is only 72639, Obviously, this is the wrong result. And I checked the file again with the following command
[yyn@localhost All]$ samtools quickcheck -qv NA12878_GRCh38.bam && echo 'all ok' || echo 'failed check'

The result is:
all ok

I checked the contents of the file again, and the result showed that there was no problem with the first 72620 lines in the file, but there was a problem with the first 72630 lines, so the file should be truncated in the 72620 to 72630 lines.
[yyn@localhost All]$ samtools view NA12878_GRCh38.bam | head -n 72610 >> head72610.sam

That's ok.
[yyn@localhost All]$ samtools view NA12878_GRCh38.bam | head -n 72620 >> head72620.sam
[E::bgzf_uncompress] Inflate operation failed: progress temporarily not possible, or in() / out() returned an error
[E::bgzf_read] Read block operation failed with error 1 after 0 of 4 bytes
[main_samview] truncated file.

samtools sort and samtools index are the same error results as above. Does anyone know what's going on? Thanks!

**Tags:** sam, samtools
> **Comments:**
> **username_1**: As you say, the file is truncated. Why are you investigating this instead of just downloading the entire file?  
> **username_0**: I downloaded it three times using lftp, all of which are like this, and I can't restore it with bamUtil. But downloading with Aspera is slower than lftp.  

---

## 0 answers

