[Bioc-devel] Problem in asBam from Rsamtools

Dear Wei,
I think the problem was due to a file system issue. I check the raid and one of the disk failed, it could be that this created some problem to the I/O also because during the run of Rsubread there were many other I/O processes running.
I run again Rsubread  and I did not got any error
Thanks for the help
Raf

On 6/2/13 1:22 AM, Wei Shi wrote:

Dear Raf,

As Martin pointed, that line seems to be the concatenation of two records. But the second record is incomplete (it doesn't have the read identifier). It seems more likely to be a file system problem rather than Rsubread problem. Could you please also provide the line before the problematic line? You may also rerun the alignment on a different disk to see if you will see this problem again.

Hope this helps.


Best wishes,

Wei


On Jun 2, 2013, at 2:35 AM, Martin Morgan wrote:

On 06/01/2013 08:04 AM, rcaloger wrote:

Hi,
I am using the devel version of Bioconductor as part of the development of my
package chimera.
Testing a new function in chimera, that uses Rsubread package, I encountered a
problem in converting a sam file generated by Rsubread in a bam file.
I used the function asBam from Rsamtools and I got the following error:

In doTryCatch(return(expr), name, parentenv, handler) :
  Parse error at line 14667325: sequence and quality are inconsistent

I managed to run asBam if I use only the sam file till line 14667324
Instead I get the above error if I use a sam file finishing at line 14667325

The line that create the problem is the following:

HWI-ST169:273:D0YW6ACXX:2:1201:4070:162856    141    *    0    0 * *    0    0
AAAAAAGGGTTGAATTATTTTCACTTGCCCACGTAGTTTATGAATGTGGGAAATAGCTTCAAAGACAGATTAAATGATTTGCCCAAGGCCACAGAAAAGAG
@@@FFFFFHABHHJGGBFIGIFHGIJHGJGJIFBGHDBG9BDAFIIDHIIGCHCHI<GACC at ADHHHE;7?@DEFED>@;ACCC>ABB;AAD<BC>
77    *    0    0    *    *    0    0
CATGGATGAGGAGAATGAGGATTTTGCGCCGGCTGCTCAGAAGATACCGTGAATCTAAGAAGATCGATCGCCACATGTATCACAGCCTGTACCTGAAGGGG
@@@DD?BADHF<D<ACG>FFE;BBF at B?@C at F:(?1.=)))883)8=7@(65??EEBDEC37;;>???=BB@<BBCCACBDDCC:?BCBC:@#########

This looks like two separate records have been concatenated; it's really hard to know whether this is Rsubread or some aspect of the file system or the way the file has been handled after creation by Rsubread. Picard is one commonly used tool for validation. Martin

Does anybody has an idea of what is wrong in this line?
There is any way to validate the sam file before running asBam to detect and
filtered out lines that might create problems in the conversion into Bam?
Cheers
Raf

########
sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets methods
[8] base

other attached packages:
[1] Rsamtools_1.13.16     Biostrings_2.29.3 GenomicRanges_1.13.15
[4] XVector_0.1.0         IRanges_1.19.8        BiocGenerics_0.7.2

loaded via a namespace (and not attached):
[1] bitops_1.0-5   stats4_3.0.0   zlibbioc_1.7.0

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-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
MBC Centro di Biotecnologie Molecolari
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email: raffaele.calogero at unito.it
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