Permission denied errors during rsync

[Mike Rightmire]

Hey,

So I'm using a manual rsync to download the /gbdb and /mysql files from the european server.

I'm noting in the output from rsync a lot of permission denied errors...
   
+ rsync --progress -avzp hgdownload-euro.soe.ucsc.edu::mysql/mm10/ /var/lib/mysql//mm10/
    receiving incremental file list
    ./
    rsync: send_files failed to open "/mm10/all_mrna.MYD" (in mysql): Permission denied (13)
    (snip)
    rsync: send_files failed to open "/mm10/xenoRefSeqAli.MYI" (in mysql): Permission denied (13)

    sent 1,065,941 bytes  received 88,990 bytes  18,478.90 bytes/sec
    total size is 202,551,408,665  speedup is 175,379.66
    rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1655) [generator=3.1.1]
    + rsync --progress -avp hgdownload-euro.soe.ucsc.edu::gbdb/mm10/ /gbdb-data1//mm10/
    receiving incremental file list

It doesn't SEEmM to be on my end (I can't find these files on my server). Is this an issue on the server side?

Thanks!
Mike

--

Universitäts Klinikum Heidelberg - University Hospital Heidelberg

Section of Bioinformatics and Systems Cardiology
Analysezentrum III - Klaus Tschira Institute

Mike Rightmire 

Bioinformatics and IT

Im Neuenheimer Feld 669

69120 Heidelberg

Tel.: +49 6221 56 - 34213

Fax.: +49 6221 56 - 6868

Cell: +49 176 7131 8758

Michael....@uni-heidelberg.de


http://www.klinikum.uni-heidelberg.de

[Christopher Lee]

Hello Mike,

Thanks for the note about hgdownload-euro, there was indeed an error
on our end, which should be resolved now. Can you please try again and
let us know if everything is working?

Please let us know if you have any further questions!

Thanks,

Christopher Lee
UCSC Genomics Institute

Want to share the Browser with colleagues?
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> Universitäts Klinikum Heidelberg - University Hospital Heidelberg
> Section of Bioinformatics and Systems Cardiology
> Analysezentrum III - Klaus Tschira Institute
>
> Mike Rightmire
> Bioinformatics and IT
> Im Neuenheimer Feld 669
> 
69120 Heidelberg
> 
Tel.: +49 6221 56 - 34213
> Fax.: +49 6221 56 - 6868
> 
Cell: +49 176 7131 8758
> Michael....@uni-heidelberg.de
> 
http://www.klinikum.uni-heidelberg.de
>

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[Mike Rightmire]

Hi Christopher,

No worries. I have it running now. I'll check the logs when I get back to work tomorrow.

BTW, I don't know if it's related - but the files from the rsync for MySQL used to come in with ownership mysql:mysql. Now they are coming in with a numeric user:group (9xx:9xx ... I can't remember exactly right now :D )

This breaks up unless we do a chown -R on them when theyre done downloading.

Could this be the same issue?

Best!
Mike

Christopher Lee

21 February 2018 at 18:34

Hello Mike,

Thanks for the note about hgdownload-euro, there was indeed an error
on our end, which should be resolved now. Can you please try again and
let us know if everything is working?

Please let us know if you have any further questions!

Thanks,

Christopher Lee
UCSC Genomics Institute

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

On Wed, Feb 21, 2018 at 6:01 AM, Mike Rightmire

Mike Rightmire

21 February 2018 at 15:01

Hey,

So I'm using a manual rsync to download the /gbdb and /mysql files from the european server.

I'm noting in the output from rsync a lot of permission denied errors...
   
+ rsync --progress -avzp hgdownload-euro.soe.ucsc.edu::mysql/mm10/ /var/lib/mysql//mm10/
    receiving incremental file list
    ./
    rsync: send_files failed to open "/mm10/all_mrna.MYD" (in mysql): Permission denied (13)
    (snip)
    rsync: send_files failed to open "/mm10/xenoRefSeqAli.MYI" (in mysql): Permission denied (13)

    sent 1,065,941 bytes  received 88,990 bytes  18,478.90 bytes/sec
    total size is 202,551,408,665  speedup is 175,379.66
    rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1655) [generator=3.1.1]
    + rsync --progress -avp hgdownload-euro.soe.ucsc.edu::gbdb/mm10/ /gbdb-data1//mm10/
    receiving incremental file list

It doesn't SEEmM to be on my end (I can't find these files on my server). Is this an issue on the server side?

Thanks!
Mike

--

[Christopher Lee]

Hi Mike,

The numeric owner:group is expected and you should perform the chown after the download as you are already doing.

Please let us know if you have any further questions!

Thanks,

Christopher Lee
UCSC Genomics Institute

--

Michael.Rightmire@uni-heidelberg.de


http://www.klinikum.uni-heidelberg.de