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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi all, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I am attempting the ImportArrays function and am having
problems. The job seems to hang and when I check the error files I see the output
at the end of this mail. The error being reported is at the last line in the
PROBES file but there is nothing wrong with this file. I have used it with previous
versions of the mapping environment with no problems. Has anyone got any ideas
what is happening?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Best, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Gavin<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Running job 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Module is ImportArrays<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Input id is AFFY_UTR:genome<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Analysis is Import_AFFY_UTR_Arrays<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Files are
/cluster_progs/data/Ensembl/59/process_dirs/lsf_default_output_dir/Import_AFFY_UTR_Arrays/5/AFFY_UTR:genome.Import_AFFY_UTR_Arrays.230.out
/cluster_progs/da<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>ta/Ensembl/59/process_dirs/lsf_default_output_dir/Import_AFFY_UTR_Arrays/5/AFFY_UTR:genome.Import_AFFY_UTR_Arrays.230.err<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>NOTE: rollback_ArrayChips. Need to implement ExperimentlChip
check, is the problem that ExperimentalChips are registered before ArrayChips
imported? at /cluster_progs<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>/data/Ensembl/59/ensembl-functgenomics/modules//Bio/EnsEMBL/Funcgen/Utils/Helper.pm
line 1957, <PROBES> line 1.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>DBD::mysql::st bind_param failed: Illegal parameter number
at /cluster_progs/data/Ensembl/59/ensembl-functgenomics/modules//Bio/EnsEMBL/Funcgen/DBSQL/ProbeAdaptor.pm
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>line 569, <PROBES> line 548.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>WRITING: Lost the will to live Error<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Job 1 failed: [<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>-------------------- EXCEPTION --------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>MSG: Problems for ImportArrays writing output for
AFFY_UTR:genome [DBD::mysql::st bind_param failed: Illegal parameter number at
/cluster_progs/data/Ensembl/59/ensemb<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>l-functgenomics/modules//Bio/EnsEMBL/Funcgen/DBSQL/ProbeAdaptor.pm
line 569, <PROBES> line 548.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>]<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>STACK Bio::EnsEMBL::Pipeline::Job::run_module /cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pipeline/Job.pm:662<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>STACK (eval)
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pipeline/runner.pl:219<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>STACK main::run_jobs_with_lsfcopy
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pipeline/runner.pl:218<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>STACK toplevel
/cluster_progs/data/Ensembl/59/ensembl-pipeline/modules//Bio/EnsEMBL/Pipeline/runner.pl:128<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>---------------------------------------------------<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>]Finished job 1<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Gavin Oliver, MSc<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Team Leader Genomic
Research<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Almac<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Diagnostics<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Tel: +44 (0)28
38395792<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Fax: +44 (0)28
38398676<o:p></o:p></span></font></p>
<p class=MsoNormal style='line-height:150%'><font size=2 face=Arial><span
style='font-size:10.0pt;line-height:150%;font-family:Arial'>Visit our website
at: <a href="http://www.almacgroup.com/">http://www.almacgroup.com</a></span></font><font
size=2 face=Arial><span style='font-size:10.0pt;line-height:150%;font-family:
Arial'><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<P class=MsoNormal><STRONG><B><SPAN style="FONT-SIZE: 12pt; COLOR: blue"><FONT face="Times New Roman"> </FONT></P>
<P class=MsoNormal><FONT color=#000000><SPAN lang=EN-GB style="FONT-FAMILY: 'Times New Roman'">The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><FONT color=#0000ff><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Sciences Limited, registered no. NI041550.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Discovery Limited, registered no. NI046249. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Pharma Services Limited, registered no. NI045055.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Services Limited, registered no. NI041905.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Technologies Limited, registered no. NI061202. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Diagnostics Limited, registered no. NI043067.<SPAN style="mso-spacerun: yes"> </SPAN>All preceding companies are registered in <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:country-region w:st="on">Northern Ireland</st1:country-region> with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>. <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no. SC154034. <o:p></o:p></SPAN></P>
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<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are <st1:State w:st="on"><st1:place w:st="on">Delaware</st1:place></st1:State> limited liability companies and Almac Group Incorporated is a Delaware Corporation.<SPAN style="mso-spacerun: yes"> </SPAN>More information on the Almac Group can be found on the Almac website: www.almacgroup.com<o:p></o:p></SPAN></P></SPAN></B></STRONG></FONT></body>
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