Hi,
> quickBamFlagSummary(eh[["EH8081"]])
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for
documentation
loading from cache
[E::hts_hopen] Failed to open file
/home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133
[E::hts_open_format] Failed to open file
"/home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133" : Exec format
error
Error in value[[3L]](cond) :
failed to open BamFile: failed to open SAM/BAM file
file: '/home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133'
> eh[["EH8081", force=TRUE]]
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for
documentation
downloading 2 resources
retrieving 2 resources
|======================================================================|
100%
|======================================================================|
100%
loading from cache
class: BamFile
path: /home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133
index: /home/biocbuild/.cache/R/ExperimentHub/1d1f2d19075fb4_8134
isOpen: FALSE
yieldSize: NA
obeyQname: FALSE
asMates: FALSE
qnamePrefixEnd: NA
qnameSuffixStart: NA
> quickBamFlagSummary(eh[["EH8081"]])
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for
documentation
loading from cache
[E::idx_find_and_load] Could not retrieve index file for
'/home/biocbuild/.cache/R/ExperimentHub/1d1f2d19075fb4_8134'
group | nb of | nb of | mean / max
of | records | unique | records per
records | in group | QNAMEs | unique QNAME
All records........................ A | 215602 | 100000 | 2.16 / 20
o template has single segment.... S | 0 | 0 | NA / NA
o template has multiple segments. M | 215602 | 100000 | 2.16 / 20
- first segment.............. F | 107801 | 100000 | 1.08 / 10
- last segment............... L | 107801 | 100000 | 1.08 / 10
- other segment.............. O | 0 | 0 | NA / NA
Note that (S, M) is a partitioning of A, and (F, L, O) is a partitioning of
M.
Indentation reflects this.
Details for group M:
o record is mapped.............. M1 | 215602 | 100000 | 2.16 / 20
- primary alignment......... M2 | 200000 | 100000 | 2 / 2
- secondary alignment....... M3 | 15602 | 4085 | 3.82 / 18
o record is unmapped............ M4 | 0 | 0 | NA / NA
Details for group F:
o record is mapped.............. F1 | 107801 | 100000 | 1.08 / 10
- primary alignment......... F2 | 100000 | 100000 | 1 / 1
- secondary alignment....... F3 | 7801 | 4085 | 1.91 / 9
o record is unmapped............ F4 | 0 | 0 | NA / NA
Details for group L:
o record is mapped.............. L1 | 107801 | 100000 | 1.08 / 10
- primary alignment......... L2 | 100000 | 100000 | 1 / 1
- secondary alignment....... L3 | 7801 | 4085 | 1.91 / 9
o record is unmapped............ L4 | 0 | 0 | NA / NA
Looks good ?
Regards,
Martin
On Mon, Oct 23, 2023 at 7:26 PM Hervé Pagès <hpages.on.git...@gmail.com>
wrote:
> Hi Robert,
>
> There's the possibility that some of these BAM files got corrupted when
> downloaded to kunpeng2 local cache.
>
> @Martin Gregorov: Would you be able to try to run the following on
> kunpeng2?
>
> library(Rsamtools)
> library(ExperimentHub)
> eh <- ExperimentHub()
> quickBamFlagSummary(eh[["EH8081"]])
>
> If you get an error that the file cannot be opened, then maybe try to
> re-download it with:
>
> eh[["EH8081", force=TRUE]]
>
> Then try quickBamFlagSummary(eh[["EH8081"]]) again and hopefully it will
> work.
>
> Thanks,
>
> H.
>
> On 10/23/23 08:03, Robert Castelo wrote:
> > hi,
> >
> > our package atena fails to build **only** in kunpeng2 Linux openEuler
> > 22.03 LTS-SP1 / aarch64:
> >
> >
> https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx/kunpeng2-buildsrc.html
> >
> >
> > concretely, the vignette fails to find a BAM file downloaded via
> > ExperimentHub. This does not happen in any of the other platforms.
> > Should we do anything about this?
> >
> > Thanks!
> >
> > robert.
> >
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.git...@gmail.com
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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