choosehappy
commented
3 days ago Looks like a tcga file, have you checked the md5sum to rule out corruption ?
On Jul 3, 2024 21:46, suminwei @.***> wrote:
Hi, I am getting the following error when trying to run histoqc on .svs files.
Command: python -m histoqc -c v2.1 -n 3 "./input_svs_test/*.svs"
Error: 2024-07-03 15:43:52,680 - INFO - -----Working on: ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs 1 of 15 2024-07-03 15:43:52,685 - INFO - -----Working on: ./input_svs_test/TCGA-EJ-5532-01Z-00-DX1.07548d1f-867f-4bca-a9f3-aaed043b8753.svs 2 of 15 2024-07-03 15:43:52,689 - INFO - -----Working on: ./input_svs_test/TCGA-EJ-A46E-01Z-00-DX1.DBF5A5EC-DCD9-44E9-8303-9F61BEAE44D0.svs 3 of 15 TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b) encountered. TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b) encountered. ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs: JPEG compression support is not configured. 2024-07-03 15:43:52,701 - ERROR - ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs - Error analyzing file (skipping): <class 'openslide.lowlevel.OpenSlideError'> An error produced by the OpenSlide library. Import this from openslide rather than from openslide.lowlevel. Unsupported TIFF compression: 7 ./input_svs_test/TCGA-EJ-A46E-01Z-00-DX1.DBF5A5EC-DCD9-44E9-8303-9F61BEAE44D0.svs: JPEG compression support is not configured. TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b) encountered. 2024-07-03 15:43:52,704 - ERROR - ./input_svs_test/TCGA-EJ-A46E-01Z-00-DX1.DBF5A5EC-DCD9-44E9-8303-9F61BEAE44D0.svs - Error analyzing file (skipping): <class 'openslide.lowlevel.OpenSlideError'> An error produced by the OpenSlide library. Import this from openslide rather than from openslide.lowlevel. Unsupported TIFF compression: 7 ./input_svs_test/TCGA-EJ-5532-01Z-00-DX1.07548d1f-867f-4bca-a9f3-aaed043b8753.svs: JPEG compression support is not configured. 2024-07-03 15:43:52,708 - ERROR - ./input_svs_test/TCGA-EJ-5532-01Z-00-DX1.07548d1f-867f-4bca-a9f3-aaed043b8753.svs - Error analyzing file (skipping): <class 'openslide.lowlevel.OpenSlideError'> An error produced by the OpenSlide library. Import this from openslide rather than from openslide.lowlevel. Unsupported TIFF compression: 7 20
I don't quite understand why it's not recognizing the .svs files? Thank you.
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suminwei
Hi, I am getting the following error when trying to run histoqc on .svs files.
Command:
python -m histoqc -c v2.1 -n 3 "./input_svs_test/*.svs"Error:
2024-07-03 15:43:52,680 - INFO - -----Working on: ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs 1 of 15 TIFFReadDirectory: Warning, Unknown field with tag 347 (0x15b) encountered. ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs: JPEG compression support is not configured. 2024-07-03 15:43:52,701 - ERROR - ./input_svs_test/TCGA-CH-5765-01Z-00-DX1.ee77679a-ef5a-4326-b72c-497532f60fb0.svs - Error analyzing file (skipping): <class 'openslide.lowlevel.OpenSlideError'> An error produced by the OpenSlide library. Import this from openslide rather than from openslide.lowlevel. Unsupported TIFF compression: 7I don't quite understand why it's not recognizing the .svs files? Thank you.