rsync error: : some files/attrs were not transferred (see previous errors) (code 23) at main.c(1505) [receiver=3.0.6]

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Ho, Eric

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Jul 11, 2016, 12:36:52 PM7/11/16
to genome...@soe.ucsc.edu

I encountered errors this morning when I wanted to fetch eboVir3 and hg19. But I was able to fetch hg18, meaning that it wasn't due to setup issue. Here's the hg18 files:
-rw-rw-r-- 1 ericho ericho 11867827 Jun 21 15:08 trackDb.ix
-rw-rw-r-- 1 ericho ericho 2224 Jun 21 15:08 trackDb.ixx
drwxrwxr-x 2 ericho ericho 4096 Oct 9 2015 html
drwxrwxr-x 2 ericho ericho 4096 Dec 30 2007 nib
-rw-rw-r-- 1 ericho ericho 807604784 Dec 20 2005 hg18.2bit


I fetched them via the kent script:

./fetchMinimalGbdb.sh browserEnvironment.txt eboVir3

My /gbdb/eboVir3 contained only these files (no nib):

-rw-rw-r-- 1 ericho ericho 286802 May 25 12:17 trackDb.ix
-rw-rw-r-- 1 ericho ericho 80 May 25 12:17 trackDb.ixx
drwxrwxr-x 2 ericho ericho 4096 Oct 9 2015 html
-rw-rw-r-- 1 ericho ericho 4787 Sep 18 2014 eboVir3.2bit

Any idea appreciated.

Eric.

PS.
Centos 6.8
Mysql 5.5
Apache 2.2
kentsrc is 1 day old.

Matthew Speir

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Jul 12, 2016, 2:55:00 PM7/12/16
to Ho, Eric, genome...@soe.ucsc.edu
Hi Eric,

Thank you for your question about syncing the directories for hg19 and
eboVir3.

Neither hg19 or eboVir3 are expected to have nib files/directories. Nib
files were previously used to store the genomic sequence for some
assemblies but have since been replaced by the 2bit format.

The errors that you were seeing were likely due to the fact that the
script was attempting to rsync the nib directories for these assemblies
when they didn't have one. One of our engineers has fixed up the script
so that you shouldn't see these errors anymore.

I hope this is helpful. If you have any further questions, please reply
to genome...@soe.ucsc.edu. All messages sent to that address are
archived on a publicly-accessible Google Groups forum. If your question
includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group
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