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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!

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    $\begingroup$ As you say, the file is truncated. Why are you investigating this instead of just downloading the entire file? $\endgroup$
    – terdon
    Apr 12, 2021 at 9:33
  • $\begingroup$ 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. $\endgroup$
    – yyn
    Apr 12, 2021 at 23:58

1 Answer 1

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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.

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  • $\begingroup$ Thanks for your advice, I will redownload it by using Aspera instead of lftp. $\endgroup$
    – yyn
    Apr 13, 2021 at 0:25

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