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Error Building GKNO due to tutorial retrieval failure #68

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mcnaircm opened this issue Jun 20, 2016 · 7 comments
Open

Error Building GKNO due to tutorial retrieval failure #68

mcnaircm opened this issue Jun 20, 2016 · 7 comments

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@mcnaircm
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I am currently having an issue in building gkno, and weirdly enough it seems to be with the retrieval of the tutorial after everything esle is done which terminates the process. The following is what I see when I try to run the build:
./gkno build [ 1:35PM]

University of Utah gkno package

version: 2.57.0
date: June 2016

git commit: de31cc5

Checking dependencies...done.
Initializing component data...done.
Building tools:
bamaddrg...done.
bamtools...done.
bedtools...done.
blast...done.
bwa...done.
freebayes...done.
htslib...done.
samtools...done.
pindel...done.
libStatGen...done.
bamUtil...done.
fastQValidator...done.
qplot...done.
verifyBamID...done.
mosaik...done.
mutatrix...done.
picard...done.
samblaster...done.
seqan...done.
snpEff...done.
tabix...done.
tangram...done.
vcflib...done.
vt...done.
wham...done.
Fetching default resources:
tutorial:
Downloading files... 0%ERROR: Could not retrieve file at http://marth-award.genetics.utah.edu:8089/version_10.tar.gz
ERROR: See logs/build_tutorial.* files for more details.

TERMINATED: Errors found in running gkno. See specific error messages above for resolution.

I'm not really sure why not having the tutorial file would terminate the whole process, but there you have it. Any help in figuring out how to get around this issue would be much appreciated!

Cheers,
Chris

@AlistairNWard
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Hi Chris,

I'm unsure why downloading the tutorial data would have failed. Can you
access the data by just trying a wget (e.g. wget
http://marth-award.genetics.utah.edu:8089/version_10.tar.gz)? If you can,
maybe there was an odd error when you tried the build and you can just try
and rebuild gkno. Either way, you're right that failure to get the
resources shouldn't stop you being able to run gkno since everything else
is actually available (although none of the 'test' parameter sets in the
pipelines would work). I have updated the code, to ensure that the final
configuration file is still created on failure to download resources
ensuring that gkno will still run. Please try recloning and build again and
even if the resource download fails, gkno should still be executable.

Please let me know if this doesn't work, or if you have any
questions/comments about using gkno.

Al

Alistair Ward, PhD
Director, Research and Science
Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine​
15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Mon, Jun 20, 2016 at 2:00 PM, mcnaircm [email protected] wrote:

I am currently having an issue in building gkno, and weirdly enough it
seems to be with the retrieval of the tutorial after everything esle is
done which terminates the process. The following is what I see when I try
to run the build:
./gkno build [ 1:35PM]

University of Utah gkno package

version: 2.57.0
date: June 2016
git commit: de31cc5
de31cc5

Checking dependencies...done.
Initializing component data...done.
Building tools:
bamaddrg...done.
bamtools...done.
bedtools...done.
blast...done.
bwa...done.
freebayes...done.
htslib...done.
samtools...done.
pindel...done.
libStatGen...done.
bamUtil...done.
fastQValidator...done.
qplot...done.
verifyBamID...done.
mosaik...done.
mutatrix...done.
picard...done.
samblaster...done.
seqan...done.
snpEff...done.
tabix...done.
tangram...done.
vcflib...done.
vt...done.
wham...done.
Fetching default resources:
tutorial:
Downloading files... 0%ERROR: Could not retrieve file at
http://marth-award.genetics.utah.edu:8089/version_10.tar.gz
ERROR: See logs/build_tutorial.* files for more details.
TERMINATED: Errors found in running gkno. See specific error messages
above for resolution.

I'm not really sure why not having the tutorial file would terminate the
whole process, but there you have it. Any help in figuring out how to get
around this issue would be much appreciated!

Cheers,
Chris


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@mcnaircm
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Hey Alistair,
I probably should have said in the initial post but I did in fact attempt to do this when I had the issue initially and I keep getting a connection time out error when I try to wget the tutorial directly. I re-cloned gkno and although the tutorial still didn't download it seems that gkno will run now! Thanks!

@AlistairNWard
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That's strange. Do you have any odd firewalls or anything? I've tried doing
a build and getting the resources myself a couple of times to check and
have no problems getting the resources to download.

Can you add other resources, e.g. ./gkno add-resource grch37?

Alistair Ward, PhD
Director, Research and Science
Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine​
15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330

Co-founder, Frameshift labs, LLC

On Wed, Jun 22, 2016 at 12:07 PM, mcnaircm [email protected] wrote:

Hey Alistair,
I probably should have said in the initial post but I did in fact attempt
to do this when I had the issue initially and I keep getting a connection
time out error when I try to wget the tutorial directly. I re-cloned gkno
and although the tutorial still didn't download it seems that gkno will run
now! Thanks!


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@hideoimamura
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hideoimamura commented Nov 25, 2016

Hi Alistair, I have the same problem. I am repeated this installation a few times but I got to the same point.
And because the installation stops there, I cannot install the entire packet. Can I skip this downloading?
thank you,
Hideo
mac-C02N1289FH05:gkno_launcher himamura$ ./gkno build

University of Utah gkno package

version: 2.63.7
date: November 2016
git commit: 0274e25

Checking dependencies...done.
Initializing component data...
done.
Building tools:
bamaddrg...done.
bamtools...done.
bedtools...done.
blast...done.
bwa...done.
freebayes...done.
htslib...done.
samtools...done.
pindel...ERROR: See logs/build_pindel.* files for more details.
libStatGen...done.
bamUtil...done.
fastQValidator...done.
qplot...done.
verifyBamID...done.
mosaik...ERROR: See logs/build_mosaik.* files for more details.
mutatrix...ERROR: See logs/build_mutatrix.* files for more details.
picard...done.
samblaster...done.
seqan...done.
snpEff...done.
tabix...done.
tangram...done.
vcflib...done.
vt...done.
wham...ERROR: See logs/build_wham.* files for more details.
Fetching default resources:
tutorial:
Downloading files... 0%

@AlistairNWard
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AlistairNWard commented Nov 25, 2016 via email

@hideoimamura
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Hi Alistair, thank you for a quick response.
When I type .
/gkno
ERROR: gkno not built.
Because
Downloading files... 0%
stops the building process every time I gkno build.
So gkno is not built successfully.
It always stops at
Downloading files... 0%
It does not go any further.
I worked at Boston college when Mike S was there and Gabor knows me as well. I can run most of the programs by myself and I am just testing how gkno works. So far I cannot test since it cannot be built.
Thank you.
Hideo

@AlistairNWard
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AlistairNWard commented Nov 25, 2016 via email

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