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Hi Johanne,<br>
I have also been having an intermittent problem where the code dies
while executing exactly the same line as Anja had. <br>
In my case I am trying to get all the homologues for a given gene.<br>
Here is the stack trace:<br>
<br>
<meta http-equiv="content-type" content="text/html;
charset=windows-1252">
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</style>DBD::mysql::st execute failed: Lost connection to MySQL server
during query at
/home/john.samuel/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
line 482, <RE1_IN> line 205.<br>
<br>
-------------------- EXCEPTION --------------------<br>
MSG: Detected an error whilst executing SQL 'SELECT g.gene_id,
g.seq_region_id, g.seq_region_start, g.seq_region_end,
g.seq_region_strand, g.analysis_id, g.biotype, g.display_xref_id,
g.description, g.status, g.source, g.is_current,
g.canonical_transcript_id, g.stable_id, g.version,
UNIX_TIMESTAMP(g.created_date), UNIX_TIMESTAMP(g.modified_date),
x.display_label, x.dbprimary_acc, x.description, x.version,
exdb.db_name, exdb.status, exdb.db_release, exdb.db_display_name,
x.info_type, x.info_text <br>
FROM (( (gene g) <br>
LEFT JOIN xref x ON x.xref_id = g.display_xref_id ) <br>
LEFT JOIN external_db exdb ON exdb.external_db_id =
x.external_db_id ) <br>
WHERE g.stable_id = ? AND g.is_current = 1 <br>
': DBD::mysql::st execute failed: Lost connection to MySQL server
during query at
/home/john.samuel/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
line 482, <RE1_IN> line 205.<br>
<br>
STACK Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch
/home/john.samuel/src/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm:483<br>
STACK Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_by_stable_id
/home/john.samuel/src/ensembl/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm:249<br>
STACK Bio::EnsEMBL::Compara::GeneMember::get_Gene
/home/john.samuel/src/ensembl-compara/modules/Bio/EnsEMBL/Compara/GeneMember.pm:183<br>
STACK main::get_homologues slartibartfast.pl:488<br>
STACK toplevel slartibartfast.pl:348<br>
Date (localtime) = Mon May 9 17:05:48 2016<br>
Ensembl API version = 80<br>
---------------------------------------------------<br>
<br>
Any ideas about the cause of this problem, and a possible fix? I
haven't had problems like this before, even with other programs with
run times of many hours, only when trying to get homologues.<br>
My program does run for a long time too (> 2 hours) before this
occurs, and some of the genes (zebrafish) have a lot of homologues.<br>
<br>
Regards,<br>
John<br>
<br>
<br>
<div class="moz-cite-prefix">On 16-05-24 07:48 AM, Anja Thormann
wrote:<br>
</div>
<blockquote
cite="mid:400023A0-5B0F-4310-926A-4F5B2AE8B64D@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div>Hello Johanne,<br class="">
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div class="">
</div>
<div class="">The only exception I get now from time to
time, is:</div>
<div class="">DBD::mysql::st execute failed: Lost
connection to MySQL server during query at
/Users/Johanne/src/ensembl/modules//Bio/EnsEMBL/DBSQL/BaseAdaptor.pm
line 482. </div>
<div class=""><br class="">
</div>
<div class="">Is it caused by something concerning my
local MySQL installation or Internet connection?</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>This is probably related to a long run time of the script.
I will look into this.</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div class="">As our thread contained two conversations, I
wonder if you got the same results on the LD variant
expansion script as I did with the two reference
genomes?</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
I still need to run the comparison. But a difference of 13
variants in the results doesn’t seem to be a problem to me. You
are using an updated assembly with hg38 which has consequences
on the set of variants you are looking at. The blog post (<a
moz-do-not-send="true"
href="http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html"
class=""><a class="moz-txt-link-freetext" href="http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html">http://genomeref.blogspot.co.uk/2013/12/announcing-grch38.html</a></a>)
explains this in more detail in the section 'General assembly
updates'. </div>
<div>
<div><br class="">
</div>
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div class="">
</div>
<div class="">And does your database contain all
information from dbSNP + 1000G? I have set the script to
use both database and VCF data
($variation_adaptor->db->use_vcf(1);), but did not
find info on where exactly the data in the database
comes from.</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
We store all 1000G variants in our database. The variants are
imported from dbSNP. The genotypes for 1000G variants are stored
in VCF files. To use the genotypes from VCF files you need to
set use_vcf to 1.<br class="">
<div><br class="">
</div>
<div><br class="">
</div>
<div>Best,</div>
<div>Anja</div>
<div><br class="">
</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div class="">
</div>
<div class="">Best,</div>
<div class="">Johanne</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">23. mai 2016 kl. 16.45 skrev Will
McLaren <<a moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" class="">wm2@ebi.ac.uk</a>>:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello,
<div class=""><br class="">
</div>
<div class="">The files there are symbolic links
to another directory - it's possible your FTP
client is not following these links.</div>
<div class=""><br class="">
</div>
<div class="">The "real" files are here:</div>
<div class=""><br class="">
</div>
<div class=""><a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/"
class="">ftp://ftp.ensembl.org/pub/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/</a><br
class="">
</div>
<div class=""><br class="">
</div>
<div class="">Try downloading from that path
instead.</div>
<div class=""><br class="">
</div>
<div class="">Regards</div>
<div class=""><br class="">
</div>
<div class="">Will</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 23 May 2016 at
15:31, Johanne Håøy Horn <span dir="ltr"
class="">
<<a moz-do-not-send="true"
href="mailto:johannhh@ifi.uio.no"
target="_blank" class="">johannhh@ifi.uio.no</a>></span>
wrote:<br class="">
<blockquote class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px
#ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi,
<div class=""><br class="">
</div>
<div class="">I got the same error message
with the full path.
<div class="">
<div class=""><br class="">
</div>
<div class="">I think the problem is
with the hg38 .gz and .gz.tbi files.
I went back to the URL you gave me:
<a moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/"
target="_blank" class="">ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/</a></div>
<div class="">But when I click any of
the files, I get the error message
"The operation can’t be completed
because the original item for
<file name> can’t be found».
This is not a problem for the hg19
ftp connection, whose files I can
open just fine.</div>
<div class="">I have restarted my
computer (Max OS X 10.11.5) and
remounted the connection several
times. I log on using guest.</div>
<div class=""><br class="">
</div>
<div class="">So the files I
downloaded were not existing after
all, and the error message were
correct.</div>
<div class=""><br class="">
</div>
<div class="">Do you have any
suggestions as to how I can mount it
correctly?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Johanne</div>
<div class="">
<div class="h5">
<div class=""><br class="">
<div class="">
<blockquote type="cite"
class="">
<div class="">23. mai 2016
kl. 15.31 skrev Will
McLaren <<a
moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk"
target="_blank" class=""><a class="moz-txt-link-abbreviated" href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a></a>>:</div>
<br class="">
<div class="">
<div dir="ltr" class="">I
think possibly Perl
doesn't like using "~"
to represent your home
directory - try
replacing it with the
full path, or possibly
$ENV{HOME}
<div class=""><br
class="">
</div>
<div class="">Will</div>
</div>
<div class="gmail_extra"><br
class="">
<div class="gmail_quote">On
23 May 2016 at 13:59,
Johanne Håøy Horn <span
dir="ltr" class="">
<<a
moz-do-not-send="true"
href="mailto:johannhh@ifi.uio.no" target="_blank" class=""><a class="moz-txt-link-abbreviated" href="mailto:johannhh@ifi.uio.no">johannhh@ifi.uio.no</a></a>></span>
wrote:<br class="">
<blockquote
class="gmail_quote"
style="margin:0 0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
style="word-wrap:break-word"
class="">Thank you
for your wonderful
support!
<div class=""><br
class="">
</div>
<div class="">I
tried now with
the following
JSON struct:
<div class=""><span
class="">
<div class="">{</div>
<div class="">
"id":
"1000genomes_phase3",</div>
<div class="">
"species":
"homo_sapiens",</div>
<div class="">
"assembly":
"GRCh38",</div>
<div class="">
"type":
"local",</div>
<div class="">
"strict_name_match":
1,</div>
</span>
<div class="">
"filename_template":
"~/src/ensembl-vcf/ALL.chr###CHR###.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz",</div>
<span class="">
<div class="">
"chromosomes":
[</div>
<div class="">
"1",
"2", "3", "4",
"5", "6", "7",
"8", "9",
"10", "11",
"12", "13",
"14",</div>
<div class="">
"15",
"16", "17",
"18", "19",
"20", "21",
"22", "X", "Y"</div>
<div class="">
],</div>
<div class="">
"sample_prefix":
"1000GENOMES:phase_3:"</div>
<div class="">
},</div>
</span></div>
<div class=""><br
class="">
</div>
<div class="">I
got this error
message:</div>
<div class="">MSG:
ERROR: VCF
file
~/src/ensembl-vcf/ALL.chr1.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz
not found</div>
<div class=""><br
class="">
</div>
<div class="">Should
the tbi files
be where I
call the
script? Or is
it something
else I am
doing wrong?</div>
<div class=""><br
class="">
</div>
<div class="">Best,</div>
<div class="">Johanne</div>
<div class="">
<div class="">
<div class=""><br
class="">
<div class="">
<blockquote
type="cite"
class="">
<div class="">23.
mai 2016 kl.
14.04 skrev
Will McLaren
<<a
moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank" class=""><a class="moz-txt-link-abbreviated" href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a></a>>:</div>
<br class="">
<div class="">
<div dir="ltr"
class="">Hi
Johanne,
<div class=""><br
class="">
</div>
<div class="">You
need the
filename part
of the
template too,
so:</div>
<div class=""><br
class="">
</div>
<div class=""><span
style="font-size:12.8px" class=""> "filename_template":
"~/src/ensembl-vcf/ALL.chr###CHR###.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz",</span></div>
<div class=""><span
style="font-size:12.8px" class=""><br class="">
</span></div>
<div class=""><span
style="font-size:12.8px" class="">Regards</span></div>
<div class=""><span
style="font-size:12.8px" class=""><br class="">
</span></div>
<div class=""><span
style="font-size:12.8px" class="">Will</span></div>
</div>
<div
class="gmail_extra"><br
class="">
<div
class="gmail_quote">On
23 May 2016 at
12:57, Johanne
Håøy Horn <span
dir="ltr"
class="">
<<a
moz-do-not-send="true"
href="mailto:johannhh@ifi.uio.no" target="_blank" class=""><a class="moz-txt-link-abbreviated" href="mailto:johannhh@ifi.uio.no">johannhh@ifi.uio.no</a></a>></span>
wrote:<br
class="">
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
style="word-wrap:break-word"
class="">Hello
again!
<div class=""><br
class="">
</div>
<div class="">I
tried set the
following in
the JSON file:</div>
<div class=""><br
class="">
</div>
<div class="">
<div class=""> {</div>
<div class="">
"id":
"1000genomes_phase3",</div>
<div class="">
"species":
"homo_sapiens",</div>
<div class="">
"assembly":
"GRCh38",</div>
<div class="">
"type":
"local",</div>
<div class="">
"strict_name_match":
1,</div>
<div class="">
"filename_template":
"~/src/ensembl-vcf/",</div>
<div class="">
"chromosomes":
[</div>
<div class="">
"1",
"2", "3", "4",
"5", "6", "7",
"8", "9",
"10", "11",
"12", "13",
"14",</div>
<div class="">
"15",
"16", "17",
"18", "19",
"20", "21",
"22", "X", "Y"</div>
<div class="">
],</div>
<div class="">
"sample_prefix":
"1000GENOMES:phase_3:"</div>
<div class="">
},</div>
<div class=""><br
class="">
</div>
<div class="">But
I get this
error message:</div>
<div class="">MSG:
ERROR: VCF
file
~/src/ensembl-vcf/
not found</div>
<div class=""><br
class="">
</div>
<div class="">I
downloaded all
the hg38 files
you linked to
in the
folder ~/src/ensembl-vcf/.
When you say
that I need to
change
filename_template
to the path
where the
files were
downloaded, is
it the full
path of all
the 48 files
rather than
the path to
the folder
they are in?</div>
<div class=""><br
class="">
</div>
<div class="">Best,</div>
<div class="">Johanne</div>
<div class=""><br
class="">
</div>
<div class="">
<blockquote
type="cite"
class=""><span
class="">
<div class="">23.
mai 2016 kl.
11.57 skrev
Will McLaren
<<a
moz-do-not-send="true"
href="mailto:wm2@ebi.ac.uk" target="_blank" class=""><a class="moz-txt-link-abbreviated" href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a></a>>:</div>
<br class="">
</span>
<div class="">
<div class="">
<div class="">
<div dir="ltr"
class="">Hi
Johanne,
<div class=""><br
class="">
</div>
<div class="">It
looks like the
API is
intermittently
losing
connection to
the remote VCF
files hosted
on our FTP
site.</div>
<div class=""><br
class="">
</div>
<div class="">You
can bypass
this
connection by
downloading
the files to
your local
machine:</div>
<div class=""><br
class="">
</div>
<div class="">GRCh38:
<a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/"
target="_blank"
class="">
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/">ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/</a></a><br
class="">
</div>
<div class="">GRCh37:
<a
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/"
target="_blank" class="">
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/">ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/</a></a><br
class="">
</div>
<div class=""><br
class="">
</div>
<div class="">You
will then need
to edit
[module_path]/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json,
changing the
"filename_template"
entry to the
path where you
downloaded the
files, and
"type" from
"remote" to
"local".</div>
<div class=""><br
class="">
</div>
<div class="">Regarding
the warning
message, this
should not
affect your
analyses in
any way, but I
have put in a
fix on
release/84 of
ensembl-variation
to suppress
it.</div>
<div class=""><br
class="">
</div>
<div class="">Regards</div>
<div class=""><br
class="">
</div>
<div class="">Will
McLaren</div>
<div class="">Ensembl
Variation</div>
</div>
<div
class="gmail_extra"><br
class="">
<div
class="gmail_quote">On
21 May 2016 at
12:57, Johanne
Håøy Horn <span
dir="ltr"
class="">
<<a
moz-do-not-send="true"
href="mailto:johannhh@ifi.uio.no" target="_blank" class=""><a class="moz-txt-link-abbreviated" href="mailto:johannhh@ifi.uio.no">johannhh@ifi.uio.no</a></a>></span>
wrote:<br
class="">
<blockquote
class="gmail_quote"
style="margin:0
0 0
.8ex;border-left:1px
#ccc
solid;padding-left:1ex">
<div
style="word-wrap:break-word"
class="">Dear
ensembl dev
team,
<div class=""><br
class="">
</div>
<div class="">I
have been
using your
variation API
for some time
now, and get a
range of
errors from
time to time,
without
knowing
exactly why.
It is not
because of the
scripts, I
think, as the
same script
producing the
error can work
just fine if I
run it again.</div>
<div class=""><br
class="">
</div>
<div class="">The
different
error messages
are:</div>
<div class="">
<div class=""><font
class=""
face="Courier
New">/Parser/BaseVCF4.pm
line 891,
<IN>
line 5.</font></div>
<div class=""><font
class=""
face="Courier
New">Use of
uninitialized
value in list
assignment at
/Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm
line 891,
<IN>
line 5.</font></div>
<div class=""><span style="white-space:pre-wrap" class=""></span></div>
<div class=""><font
class=""
face="Courier
New">connect:
Operation
timed out</font></div>
<div class=""><font
class=""
face="Courier
New">[kftp_connect_file]
350 Restarting
at 654385206.
Send STORE or
RETRIEVE to
initiate
transfer</font></div>
<div class=""><font
class=""
face="Courier
New"> </font></div>
<div class=""><font
class=""
face="Courier
New">[kftp_connect_file]
227 Entering
Passive Mode
(193,62,203,85,220,250).</font></div>
<div class=""><font
class=""
face="Courier
New">Tabix::tabix_query:
t is not of
type
tabix_tPtr at
/Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm
line 70.</font></div>
<div class=""><font
class=""
face="Courier
New"> </font></div>
<div class=""><font
class=""
face="Courier
New">[kftp_connect_file]
227 Entering
Passive Mode
(193,62,203,85,157,134).</font></div>
<div class=""><font
class=""
face="Courier
New">[main]
fail to open
the data file.</font></div>
<div class=""><font
class=""
face="Courier
New">Can't use
an undefined
value as an
ARRAY
reference at
/Users/Johanne/src/ensembl-io/modules/Bio/EnsEMBL/IO/Parser/BaseVCF4.pm
line 730.</font></div>
</div>
<div class=""><br
class="">
</div>
<div class="">Usually
just one of
these error
occur at a
time. I
suspect it
might have
something to
do with the
connection
between my
computer and
the ensembl
database, as
the first
error at least
always show up
in repeats
when I lose my
Internet
connection.
However, are
all of them
caused by
Internet
trouble? I
have checked
that the MySQL
instance is up
and running,
and can visit
web pages
through a
browser when
some of the
errors occur.
Could it be
something on
the
server/database
side?</div>
<div class=""><br
class="">
</div>
<div class="">Also,
if I use the
GRCh37
database:</div>
<div class=""><br
class="">
</div>
<div class="">
<div class=""><font
class=""
face="Courier
New">$registry->load_registry_from_db(</font></div>
<div class=""><font
class=""
face="Courier
New"> -host
=> '<a
moz-do-not-send="true"
href="http://ensembldb.ensembl.org/" target="_blank" class="">ensembldb.ensembl.org</a>',</font></div>
<div class=""><font
class=""
face="Courier
New"> -user
=>
'anonymous',</font></div>
<div class=""><font
class=""
face="Courier
New"> -port
=> 3337,</font></div>
<div class=""><font
class=""
face="Courier
New">);</font></div>
</div>
<div class=""><font
class=""
face="Courier
New"><br
class="">
</font></div>
<div class="">I
get this
warning/printout:</div>
<div class=""><font
class=""
face="Courier
New">Use of
uninitialized
value
$nums{"."} in
numeric
comparison
(<=>) at
/Users/Johanne/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VCFCollection.pm
line 770,
<IN>
line 6.</font></div>
<div class=""><font
class=""
face="Courier
New"><br
class="">
</font></div>
<div class="">I
use version 84
of the Ensembl
API, OS X
10.11.5, and
the script I
use when all
of these
errors occur,
is attached.
Note that the
attached
script by
default uses
hg38, but will
produce the
last printout
mentioned when
switching to
hg37.</div>
<div class=""><br
class="">
</div>
<div class="">And
something
different I
have been
wondering
about:</div>
<div class="">The
VCF files that
are downloaded
locally
(ALL.chr1.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi,
for instance)
- should they
be deleted and
re-downloaded
from time to
time to get
the latest
1000G data?
And where
exactly are
the VCFs
downloaded
from? Is it
dbSNP, as
indicated in
the file name?</div>
<div class=""><br
class="">
</div>
<div class="">Best,</div>
<div class="">Johanne
Håøy Horn</div>
</div>
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<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
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