[BioC] Problem with BAM header in GAlignments

Tue Jan 7 23:52:53 CET 2014

The thought did occur to me that these might be SAM format, but its odd because the information beyond the header appears to be binary. The files also came with accompanying .bai index files as well. I have never had cause to carefully examine the header, so I didn't know what to expect. I take it thought that the header in a BAM file is also supposed to in binary? 

Sean
> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: Tuesday, January 07, 2014 2:45 PM
> To: Taylor, Sean D; bioconductor at r-project.org
> Subject: Re: [BioC] Problem with BAM header in GAlignments
> 
> On 01/07/2014 02:31 PM, Taylor, Sean D wrote:
> > I have received some BAM files from a colleague that were produced from
> an Illumina HiSeq instrument. When I try to read them as a GAlignments
> object, I get the following error:
> >> bamfile<-'03-192B3_lung.sort.nodup.bam.realigned.bam'
> >> gal<-readGAlignments(bamfile)
> > Error in value[[3L]](cond) :
> >    failed to open BamFile: SAM/BAM header missing or empty
> >    file: '03-192B3_lung.sort.nodup.bam.realigned.bam'
> > In addition: Warning message:
> > In doTryCatch(return(expr), name, parentenv, handler) :
> >    [bam_header_read] invalid BAM binary header (this is not a BAM file).
> >
> >
> > I looked at the header data this way:
> >> strsplit(readLines(bamfile, 10), '\t')
> 
> this (using readLines on bamfile) implies that it is actually a sam (text) file
> rather than a bam (binary) file, despite the .bam extension! Convert it to
> bam and optionally generate an index with
> 
>    asBam(bamfile, "some_file_name.bam", indexDestination=TRUE)
> 
> or, better, get your upstream provider to generate bam files for you.
> 
> The funky information in the first line looks like the file has been corrupted in
> some way, too; you'll need to get that fixed first, which probably means
> coordinating with whomever is providing you with files. Probably you want to
> make sure that the 'checksums' on the file are the same before and after any
> copy, e.g., running the linux command md5sum *bam or from within R using
> tools::md5sum().
> 
> Martin
> 
> > [[1]]
> > [1] NA
> >
> > [[2]]
> > [1] "@SQ"          "SN:1"         "LN:249250621"
> >
> > [[3]]
> > [1] "@SQ"          "SN:2"         "LN:243199373"
> >
> > [[4]]030
> > [1] "@SQ"          "SN:3"         "LN:198022430"
> >
> > [[5]]
> > [1] "@SQ"          "SN:4"         "LN:191154276"
> >
> > [[6]]
> > [1] "@SQ"          "SN:5"         "LN:180915260"
> >
> > [[7]]
> > [1] "@SQ"          "SN:6"         "LN:171115067"
> >
> > [[8]]
> > [1] "@SQ"          "SN:7"         "LN:159138663"
> >
> > [[9]]
> > [1] "@SQ"          "SN:8"         "LN:146364022"
> >
> > [[10]]
> > [1] "@SQ"          "SN:9"         "LN:141213431"
> > Warning message:
> > In strsplit(readLines(bamfile, 10), "\t") :
> >    input string 1 is invalid in this locale
> >
> > And then from the command  line:
> > $ less 03-192B3_lung.sort.nodup.bam.realigned.bam
> > BAM^A<CA>^K^@^@@HD      VN:1.4  GO:none SO:coordinate
> > @SQ     SN:1    LN:249250621
> > @SQ     SN:2    LN:243199373
> > @SQ     SN:3    LN:198022430
> > @SQ     SN:4    LN:191154276
> > @SQ     SN:5    LN:180915260
> > @SQ     SN:6    LN:171115067
> > @SQ     SN:7    LN:159138663
> > @SQ     SN:8    LN:146364022
> > @SQ     SN:9    LN:141213431
> > @SQ     SN:10   LN:135534747
> >
> > I'm not sure what that first line is, but I think that is the problem. The bam
> file itself is 18 GB, so it is difficult to edit directly. Is there a way I can direct
> readGAlignments to skip the first line? Or is there a different solution, eg
> filterBam? Ultimately I am going to be sifting through many such BAM files so
> I'm hoping for a general solution that doesn't involve manual editing if
> possible.
> >
> > Thanks,
> > Sean
> >
> >> sessionInfo()
> > R version 3.0.2 (2013-09-25)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8
> >   [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
> LC_MESSAGES=en_US.UTF-8
> >   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C
> > [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
> LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] latticeExtra_0.6-26  RColorBrewer_1.0-5   ShortRead_1.20.0
> lattice_0.20-24
> >   [5] Rsamtools_1.14.1     Biostrings_2.30.0    GenomicRanges_1.14.3
> XVector_0.2.0
> >   [9] IRanges_1.20.5       BiocGenerics_0.8.0
> >
> > loaded via a namespace (and not attached):
> > [1] Biobase_2.21.7 bitops_1.0-6   grid_3.0.2     hwriter_1.3    stats4_3.0.2
> tools_3.0.2
> > [7] zlibbioc_1.7.0
> >
> >
> > Sean Taylor
> > Post-doctoral Fellow
> > Fred Hutchinson Cancer Research Center
> > 206-667-5544
> >
> >
> > 	[[alternative HTML version deleted]]
> >
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> >
> 
> 
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