text: user12006: 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!
  
  user-1: My best guess would be a corruption during download as:
  samtools quickcheck -qvvvv ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam                
  verbosity set to 4
  checking ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam
  opened ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam
  ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam is sequence data
  ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam has 196 targets in header.
  ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam has good EOF block.
  
  Plus I can successfully run idxstats from remote and fetch individual chromosomes without error via samtools view. Try redownloading before digging deeper.
  
original_text: 12006: <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>
   -1: <p>My best guess would be a corruption during download as:</p>
  <pre><code>samtools quickcheck -qvvvv ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam                
  verbosity set to 4
  checking ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam
  opened ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam
  ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam is sequence data
  ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam has 196 targets in header.
  ftp://ftp-trace.ncbi.nlm.nih.gov:/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.0_06202016/NA12878_GRCh38.bam has good EOF block.
  </code></pre>
  <p>Plus I can successfully run <code>idxstats</code> from remote and fetch individual chromosomes without error via <code>samtools view</code>. Try redownloading before digging deeper.</p>
  