Error in CreateSnap

[yasserIRCM]

Hi there

I have an error message that looks like this after running the very first command on your analysis pipeline

Epoch: reading the barcode session ...
[1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap"
[1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap"
Error in data.frame(barcode, TN, UM, PP, UQ, CM) :
arguments imply differing number of rows: 0, 6641
In addition: Warning messages:
1: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
2: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
3: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
4: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
5: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
6: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
7: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :

Show Traceback

Rerun with Debug
Error in data.frame(barcode, TN, UM, PP, UQ, CM) :
arguments imply differing number of rows: 0, 6641

on the other, we have updated the rhdf5 package to 2.29.2
and
Rhdf5lib to 1.7.4

and we are still getting the same error.
also, we tried to troubleshoot by using your snap files but we can't download them (we can see them but not download them).

please let us know how we can fix this.

regards

[r3fang]

can you reinstall “rhdf5” package and its dependencies. It seems that the installation of this package failed

…

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Aug 28, 2019, at 2:45 PM, yasserIRCM ***@***.***> wrote: Hi there I have an error message that looks like this after running the very first command on your analysis pipeline Epoch: reading the barcode session ... [1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap" [1] "Warning @readSnap: 'BD/name' not found in possorted_bamko.snap" Error in data.frame(barcode, TN, UM, PP, UQ, CM) : arguments imply differing number of rows: 0, 6641 In addition: Warning messages: 1: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 2: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 3: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 4: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 5: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 6: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 7: In h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : Show Traceback Rerun with Debug Error in data.frame(barcode, TN, UM, PP, UQ, CM) : arguments imply differing number of rows: 0, 6641 on the other, we have updated the rhdf5 package to 2.29.2 and Rhdf5lib to 1.7.4 and we are still getting the same error. also, we tried to troubleshoot by using your snap files but we can't download them (we can see them but not download them). please let us know how we can fix this. regards — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#78?email_source=notifications&email_token=ABT6GG5EG7NGMHRDXKTIANLQG3WVZA5CNFSM4IRUQFWKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HIBJWVQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABT6GGYDNPMVWVTFGIVIGXTQG3WVZANCNFSM4IRUQFWA>.

[yasserIRCM]

ERRATUM

correction.
it didn't work with rhdf5 2.26.2
but it worked with rhdf5 2.28.0 (and Rhdf5lib 1.6.0).

PS: my installation didn't fail. that was what I suspected, I think it more of a issue with version

thanks a lot for your help