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<div>Hi John</div>
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<div>Could you try adding --debug DEBUG to your import command, and see if it gives any more information? If that doesn't help could you send us cli.err and cli.out?</div>
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<div>Many thanks</div>
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<div>Simon</div>
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<div>On 25 Mar 2014, at 15:46, "John Webber (NBI)" <<a href="mailto:John.Webber@nbi.ac.uk">John.Webber@nbi.ac.uk</a>></div>
<div> wrote:</div>
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Hi,<o:p></o:p></div>
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<o:p> </o:p></div>
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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></div>
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<o:p> </o:p></div>
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I am seeing the following errors, and my bulk upload fails:<o:p></o:p></div>
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<o:p> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
<span style="font-size: 9pt; "> cli.invoke(import_args, strict=True)<o:p></o:p></span></div>
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<span style="font-size: 9pt; "> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 749, in invoke<o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
<span style="font-size: 9pt; "> self.assertRC()<o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
<span style="font-size: 9pt; "> File "/opt/OMERO.server-4.4.8p1-ice33-b304/lib/python/omero/cli.py", line 738, in assertRC<o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
<span style="font-size: 9pt; "> raise NonZeroReturnCode(self.rv, "assert failed")<o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
<span style="font-size: 9pt; ">omero.cli.NonZeroReturnCode: assert failed<o:p></o:p></span></div>
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<o:p> </o:p></div>
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The bulk upload failed while writing an image, with the following arguments:<o:p></o:p></div>
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<o:p> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt 36pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
<span style="font-size: 9pt; ">['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></div>
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<o:p> </o:p></div>
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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></div>
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<o:p> </o:p></div>
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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></div>
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<o:p> </o:p></div>
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Please can you point me in the right direction as to how I can debug this issue further?<o:p></o:p></div>
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<br>
Thanks<o:p></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">
John<o:p></o:p></div>
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<o:p> </o:p></div>
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<o:p> </o:p></div>
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<o:p> </o:p></div>
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<b><span style="font-size: 10pt; font-family: Arial, sans-serif; color: rgb(79, 129, 189); ">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<b><span style="font-family: Arial, sans-serif; color: rgb(84, 141, 212); ">John Webber<br>
</span></b><span style="color: rgb(31, 73, 125); ">Computing and Information Services</span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); ">NBI Partnership Ltd</span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); ">Norwich Research park</span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); ">Colney Lane</span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 12pt; background-color: white; ">
<span style="color: rgb(31, 73, 125); ">Norwich</span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 12pt; background-color: white; ">
<span style="color: rgb(31, 73, 125); ">NR4 7UH</span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); "> </span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); ">E-Mail:</span><span> </span><span style="color: rgb(31, 73, 125); "><a href="mailto:john.webber@nbi.ac.uk" style="color: rgb(149, 79, 114); text-decoration: underline; "><span style="color: blue; ">john.webber@nbi.ac.uk</span></a></span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); ">Web:</span><span> </span><span style="color: rgb(31, 73, 125); "> <span class="Apple-converted-space"> </span><a href="http://www.nbi.ac.uk/" style="color: rgb(149, 79, 114); text-decoration: underline; "><span style="color: blue; ">http://www.nbi.ac.uk</span></a></span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; line-height: 12pt; background-color: white; ">
<span style="color: rgb(31, 73, 125); ">Tel:</span><span> </span><span style="color: rgb(31, 73, 125); "> +44(0)1603 450 818<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); "> </span></div>
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<span style="color: rgb(31, 73, 125); ">Helpdesk (Tel): 1234</span><span> </span><span style="color: rgb(31, 73, 125); "> HPC Support (Web):</span><span> </span><span style="color: rgb(31, 73, 125); "> <span class="Apple-converted-space"> </span><a href="http://hpc.nbi.ac.uk/" style="color: rgb(149, 79, 114); text-decoration: underline; "><span style="color: blue; ">http://hpc.nbi.ac.uk</span></a>
(NBI internal)<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); "> HPC Support (Tel):</span><span> </span><span style="color: rgb(31, 73, 125); "> 2003 (NBI internal)<o:p></o:p></span></div>
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<span style="color: rgb(31, 73, 125); "> </span><span style="color: rgb(15, 18, 111); "><o:p></o:p></span></div>
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<i><span style="color: rgb(31, 73, 125); ">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: rgb(15, 18, 111); "><o:p></o:p></span></div>
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