<div dir="ltr">Glad that seems to be working.<div><br></div><div>Do keep us posted if you encounter any more problems.</div><div><br></div><div>Cheers</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 12 July 2016 at 11:32, <span dir="ltr"><<a href="mailto:andrew126@mac.com" target="_blank">andrew126@mac.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Will,<div><br></div><div>I think I've solved it .. I didn't realize/notice, by default, VirtualBox puts VMs on a different network than the host .. putting the VM in bridged mode gets it on the same network as the host (and the rest of my network), and that seems to have resolved things (so far .. knock on wood). I'm surprised so much worked with the VM being on a different network (?), but I'm happy things are working at the moment.</div><div><br></div><div>Thanks for all the help.</div><div><br></div><div>Cheers,</div><div><br></div><div>Andrew</div><div><div class="h5"><div><br></div><div><br><div><blockquote type="cite"><div>On Jul 12, 2016, at 5:25 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><div><div dir="ltr">Try this path for the downloads:<div><br></div><div><a href="ftp://ftp.ensembl.org/pub/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/" target="_blank">ftp://ftp.ensembl.org/pub/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/</a><br></div><div><br></div><div>It works fine for me.</div><div><br></div><div>I'll have a look into your VM test, though this sounds like low level network stuff that I would have no idea how to debug!</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 12 July 2016 at 02:04, <span dir="ltr"><<a href="mailto:andrew126@mac.com" target="_blank">andrew126@mac.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div><font face="Courier">Hi Will,</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Here's some more that I've done.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">I was unable to download the VCFs locally based on the link you provided (<a href="ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/" target="_blank">ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/</a>), since those files are small (~170-byte), I assume they are links to other files, but I couldn't establish the location of the linked-to files.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">For example, it appears that variation_genotype/homo_sapiens/ALL.chr4.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi points to release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/ALL.chr4.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi</font></div><div><font face="Courier">... but <a href="http://ftp.ensembl.org/pub/release-82" target="_blank">ftp.ensembl.org/pub/release-82</a> is an empty directory (to my browser).</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">To standardize things as much as possible, I downloaded/installed Ensembl84VirtualMachine.ova. Note that it didn't have IPC-Run installed on it. I installed IPC-Run 0.79, updated the ensembl 84 git, and then ran the test code.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">On the first run after booting, the test code runs successfully for a short period of time before crashing.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Before crashing stderr reports these messages:</font></div><div><div><font face="Courier"><span style="white-space:pre-wrap"> </span>[get_local_version] downloading the index file...</font></div><div><font face="Courier"><span style="white-space:pre-wrap"> </span>[get_local_version] downloading the index file...</font></div></div><div><font face="Courier"><br></font></div><div><font face="Courier">which seem to refer to these files getting downloaded:</font></div><div><font face="Courier"><span style="white-space:pre-wrap"> </span>ALL.chr1.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi</font></div><div style="margin:0px"><font face="Courier"><span style="white-space:pre-wrap"> </span>ALL.chr4.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP.vcf.gz.tbi</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Given that the slice referenced in the perl script is chr 4, I have no idea why chr 1 is getting downloaded (?) .. do you see the same thing when you run the script?</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">After the crash, netstat shows large number of ensembl connections, most in FIN_WAIT2 state:</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">...</font></div><div><div style="margin:0px"><font face="Courier">7fff629ec000-7fff629ee000 r--p 00000000 00:00 0 [vvar]</font></div><div style="margin:0px"><font face="Courier">7fff629ee000-7fff629f0000 r-xp 00000000 00:00 0 [vdso]</font></div><div style="margin:0px"><font face="Courier">ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]</font></div><div style="margin:0px"><font face="Courier">Aborted (core dumped)</font></div><div style="margin:0px"><font face="Courier">ensembl@ensembl:~$ netstat | more</font></div><div style="margin:0px"><font face="Courier">Active Internet connections (w/o servers)</font></div><div style="margin:0px"><font face="Courier">Proto Recv-Q Send-Q Local Address Foreign Address State </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44305/" target="_blank">10.0.2.15:44305</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44321/" target="_blank">10.0.2.15:44321</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:43142/" target="_blank">10.0.2.15:43142</a> ec2-50-16-247-22.:mysql TIME_WAIT </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44303/" target="_blank">10.0.2.15:44303</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44313/" target="_blank">10.0.2.15:44313</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44289/" target="_blank">10.0.2.15:44289</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:35143/" target="_blank">10.0.2.15:35143</a> ec2-23-21-181-179:mysql TIME_WAIT </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44295/" target="_blank">10.0.2.15:44295</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44309/" target="_blank">10.0.2.15:44309</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44319/" target="_blank">10.0.2.15:44319</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44293/" target="_blank">10.0.2.15:44293</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44287/" target="_blank">10.0.2.15:44287</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44323/" target="_blank">10.0.2.15:44323</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44283/" target="_blank">10.0.2.15:44283</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44269/" target="_blank">10.0.2.15:44269</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:44317/" target="_blank">10.0.2.15:44317</a> ftp-ensembl-ext.san:ftp FIN_WAIT2 </font></div><div style="margin:0px"><font face="Courier">tcp6 0 0 localhost:48000 localhost:ipp ESTABLISHED</font></div><div style="margin:0px"><font face="Courier">tcp6 0 0 localhost:ipp localhost:48000 ESTABLISHED</font></div><div style="margin:0px"><font face="Courier">Active UNIX domain sockets (w/o servers)</font></div><div style="margin:0px"><font face="Courier">Proto RefCnt Flags Type State I-Node Path</font></div><div style="margin:0px"><font face="Courier">unix 18 [ ] DGRAM 10253 /dev/log</font></div></div><div><font face="Courier">Etc.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">From google (I have no idea the level of credibility):</font></div><div><font face="Courier"><span style="color:rgb(51,51,51);background-color:rgb(250,250,250)">"FIN_WAIT2 is a state when the server closes the socket on its side but</span><br style="color:rgb(51,51,51)"><span style="color:rgb(51,51,51);background-color:rgb(250,250,250)">does not receive an acknowledgement of the close from the client. Does</span><br style="color:rgb(51,51,51)"><span style="color:rgb(51,51,51);background-color:rgb(250,250,250)">your application open and close a lot of connections? When you close on</span><br style="color:rgb(51,51,51)"><span style="color:rgb(51,51,51);background-color:rgb(250,250,250)">the client side do you use the Connection.close() method?"</span></font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Even after the active-internet-connections table clears, I get more-instantaneous crashes. After these, netstat shows:</font></div><div><font face="Courier"><br></font></div><div><div style="margin:0px"><font face="Courier">Active Internet connections (w/o servers)</font></div><div style="margin:0px"><font face="Courier">Proto Recv-Q Send-Q Local Address Foreign Address State </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:40289/" target="_blank">10.0.2.15:40289</a> ec2-50-16-247-22.:mysql TIME_WAIT </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:59322/" target="_blank">10.0.2.15:59322</a> ec2-23-21-181-179:mysql TIME_WAIT </font></div><div style="margin:0px"><font face="Courier">tcp 0 0 <a href="http://10.0.2.15:59321/" target="_blank">10.0.2.15:59321</a> ec2-23-21-181-179:mysql TIME_WAIT </font></div><div style="margin:0px"><font face="Courier">tcp6 1 0 localhost:55452 localhost:ipp CLOSE_WAIT </font></div><div style="margin:0px"><font face="Courier">Active UNIX domain sockets (w/o servers)</font></div><div style="margin:0px"><font face="Courier">Proto RefCnt Flags Type State I-Node Path</font></div><div style="margin:0px"><font face="Courier">unix 19 [ ] DGRAM 10189 /dev/log</font></div><div style="margin:0px"><font face="Courier">unix 3 [ ] STREAM CONNECTED 14690 </font></div></div><div><font face="Courier">Etc.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">If I wait an extended period of time (~30 minutes), then the test code will not instantaneously crash and it will behave how it behaved initially: running successfully for a short period of time and then crashing (though not nec. at the exact same spot).</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Please let me know if these notes offer you any insights, or if you can suggest anything else for me to try .. I'd really like to get this working.</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Many thanks,</font></div><div><font face="Courier"><br></font></div><div><font face="Courier">Andrew</font></div><div><div><div><font face="Courier"><br></font></div><div><font face="Courier"><br></font></div><div><font face="Courier"><br></font></div><div><br></div><div><br></div><div><br></div><div><br></div><br><div><blockquote type="cite"><div>On Jul 11, 2016, at 10:44 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><div><div dir="ltr">Hi again,<div><br></div><div>I can't get the script to recreate the issue at my end.</div><div><br>I'm surprised you're getting that message as the script is querying only one chromosome, so it should only be opening one (at most two) VCFs concurrently.</div><div><br></div><div>I don't know what's happening underneath our API layer, but my guess would be some other process (possibly zombie?) has an open connection to our FTP site. It may also be there's some per-IP allowance that is being violated somehow?</div><div><br></div><div>In any case have you tried downloading the VCFs locally?</div><div><br></div><div>Cheers</div><div><br></div><div>Will</div><div class="gmail_extra"><br><div class="gmail_quote">On 11 July 2016 at 14:52, <span dir="ltr"><<a href="mailto:andrew126@mac.com" target="_blank">andrew126@mac.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div>Hi,</div><div><br></div><div>In case it helps to debug this issue, I've reattached the perl script that throws "too many connection" errors .. even with the release/84 code fix.</div><div><br></div><div>Many thanks,</div><div><div><div><br></div><div>Andrew</div><div><br></div><div><div>use strict;</div><div>$|=1;</div><div>use IPC::Run;</div><div>use Bio::EnsEMBL::Registry;</div><div>use Bio::EnsEMBL::ApiVersion; </div><div>printf( "The API version used is %s\n", software_version() ); </div><div><br></div><div>my $registry = 'Bio::EnsEMBL::Registry';</div><div>$registry->load_all();</div><div>$registry->set_reconnect_when_lost();</div><div>$registry->load_registry_from_db(</div><div> -host => '<a href="http://useastdb.ensembl.org/" target="_blank">useastdb.ensembl.org</a>',</div><div> -user => 'anonymous'</div><div> );</div><div><br></div><div>my $gene_adaptor = $registry->get_adaptor('homo_sapiens','core','gene');</div><div>my $slice_adaptor = $registry->get_adaptor('homo_sapiens','core','slice');</div><div><br></div><div>my $slice = $slice_adaptor->fetch_by_region( 'chromosome', "4", 139000000, 139100000);</div><div><br></div><div>print "Variation:\n";</div><div><br></div><div>my $vf_adaptor = $registry->get_adaptor( 'human', 'variation', 'variationfeature' );</div><div>$vf_adaptor->db->use_vcf(1);</div><div>my $vars = $vf_adaptor->fetch_all_by_Slice($slice);</div><div><br></div><div>foreach my $vf (@{$vars}){</div><div> print "\t".$vf->variation_name(),"\n";</div><div> print "\t".$vf->allele_string(),"\n";</div><div> print "\tChromosome: ".$slice->seq_region_name."\n";</div><div> print "\tStart-End: ".$vf->seq_region_start."-".$vf->seq_region_end."\n";</div><div> print "\tConsequences: ".join(",",@{$vf->consequence_type()}),"\n";</div><div> if (1==1) {</div><div><span style="white-space:pre-wrap"> </span>my $alleles = $vf->variation->get_all_Alleles();</div><div><span style="white-space:pre-wrap"> </span>foreach my $allele (@{$alleles}) {</div><div><span style="white-space:pre-wrap"> </span> next unless (defined $allele->population);</div><div><span style="white-space:pre-wrap"> </span> my $allele_string = $allele->allele;</div><div><span style="white-space:pre-wrap"> </span> my $frequency = $allele->frequency || 'NA';</div><div><span style="white-space:pre-wrap"> </span> my $population_name = $allele->population->name;</div><div><span style="white-space:pre-wrap"> </span> printf("\tAllele %s has frequency: %s in population %s.\n", $allele_string, $frequency, $po</div><div>pulation_name);</div><div><span style="white-space:pre-wrap"> </span>}</div><div> }</div><div> print "\n";</div><div>}</div></div><div><br></div><div><br></div><div><br></div><br></div></div><div><div><div><blockquote type="cite"><div>On Jul 7, 2016, at 12:51 PM, <a href="mailto:andrew126@mac.com" target="_blank">andrew126@mac.com</a> wrote:</div><br><div><div style="word-wrap:break-word"><div>Hi Will,</div><div><br></div><div>Yes, I can definitely share .. an example of a script that is throwing errors is in the original post at the start of the this thread.</div><div><br></div><div>Many thanks,</div><div><br></div><div>Andrew</div><br><div><blockquote type="cite"><div>On Jul 7, 2016, at 11:57 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><div><div dir="ltr">Hi Andrew,<div><br></div><div>Strange, are you able to share your test script?</div><div><br></div><div>Another solution is to download the VCF files that are being opened over the FTP connection [1] and modifying the config file in ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json to point to the path where you downloaded the files.</div><div><br></div><div>Cheers</div><div><br></div><div>Will</div><div><br></div><div>[1] : <a href="ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/" target="_blank">ftp://ftp.ensembl.org/pub/variation_genotype/homo_sapiens/</a> or for GRCh37 <a href="ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/" target="_blank">ftp://ftp.ensembl.org/pub/grch37/release-82/variation/vcf/homo_sapiens/1000GENOMES-phase_3-genotypes/</a> </div></div><div class="gmail_extra"><br><div class="gmail_quote">On 7 July 2016 at 13:49, <span dir="ltr"><<a href="mailto:andrew126@mac.com" target="_blank">andrew126@mac.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div>Hi Will,</div><div><br></div><div>Thanks for the response.</div><div><br></div><div>I've updated to the latest fixes, but I'm still getting these errors using the same code.</div><div><br></div><div>Is there anything else I can try?</div><div><br></div><div>Thanks,</div><div><br></div><div>Andrew</div><div><br></div><div><div>andrew@ubuntu1404-64-ak:~/gte/src$ git ensembl --pull api</div><div>* Processing 'api'</div><div><br></div><div>* Working with module 'ensembl'</div><div>* Performing pull</div><div>Already up-to-date.</div><div><br></div><div>* Working with module 'ensembl-compara'</div><div>* Performing pull</div><div>Already up-to-date.</div><div><br></div><div>* Working with module 'ensembl-funcgen'</div><div>* Performing pull</div><div>Already up-to-date.</div><div><br></div><div>* Working with module 'ensembl-io'</div><div>* Performing pull</div><div>Already up-to-date.</div><div><br></div><div>* Working with module 'ensembl-variation'</div><div>* Performing pull</div><div>Already up-to-date.</div><div><br></div></div><div><div>perl <a href="http://tryit_crash.pl/" target="_blank">tryit_crash.pl</a> > tic.out &</div><div>[2] 3517</div><span><div>andrew@ubuntu1404-64-ak:~/gte$ UNIVERSAL->import is deprecated and will be removed in a future perl at /home/andrew/gte/src/bioperl-live/Bio/Tree/TreeFunctionsI.pm line 94.</div><div>Subroutine Tabix::tabix_open redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.</div><div>Subroutine Tabix::tabix_close redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.</div><div>Subroutine Tabix::tabix_query redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.</div><div>Subroutine Tabix::tabix_read redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.</div><div>Subroutine Tabix::tabix_getnames redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.</div><div>Subroutine TabixIterator::tabix_iter_free redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.</div><div>[kftp_connect_file] 530 You may not have more than 15 concurrent connections at any time.</div><div>[kftp_connect_file] 530 You may not have more than 15 concurrent connections at any time.</div><div>[main] fail to open the data file.</div></span><div>Tabix::tabix_query: t is not of type tabix_tPtr at /home/andrew/gte/src/ensembl-io/modules/Bio/EnsEMBL/IO/TabixParser.pm line 70.</div></div><div><div><div><br></div><div><br></div><br><div><blockquote type="cite"><div>On Jul 7, 2016, at 6:35 AM, Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>> wrote:</div><br><div><div dir="ltr"><div>Hi Andrew,<br></div><div><br></div><div>We added a fix for this in the release/84 code ([1] if you're interested) that limits the number of concurrent VCF connections to 2. If you are on release/84, use git pull in the ensembl-variation directory to get the latest fixes.</div><div><br></div><div>If you are using an earlier version of the API, I'd suggest you update to 84.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div><br></div><div>[1] : <a href="https://github.com/Ensembl/ensembl-variation/commit/cd6813a66ca2cead9dc4da4e3a7bfa965b78f2ae" target="_blank">https://github.com/Ensembl/ensembl-variation/commit/cd6813a66ca2cead9dc4da4e3a7bfa965b78f2ae</a><br></div><div class="gmail_extra"><br><div class="gmail_quote">On 6 July 2016 at 20:50, <span dir="ltr"><<a href="mailto:andrew126@mac.com" target="_blank">andrew126@mac.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hi,<br>
<br>
I'm using API 84 on 64-bit Ubuntu.<br>
<br>
uname -a<br>
Linux ubuntu1404-64-ak 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux<br>
<br>
The below script reliably generates errors because of the number of concurrent connections. If get_all_Alleles() is not called, then no errors are experienced. I think other similar calls also generate these errors, but this is a simple example to get started.<br>
<br>
Posted below the script is an example of the error messages encountered.<br>
<br>
Is there a way to accomplish the same goal (summary of all alleles for each variant) without generating such errors?<br>
<br>
Please let me know if any other information would be useful.<br>
<br>
Thanks for any help,<br>
<br>
Andrew<br>
<br>
<br>
use strict;<br>
$|=1;<br>
use IPC::Run;<br>
use Bio::EnsEMBL::Registry;<br>
use Bio::EnsEMBL::ApiVersion;<br>
printf( "The API version used is %s\n", software_version() );<br>
<br>
my $registry = 'Bio::EnsEMBL::Registry';<br>
$registry->load_all();<br>
$registry->set_reconnect_when_lost();<br>
$registry->load_registry_from_db(<br>
-host => '<a href="http://useastdb.ensembl.org/" rel="noreferrer" target="_blank">useastdb.ensembl.org</a>',<br>
-user => 'anonymous'<br>
);<br>
<br>
my $gene_adaptor = $registry->get_adaptor('homo_sapiens','core','gene');<br>
my $slice_adaptor = $registry->get_adaptor('homo_sapiens','core','slice');<br>
<br>
my $slice = $slice_adaptor->fetch_by_region( 'chromosome', "4", 139000000, 139100000);<br>
<br>
print "Variation:\n";<br>
<br>
my $vf_adaptor = $registry->get_adaptor( 'human', 'variation', 'variationfeature' );<br>
$vf_adaptor->db->use_vcf(1);<br>
my $vars = $vf_adaptor->fetch_all_by_Slice($slice);<br>
<br>
foreach my $vf (@{$vars}){<br>
print "\t".$vf->variation_name(),"\n";<br>
print "\t".$vf->allele_string(),"\n";<br>
print "\tChromosome: ".$slice->seq_region_name."\n";<br>
print "\tStart-End: ".$vf->seq_region_start."-".$vf->seq_region_end."\n";<br>
print "\tConsequences: ".join(",",@{$vf->consequence_type()}),"\n";<br>
if (1==1) {<br>
my $alleles = $vf->variation->get_all_Alleles();<br>
foreach my $allele (@{$alleles}) {<br>
next unless (defined $allele->population);<br>
my $allele_string = $allele->allele;<br>
my $frequency = $allele->frequency || 'NA';<br>
my $population_name = $allele->population->name;<br>
printf("\tAllele %s has frequency: %s in population %s.\n", $allele_string, $frequency, $population_name);<br>
}<br>
}<br>
print "\n";<br>
}<br>
<br>
<br>
<br>
<br>
<br>
<br>
andrew@ubuntu1404-64-ak:~/gte$ perl <a href="http://tryit_crash.pl/" rel="noreferrer" target="_blank">tryit_crash.pl</a> > tic.out &<br>
[2] 3059<br>
andrew@ubuntu1404-64-ak:~/gte$ UNIVERSAL->import is deprecated and will be removed in a future perl at /home/andrew/gte/src/bioperl-live/Bio/Tree/TreeFunctionsI.pm line 94.<br>
Subroutine Tabix::tabix_open redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.<br>
Subroutine Tabix::tabix_close redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.<br>
Subroutine Tabix::tabix_query redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.<br>
Subroutine Tabix::tabix_read redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.<br>
Subroutine Tabix::tabix_getnames redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.<br>
Subroutine TabixIterator::tabix_iter_free redefined at /home/andrew/gte/src/lib/perl/5.18.2/Tabix.pm line 17.<br>
[kftp_connect_file] 530 You may not have more than 15 concurrent connections at any time.<br>
[main] fail to open the data file.<br>
[kftp_connect_file] 530 You may not have more than 15 concurrent connections at any time.<br>
*** buffer overflow detected ***: perl terminated<br>
======= Backtrace: =========<br>
/lib/x86_64-linux-gnu/libc.so.6(+0x7338f)[0x7f7fcd13138f]<br>
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x5c)[0x7f7fcd1c8c9c]<br>
/lib/x86_64-linux-gnu/libc.so.6(+0x109b60)[0x7f7fcd1c7b60]<br>
/lib/x86_64-linux-gnu/libc.so.6(+0x10abe7)[0x7f7fcd1c8be7]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0xaebd)[0x7f7fc8011ebd]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0xb0aa)[0x7f7fc80120aa]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(knet_read+0xb8)[0x7f7fc8012c18]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(bgzf_read_block+0x165)[0x7f7fc8010c25]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(bgzf_getline+0x37)[0x7f7fc8011cc7]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(ti_iter_read+0xd2)[0x7f7fc8010172]<br>
/home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so(+0x3368)[0x7f7fc800a368]<br>
/usr/lib/libperl.so.5.18(Perl_pp_entersub+0x596)[0x7f7fcd53c866]<br>
/usr/lib/libperl.so.5.18(Perl_runops_standard+0x16)[0x7f7fcd534e86]<br>
/usr/lib/libperl.so.5.18(perl_run+0x254)[0x7f7fcd4cd714]<br>
perl(main+0x149)[0x400dd9]<br>
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f7fcd0dfec5]<br>
perl[0x400e11]<br>
======= Memory map: ========<br>
00400000-00402000 r-xp 00000000 fc:00 133596 /usr/bin/perl<br>
00601000-00602000 r--p 00001000 fc:00 133596 /usr/bin/perl<br>
00602000-00603000 rw-p 00002000 fc:00 133596 /usr/bin/perl<br>
01805000-061dc000 rw-p 00000000 00:00 0 [heap]<br>
7f7fc4000000-7f7fc4021000 rw-p 00000000 00:00 0<br>
7f7fc4021000-7f7fc8000000 ---p 00000000 00:00 0<br>
7f7fc8007000-7f7fc8015000 r-xp 00000000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so<br>
7f7fc8015000-7f7fc8214000 ---p 0000e000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so<br>
7f7fc8214000-7f7fc8215000 r--p 0000d000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so<br>
7f7fc8215000-7f7fc8216000 rw-p 0000e000 fc:00 532847 /home/andrew/gte/src/lib/perl/5.18.2/auto/Tabix/Tabix.so<br>
7f7fc8216000-7f7fc822b000 r-xp 00000000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so<br>
7f7fc822b000-7f7fc842a000 ---p 00015000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so<br>
7f7fc842a000-7f7fc842b000 r--p 00014000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so<br>
7f7fc842b000-7f7fc842c000 rw-p 00015000 fc:00 260284 /usr/lib/perl/5.18.2/auto/Storable/Storable.so<br>
7f7fc842c000-7f7fc842e000 r-xp 00000000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so<br>
7f7fc842e000-7f7fc862d000 ---p 00002000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so<br>
7f7fc862d000-7f7fc862e000 r--p 00001000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so<br>
7f7fc862e000-7f7fc862f000 rw-p 00002000 fc:00 260313 /usr/lib/perl/5.18.2/auto/attributes/attributes.so<br>
7f7fc862f000-7f7fc863d000 r-xp 00000000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so<br>
7f7fc863d000-7f7fc883c000 ---p 0000e000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so<br>
7f7fc883c000-7f7fc883d000 r--p 0000d000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so<br>
7f7fc883d000-7f7fc883e000 rw-p 0000e000 fc:00 311765 /usr/lib/perl5/auto/JSON/XS/XS.so<br>
7f7fc883e000-7f7fc884c000 r-xp 00000000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so<br>
7f7fc884c000-7f7fc8a4b000 ---p 0000e000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so<br>
7f7fc8a4b000-7f7fc8a4c000 r--p 0000d000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so<br>
7f7fc8a4c000-7f7fc8a4d000 rw-p 0000e000 fc:00 260173 /usr/lib/perl/5.18.2/auto/Compress/Raw/Zlib/Zlib.so<br>
7f7fc8a4d000-7f7fc8a53000 r-xp 00000000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so<br>
7f7fc8a53000-7f7fc8c52000 ---p 00006000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so<br>
7f7fc8c52000-7f7fc8c53000 r--p 00005000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so<br>
7f7fc8c53000-7f7fc8c54000 rw-p 00006000 fc:00 260228 /usr/lib/perl/5.18.2/auto/File/Glob/Glob.so<br>
7f7fc8c54000-7f7fc8c5c000 r-xp 00000000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so<br>
7f7fc8c5c000-7f7fc8e5c000 ---p 00008000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so<br>
7f7fc8e5c000-7f7fc8e5e000 r--p 00008000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so<br>
7f7fc8e5e000-7f7fc8e5f000 rw-p 0000a000 fc:00 260282 /usr/lib/perl/5.18.2/auto/Socket/Socket.so<br>
7f7fc8e5f000-7f7fc8e63000 r-xp 00000000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so<br>
7f7fc8e63000-7f7fc9062000 ---p 00004000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so<br>
7f7fc9062000-7f7fc9063000 r--p 00003000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so<br>
7f7fc9063000-7f7fc9064000 rw-p 00004000 fc:00 260192 /usr/lib/perl/5.18.2/auto/Digest/MD5/MD5.so<br>
7f7fc9064000-7f7fc9066000 r-xp 00000000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so<br>
7f7fc9066000-7f7fc9265000 ---p 00002000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so<br>
7f7fc9265000-7f7fc9266000 r--p 00001000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so<br>
7f7fc9266000-7f7fc9267000 rw-p 00002000 fc:00 260176 /usr/lib/perl/5.18.2/auto/Cwd/Cwd.so<br>
7f7fc9267000-7f7fc927e000 r-xp 00000000 fc:00 395859 /lib/x86_64-linux-gnu/<a href="http://libresolv-2.19.so/" rel="noreferrer" target="_blank">libresolv-2.19.so</a><br>
7f7fc927e000-7f7fc947e000 ---p 00017000 fc:00 395859 /lib/x86_64-linux-gnu/<a href="http://libresolv-2.19.so/" rel="noreferrer" target="_blank">libresolv-2.19.so</a><br>
7f7fc947e000-7f7fc947f000 r--p 00017000 fc:00 395859 /lib/x86_64-linux-gnu/<a href="http://libresolv-2.19.so/" rel="noreferrer" target="_blank">libresolv-2.19.so</a><br>
7f7fc947f000-7f7fc9480000 rw-p 00018000 fc:00 395859 /lib/x86_64-linux-gnu/<a href="http://libresolv-2.19.so/" rel="noreferrer" target="_blank">libresolv-2.19.so</a><br>
7f7fc9480000-7f7fc9482000 rw-p 00000000 00:00 0<br>
7f7fc9482000-7f7fc9487000 r-xp 00000000 fc:00 395806 /lib/x86_64-linux-gnu/<a href="http://libnss_dns-2.19.so/" rel="noreferrer" target="_blank">libnss_dns-2.19.so</a><br>
7f7fc9487000-7f7fc9686000 ---p 00005000 fc:00 395806 /lib/x86_64-linux-gnu/<a href="http://libnss_dns-2.19.so/" rel="noreferrer" target="_blank">libnss_dns-2.19.so</a><br>
7f7fc9686000-7f7fc9687000 r--p 00004000 fc:00 395806 /lib/x86_64-linux-gnu/<a href="http://libnss_dns-2.19.so/" rel="noreferrer" target="_blank">libnss_dns-2.19.so</a><br>
7f7fc9687000-7f7fc9688000 rw-p 00005000 fc:00 395806 /lib/x86_64-linux-gnu/<a href="http://libnss_dns-2.19.so/" rel="noreferrer" target="_blank">libnss_dns-2.19.so</a><br>
7f7fc9688000-7f7fc968a000 r-xp 00000000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2<br>
7f7fc968a000-7f7fc9889000 ---p 00002000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2<br>
7f7fc9889000-7f7fc988a000 r--p 00001000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2<br>
7f7fc988a000-7f7fc988b000 rw-p 00002000 fc:00 395814 /lib/x86_64-linux-gnu/libnss_mdns4_minimal.so.2<br>
7f7fc988b000-7f7fc9896000 r-xp 00000000 fc:00 395808 /lib/x86_64-linux-gnu/<a href="http://libnss_files-2.19.so/" rel="noreferrer" target="_blank">libnss_files-2.19.so</a><br>
7f7fc9896000-7f7fc9a95000 ---p 0000b000 fc:00 395808 /lib/x86_64-linux-gnu/<a href="http://libnss_files-2.19.so/" rel="noreferrer" target="_blank">libnss_files-2.19.so</a><br>
7f7fc9a95000-7f7fc9a96000 r--p 0000a000 fc:00 395808 /lib/x86_64-linux-gnu/<a href="http://libnss_files-2.19.so/" rel="noreferrer" target="_blank">libnss_files-2.19.so</a><br>
7f7fc9a96000-7f7fc9a97000 rw-p 0000b000 fc:00 395808 /lib/x86_64-linux-gnu/<a href="http://libnss_files-2.19.so/" rel="noreferrer" target="_blank">libnss_files-2.19.so</a><br>
7f7fc9a97000-7f7fc9aad000 r-xp 00000000 fc:00 395760 /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
7f7fc9aad000-7f7fc9cac000 ---p 00016000 fc:00 395760 /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
7f7fc9cac000-7f7fc9cad000 rw-p 00015000 fc:00 395760 /lib/x86_64-linux-gnu/libgcc_s.so.1<br>
7f7fc9cad000-7f7fc9cae000 ---p 00000000 00:00 0<br>
7f7fc9cae000-7f7fca4ae000 rw-p 00000000 00:00 0<br>
7f7fca4ae000-7f7fca4c6000 r-xp 00000000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8<br>
7f7fca4c6000-7f7fca6c5000 ---p 00018000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8<br>
7f7fca6c5000-7f7fca6c6000 r--p 00017000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8<br>
7f7fca6c6000-7f7fca6c7000 rw-p 00018000 fc:00 395896 /lib/x86_64-linux-gnu/libz.so.1.2.8<br>
7f7fca6c7000-7f7fca977000 r-xp 00000000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0<br>
7f7fca977000-7f7fcab77000 ---p 002b0000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0<br>
7f7fcab77000-7f7fcab7c000 r--p 002b0000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0<br>
7f7fcab7c000-7f7fcabfa000 rw-p 002b5000 fc:00 183788 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18.0.0<br>
7f7fcabfa000-7f7fcabff000 rw-p 00000000 00:00 0<br>
7f7fcabff000-7f7fcac19000 r-xp 00000000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so<br>
7f7fcac19000-7f7fcae19000 ---p 0001a000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so<br>
7f7fcae19000-7f7fcae1b000 r--p 0001a000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so<br>
7f7fcae1b000-7f7fcae1c000 rw-p 0001c000 fc:00 183957 /usr/lib/perl5/auto/DBD/mysql/mysql.so<br>
7f7fcae1c000-7f7fcae24000 r-xp 00000000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so<br>
7f7fcae24000-7f7fcb023000 ---p 00008000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so<br>
7f7fcb023000-7f7fcb024000 r--p 00007000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so<br>
7f7fcb024000-7f7fcb025000 rw-p 00008000 fc:00 260182 /usr/lib/perl/5.18.2/auto/Data/Dumper/Dumper.so<br>
7f7fcb025000-7f7fcb02c000 r-xp 00000000 fc:00 395861 /lib/x86_64-linux-gnu/<a href="http://librt-2.19.so/" rel="noreferrer" target="_blank">librt-2.19.so</a><br>
7f7fcb02c000-7f7fcb22b000 ---p 00007000 fc:00 395861 /lib/x86_64-linux-gnu/<a href="http://librt-2.19.so/" rel="noreferrer" target="_blank">librt-2.19.so</a><br>
7f7fcb22b000-7f7fcb22c000 r--p 00006000 fc:00 395861 /lib/x86_64-linux-gnu/<a href="http://librt-2.19.so/" rel="noreferrer" target="_blank">librt-2.19.so</a><br>
7f7fcb22c000-7f7fcb22d000 rw-p 00007000 fc:00 395861 /lib/x86_64-linux-gnu/<a href="http://librt-2.19.so/" rel="noreferrer" target="_blank">librt-2.19.so</a><br>
7f7fcb22d000-7f7fcb232000 r-xp 00000000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so<br>
7f7fcb232000-7f7fcb431000 ---p 00005000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so<br>
7f7fcb431000-7f7fcb432000 r--p 00004000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so<br>
7f7fcb432000-7f7fcb433000 rw-p 00005000 fc:00 260301 /usr/lib/perl/5.18.2/auto/Time/HiRes/HiRes.so<br>
7f7fcb433000-7f7fcb435000 r-xp 00000000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so<br>
7f7fcb435000-7f7fcb634000 ---p 00002000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so<br>
7f7fcb634000-7f7fcb635000 r--p 00001000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so<br>
7f7fcb635000-7f7fcb636000 rw-p 00002000 fc:00 260297 /usr/lib/perl/5.18.2/auto/Tie/Hash/NamedCapture/NamedCapture.so<br>
7f7fcb636000-7f7fcb63b000 r-xp 00000000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so<br>
7f7fcb63b000-7f7fcb83b000 ---p 00005000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so<br>
7f7fcb83b000-7f7fcb83c000 r--p 00005000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so<br>
7f7fcb83c000-7f7fcb83d000 rw-p 00006000 fc:00 260251 /usr/lib/perl/5.18.2/auto/List/Util/Util.so<br>
7f7fcb83d000-7f7fcb85b000 r-xp 00000000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so<br>
7f7fcb85b000-7f7fcba5a000 ---p 0001e000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so<br>
7f7fcba5a000-7f7fcba5b000 r--p 0001d000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so<br>
7f7fcba5b000-7f7fcba5c000 rw-p 0001e000 fc:00 183894 /usr/lib/perl5/auto/DBI/DBI.so<br>
7f7fcba5c000-7f7fcba60000 r-xp 00000000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so<br>
7f7fcba60000-7f7fcbc5f000 ---p 00004000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so<br>
7f7fcbc5f000-7f7fcbc60000 r--p 00003000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so<br>
7f7fcbc60000-7f7fcbc61000 rw-p 00004000 fc:00 260245 /usr/lib/perl/5.18.2/auto/IO/IO.so<br>
7f7fcbc61000-7f7fcbc73000 r-xp 00000000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so<br>
7f7fcbc73000-7f7fcbe72000 ---p 00012000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so<br>
7f7fcbe72000-7f7fcbe75000 r--p 00011000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so<br>
7f7fcbe75000-7f7fcbe76000 rw-p 00014000 fc:00 260266 /usr/lib/perl/5.18.2/auto/POSIX/POSIX.so<br>
7f7fcbe76000-7f7fcbe79000 r-xp 00000000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so<br>
7f7fcbe79000-7f7fcc079000 ---p 00003000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so<br>
7f7fcc079000-7f7fcc07a000 r--p 00003000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so<br>
7f7fcc07a000-7f7fcc07b000 rw-p 00004000 fc:00 260222 /usr/lib/perl/5.18.2/auto/Fcntl/Fcntl.so<br>
7f7fcc07b000-7f7fcc75d000 r--p 00000000 fc:00 140924 /usr/lib/locale/locale-archive<br>
7f7fcc75d000-7f7fcc766000 r-xp 00000000 fc:00 395743 /lib/x86_64-linux-gnu/<a href="http://libcrypt-2.19.so/" rel="noreferrer" target="_blank">libcrypt-2.19.so</a><br>
7f7fcc766000-7f7fcc966000 ---p 00009000 fc:00 395743 /lib/x86_64-linux-gnu/<a href="http://libcrypt-2.19.so/" rel="noreferrer" target="_blank">libcrypt-2.19.so</a><br>
7f7fcc966000-7f7fcc967000 r--p 00009000 fc:00 395743 /lib/x86_64-linux-gnu/<a href="http://libcrypt-2.19.so/" rel="noreferrer" target="_blank">libcrypt-2.19.so</a><br>
7f7fcc967000-7f7fcc968000 rw-p 0000a000 fc:00 395743 /lib/x86_64-linux-gnu/<a href="http://libcrypt-2.19.so/" rel="noreferrer" target="_blank">libcrypt-2.19.so</a><br>
[2]+ Aborted (core dumped) perl <a href="http://tryit_crash.pl/" rel="noreferrer" target="_blank">tryit_crash.pl</a> > tic.out<br>
<br>
<br>
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