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<p>Dear Michael,</p>
<p>It looks like the ensembl-variation library can't find the <font
size="3" face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols" color="black"><span
id="gmail-divtagdefaultwrapper" style="font-size:12pt">Bio::DB::HTS::Faidx
module.</span></font></p>
<font size="3" face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols" color="black"><span
id="gmail-divtagdefaultwrapper" style="font-size:12pt"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols">Are <font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols">you sure that the </font></font></span></font><font
size="3" face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols" color="black"><span
id="gmail-divtagdefaultwrapper" style="font-size:12pt"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols"><span class="pl-s"><font size="3"
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols" color="black"><span
id="gmail-divtagdefaultwrapper" style="font-size:12pt">${INSTALL_DIR}/</span></font><b>biodbhts</b><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"> dire<font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">ctory i<font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">s in your PERL5LI<font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">B variable ?</font></font></font></font></span></font></font></span></font>
<p><font size="3"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols">Do you <font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols">have an other insta<font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">lla<font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">tion o<font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">f BioPerl on your
machine ?</font></font></font></font></font></font></p>
<p><font size="3"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols">Best regards,</font></font></font></font></font></font></font><br>
</p>
<font size="3" face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols" color="black"><span
id="gmail-divtagdefaultwrapper" style="font-size:12pt"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols"><font
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols"><span class="pl-s"><span class="pl-pds"></span></span></font></font></span></font>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 17/02/2018 00:07, Michael Yourshaw
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANcs_JJG7MkymQb6eB-9r8yrJ9cr99_jkbwGqDETbZdLCe768A@mail.gmail.com">
<div dir="ltr">My apologies if this is a duplicate. My other email
program seems not to have liked the "<a
href="mailto:dev@ensembl.org" moz-do-not-send="true">dev@ensembl.org</a>"
address.
<div><br>
</div>
<div>
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UI","Segoe
WP",Tahoma,Arial,sans-serif;font-size:medium">
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<div class="gmail-_rp_o5" tabindex="-1"
style="min-width:350px;clear:both">
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<div>
<div id="gmail-divtagdefaultwrapper"><font
size="3"
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
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<div
style="margin-top:0px;margin-bottom:0px">I
need to run the VEP perl
script offline but dairly
full-featured.</div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px">I
downloaded and installed the current
(91) VEP with `perl INSTALL.pl
--DESTDIR ${INSTALL_DIR} --CACHEDIR
${INSTALL_DIR} --PLUGINS all;`</div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px">No
errors were reported,, and in
particular installing Bio::DB::HTS
and htslib seemed to go well.</div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px">PERL5LIB
includes the DESTDIR for VEP and
PATH includes the htslib directory.</div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
<font size="2"
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI
Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><span
style="font-size:16px">Bio::DB::HTS::Faidx.pm
exists under the Bio directory
that the VEP installer created
in the </span></font><font
size="2"
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI
Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><span
style="font-size:16px">DESTDIR</span></font><font
size="2"
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI
Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><span
style="font-size:16px">.</span></font></div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px">--fasta
is set to
.../homo_sapiens/91_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.
The .fai and .gzi files are also
present.</div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px">Nonetheless,
when I run the VEP, I get the error
"<font size="1" face="Courier
New,monospace"><span
style="font-size:12px">Cannot
index bgzipped FASTA file with
Bio::DB::Fasta</span></font>".</div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px">It
appears that <font size="1"
face="Courier New,monospace"><span
style="font-size:12px">Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta </span></font>is
failing the test `eval { require
Bio::DB::HTS::Faidx; 1 }` and
therefore
not setting $CAN_USE_FAIDX. </div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px"><font
size="3"><span
style="font-size:12pt">The
command and error are below.</span></font><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px"><font
size="3"><span
style="font-size:12pt"><br>
</span></font></div>
<div
style="margin-top:0px;margin-bottom:0px"><font
size="2"
face="Calibri,Helvetica,sans-serif,EmojiFont,Apple
Color Emoji,Segoe UI
Emoji,NotoColorEmoji,Segoe UI
Symbol,Android Emoji,EmojiSymbols"><span
style="font-size:16px">Thanks
for your help.</span></font><font
size="3"><span
style="font-size:12pt"><br>
</span></font></div>
<div
style="margin-top:0px;margin-bottom:0px"><br>
</div>
<div
style="margin-top:0px;margin-bottom:0px"> </div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
/usr/local/bin/perl \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/vep
\</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">> -i
/gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/ff81a90d-ea94-4f33-9405-98575fd8e0af/call-VariantEffectPredictor/inputs/gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/ff81a90d-ea94-4f33-9405-98575fd8e0af/call-MakeSitesOnlyVcf/execution/AI-HEP7.lValExome0019.downsampled.recalibrated.filtered.postCGP.GQfiltered.sites.vcf
\</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--offline \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--cache \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--fasta
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/homo_sapiens/91_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
\</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--merged \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">> --dir
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91 \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--output_file
AI-HEP7.lValExome0019.downsampled.json
\</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--force_overwrite \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--json \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">>
--everything \</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">> -v</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">2018-02-16
16:03:21 - INFO: BAM-edited
cache detected, enabling
--use_transcript_ref; use
--use_given_ref to override this</span></font></div>
<div><br>
</div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">--------------------
EXCEPTION --------------------</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">MSG:
ERROR: Cannot index bgzipped
FASTA file with Bio::DB::Fasta</span></font></div>
<div><br>
</div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">STACK
Bio::EnsEMBL::Variation::Utils::FastaSequence::setup_fasta
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm:210</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">STACK
Bio::EnsEMBL::VEP::BaseVEP::fasta_db
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:477</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">STACK
Bio::EnsEMBL::VEP::Runner::init
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:129</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">STACK
Bio::EnsEMBL::VEP::Runner::run
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">STACK
toplevel
/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/vep/vep-91/ensembl-vep/vep:222</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">Date
(localtime) = Fri Feb 16
16:03:22 2018</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">Ensembl
API version = 91</span></font></div>
<div><font size="2" face="Courier
New,monospace"><span
style="font-size:9pt">---------------------------------------------------</span></font></div>
<div><br>
</div>
<br>
<div
style="margin-top:0px;margin-bottom:0px"> </div>
<div
style="margin-top:0px;margin-bottom:0px"> </div>
<div style="margin:0px"><font size="2"
face="Calibri,sans-serif"
color="#212121"><span
style="font-size:11pt">Michael
Yourshaw, JD, PhD</span></font></div>
<div style="margin:0px"><font size="2"
face="Calibri,sans-serif"
color="#212121"><span
style="font-size:11pt">Bioinformatician</span></font></div>
<div style="margin:0px"><font size="2"
face="Calibri,sans-serif"
color="#212121"><span
style="font-size:11pt">Colorado
Center for Personalized Medicine</span></font></div>
<div style="margin:0px"><font size="2"
face="Calibri,sans-serif"
color="#212121"><span
style="font-size:11pt">Colorado
Molecular Correlates</span></font></div>
<div style="margin:0px"><font size="2"
face="Calibri,sans-serif"
color="#212121"><span
style="font-size:11pt"><a
href="mailto:michael.yourshaw@ucdenver.edu"
target="_blank" rel="noopener
noreferrer"
moz-do-not-send="true">michael.yourshaw@ucdenver.edu</a></span></font></div>
</span></font></div>
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<div>
<div>ॐ<br>
Michael Yourshaw<br>
<a href="mailto:myourshaw@ucla.edu" target="_blank"
moz-do-not-send="true">myourshaw@gmail.com</a><br>
<br>
This message is intended only for the use of the
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ATTORNEY WORK PRODUCT. If you are not the intended
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