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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m currently experiencing an issue with a bulk upload of images to Omero. This is being run from the command line.<o:p></o:p></p>
<p class="MsoNormal" align="center" style="text-align:center"><o:p> </o:p></p>
<p class="MsoNormal">I am seeing the following errors, and my bulk upload fails:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"> cli.invoke(import_args, strict=True)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 749, in invoke<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"> self.assertRC()<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 738, in assertRC<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"> raise NonZeroReturnCode(self.rv, "assert failed")<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">omero.cli.NonZeroReturnCode: assert failed<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The bulk upload failed while writing an image, with the following arguments:
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">['import', '-s', 'localhost', '-u', 'upload', '-w', '<password removed>', '-p', '4064', '-d', '1687', '-n', '11_03_14_krp4_1130_b1_boundaries.inr.gz', '---errs=cli.err', '---file=cli.out',
'--', '/tmp/tmpB3u1Gn/11_03_14_krp4_1130_b1/11_03_14_krp4_1130_b1_boundaries.inr.gz']<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When I try to run the upload again, it fails for a different image – it does not fail on the same one upload time!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am unable to see much additional information: I have checked in the omero logs, (/opt/Omero/var/log), but am not able to see any additional logging. I have checked filesystem sizes, and nothing seems to have filled up!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Please can you point me in the right direction as to how I can debug this issue further?<o:p></o:p></p>
<p class="MsoNormal"><br>
Thanks<o:p></o:p></p>
<p class="MsoNormal">John<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#4F81BD;mso-fareast-language:EN-GB">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-family:"Arial","sans-serif";color:#548DD4;mso-fareast-language:EN-GB">John Webber<br>
</span></b><span style="color:#1F497D;mso-fareast-language:EN-GB">Computing and Information Services</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">NBI Partnership Ltd</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Norwich Research park</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Colney Lane</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Norwich</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">NR4 7UH</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"> </span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">E-Mail:</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"><a href="mailto:john.webber@nbi.ac.uk"><span style="color:blue">john.webber@nbi.ac.uk</span></a></span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Web:</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> <a href="http://www.nbi.ac.uk/">
<span style="color:blue">http://www.nbi.ac.uk</span></a></span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Tel:</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> +44(0)1603 450 818<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Helpdesk (Tel): 1234</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> HPC Support (Web):</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> <a href="http://hpc.nbi.ac.uk/">
<span style="color:blue">http://hpc.nbi.ac.uk</span></a> (NBI internal)<o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"> HPC Support (Tel):</span><span style="mso-fareast-language:EN-GB">
</span><span style="color:#1F497D;mso-fareast-language:EN-GB"> 2003 (NBI internal)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-GB"> </span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="color:#1F497D;mso-fareast-language:EN-GB">The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory</span></i><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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