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dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics
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Import fails with xeniumranger 3 #38

Open asmitaL99 opened 1 month ago

asmitaL99 commented 1 month ago

2024-10-02 10:35:12 [runtime] (run:local) ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_IMPORT_TRANSCRIPT_ASSIGNMENTS.fork0.join 2024-10-02 10:35:28 [runtime] (failed) ID.IMPORT_SEGMENTATION.XENIUM_RANGER_CS.XR_IMPORT_TRANSCRIPT_ASSIGNMENTS

[error] Pipestance failed. Error log at: project-id/XENIUM_RANGER_CS/XR_IMPORT_TRANSCRIPT_ASSIGNMENTS/fork0/join-u354efd682e/_errors

Log message: Traceback (most recent call last): File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/external/martian/adapters/python/martian_shell.py", line 648, in _main stage.main() File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/external/martian/adapters/python/martian_shell.py", line 617, in main self._run( File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/external/martian/adapters/python/martian_shell.py", line 564, in _run cmd() File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/external/martian/adapters/python/martian_shell.py", line 618, in lambda: self._module.join(args, outs, chunk_defs, chunk_outs) File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/mro/insitu/stages/xr_import_transcripts/init.py", line 97, in join import_transcript_assignments.join( File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/lib/python/turing/engine/xenium_ranger/stages/import_transcript_assignments.py", line 69, in join results = import_baysor_transcript_assignments( File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/lib/python/turing/engine/xenium_ranger/import_segmentation/import_transcripts.py", line 84, in import_baysor_transcript_assignments baysor_results = BaysorSegmentationResults.deserialize( File "/home/asmilags/proseg/Xen_KPMP_038/xeniumranger-xenium3.0/lib/python/turing/engine/xenium_ranger/import_segmentation/baysor.py", line 389, in deserialize raise MissingCellPolygon(cell_id_diffs) turing.engine.xenium_ranger.import_segmentation.baysor.MissingCellPolygon: Found cell IDs in transcript-assignments that are not present in viz-polygons. All cell IDs from transcript-assignments must be present in viz-polygons. The following IDs are missing from viz-polygons: [ 2014 8653 9317 11058 11135 11175 12519 12586 15077 15091 16187 18530 19737 20041 20480 20581 23401 23738 24371 25229 26995 27589 29680 29893 29924 31984 33471 35002 39114 40135 43175 43442 44532 45535 45673 47263 52194 52457 53885 54509 54610 55001 55512 55601 58065 62005 63196 63790 63835 65668 65849 66316 68669 69243 70346 72397 72480 73470 74226 74714 76743 77135 78034 78890 80067 80098 80197 80342 80388 81917 82369 82549 82603 83755 84603 85177 85245 86150 86219 87024 87368 87554 89464 92239 93249 93280 94134 94587 94820 95007 95511 95737 98843 101275 101555 101772 102601 102769 103061 103427 103439 104129 104145 104454 104706 104807 104969 106869 107207 107527 108525 108806 109009 109787 110235 110374 110717 111191 111586 111793 111897 112284 113081 114035 115060 115426 115428 115766 115868 116314 116319 116811 116886 116907 117049 118265 118646 118847 120235 120389 120629 121239 121437 121787 121951 122237 122901 123328 123669 123701 124447 125126 125302 125888 126099 126257 126563 126766 127044 127350 127838 128136 128687 128787 128916 129403 129626 129674 129862 130002 130256 130280 130612 130770 130970 131292 131432 132197 132513 132721 132788 132959 133072 133079 133080 133606 133820 133896 134048 134068 134171 134519 134584 135223 135241 135292 135487 136036 136402 136709 136839 136882 136935 137000 137227 137375 137511 138148 138258 138352 138481 138483 138677 138899 138929 139070 139375 139648 139861 139981 140095 140267 140394 140403 140493 140685 141054 141120 141342 141393 141522 141545]

Waiting 6 seconds for UI to do final refresh. Pipestance failed. Use --noexit option to keep UI running after failure.

2024-10-02 10:35:34 Shutting down. Saving pipestance info to "/home/asmilags/proseg/Xen_KPMP_038/project-id/project-id.mri.tgz" tar: Removing leading /' from member names tar: Removing leading/' from hard link targets For assistance, upload this file to 10x Genomics by running:

xeniumranger upload "/home/asmilags/proseg/Xen_KPMP_038/project-id/project-id.mri.tgz"

dcjones commented 1 month ago

It seems xeniumranger 3 introduced some incompatibilities. I just released proseg 1.1.6 which should fix these issues. Thanks for reporting!