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Re: [scipion-users] Cryosparc 2D - Scipion issue
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From: <pc...@cn...> - 2021-08-25 06:08:03
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<div dir='auto'>Hi Dmitry, give us some time. Probably until next week to investigate.</div><div class="gmail_extra"><br><div class="gmail_quote">El 23 ago. 2021 22:22, "Dmitry A. Semchonok" <sem...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div> <div dir="auto"><br /></div><div dir="auto"><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Dear colleagues,</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">After the installation of the latest modules for the cryosparc//relion the 2D classification in SCIPION3 is finishing with the error, although in cryosparc itself the 2D classification finished correctly.</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Could you please advice how to fix that?</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Thank you</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Sincerely,</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Dmitry</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important"> </span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">Creating the output...</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00032: Traceback (most recent call last):</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00033: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 197, in run</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00034: self._run()</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00035: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _run</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00036: resultFiles = self._runFunc()</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00037: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 244, in _runFunc</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00038: return self._func(*self._args)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00039: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/protocols/protocol_cryosparc2d.py", line 282, in createOutputStep</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00040: convertCs2Star(args)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00041: File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/cryosparc2/convert/convert.py", line 99, in convertCs2Star</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00042: df = star.remove_deprecated_relion2(df, inplace=True)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00043: AttributeError: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00044: Protocol failed: module 'pyem.star' has no attribute 'remove_deprecated_relion2'</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00045: FAILED: createOutputStep, step 3, time 2021-08-22 13:57:<a href="tel:23.830243" style="overflow-wrap:!important;color:rgb( 0 , 151 , 167 ) !important">23.830243</a></span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00046: *** Last status is failed</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00047: Not cleaning temp folder since SCIPION_DEBUG_NOCLEAN is set to True.</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"><span style="overflow-wrap:!important">00048: ------------------- PROTOCOL FAILED (DONE 3/3)</span></p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"> </p><p style="margin:0cm;font-size:11pt;font-family:'calibri' , sans-serif;overflow-wrap:!important"> </p></div></div> </blockquote></div><br></div> |
