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updated .gitignore to ignore samui output directory and modified scri…
…pt to make samui directories for xenium samples
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935958 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 10 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X99_1225A' Executing queued functions logger.py:27 | ||
| INFO X99_1225A Adding coords 'coords' logger.py:27 | ||
| INFO X99_1225A Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:33] INFO X99_1225A Concatenating and compressing chunks logger.py:27 | ||
| [11:23:35] INFO Writing compressed chunks for Genes: 8861839 logger.py:27 | ||
| bytes | ||
| INFO X99_1225A Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X99_1225A Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| INFO X99_1225A Adding csv feature 'Domain of Cell' logger.py:27 | ||
| [11:23:36] INFO X99_1225A Adding csv feature 'nCounts' logger.py:27 | ||
| INFO X99_1225A Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X99_1225A Adding csv feature 'Cell Area' logger.py:27 | ||
| INFO X99_1225A Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X99_1225A' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X99_1225A | ||
| **** Job ends **** | ||
| Wed Nov 27 11:23:37 AM EST 2024 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935959 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 11 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X99_1225B' Executing queued functions logger.py:27 | ||
| INFO X99_1225B Adding coords 'coords' logger.py:27 | ||
| INFO X99_1225B Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:22] INFO X99_1225B Concatenating and compressing chunks logger.py:27 | ||
| [11:23:07] INFO Writing compressed chunks for Genes: 6352598 logger.py:27 | ||
| bytes | ||
| [11:23:08] INFO X99_1225B Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X99_1225B Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| INFO X99_1225B Adding csv feature 'Domain of Cell' logger.py:27 | ||
| INFO X99_1225B Adding csv feature 'nCounts' logger.py:27 | ||
| INFO X99_1225B Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X99_1225B Adding csv feature 'Cell Area' logger.py:27 | ||
| INFO X99_1225B Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X99_1225B' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X99_1225B | ||
| **** Job ends **** | ||
| Wed Nov 27 11:23:09 AM EST 2024 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935960 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 12 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X99_8741C' Executing queued functions logger.py:27 | ||
| INFO X99_8741C Adding coords 'coords' logger.py:27 | ||
| INFO X99_8741C Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:16] INFO X99_8741C Concatenating and compressing chunks logger.py:27 | ||
| [11:22:51] INFO Writing compressed chunks for Genes: 4962067 logger.py:27 | ||
| bytes | ||
| INFO X99_8741C Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X99_8741C Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| INFO X99_8741C Adding csv feature 'Domain of Cell' logger.py:27 | ||
| INFO X99_8741C Adding csv feature 'nCounts' logger.py:27 | ||
| INFO X99_8741C Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X99_8741C Adding csv feature 'Cell Area' logger.py:27 | ||
| INFO X99_8741C Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X99_8741C' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X99_8741C | ||
| **** Job ends **** | ||
| Wed Nov 27 11:22:52 AM EST 2024 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935948 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 13 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X99_8741D' Executing queued functions logger.py:27 | ||
| INFO X99_8741D Adding coords 'coords' logger.py:27 | ||
| INFO X99_8741D Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:14] INFO X99_8741D Concatenating and compressing chunks logger.py:27 | ||
| [11:22:43] INFO Writing compressed chunks for Genes: 4350402 logger.py:27 | ||
| bytes | ||
| INFO X99_8741D Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X99_8741D Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| [11:22:44] INFO X99_8741D Adding csv feature 'Domain of Cell' logger.py:27 | ||
| INFO X99_8741D Adding csv feature 'nCounts' logger.py:27 | ||
| INFO X99_8741D Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X99_8741D Adding csv feature 'Cell Area' logger.py:27 | ||
| INFO X99_8741D Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X99_8741D' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X99_8741D | ||
| **** Job ends **** | ||
| Wed Nov 27 11:22:44 AM EST 2024 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935950 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 2 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X36_5459B' Executing queued functions logger.py:27 | ||
| INFO X36_5459B Adding coords 'coords' logger.py:27 | ||
| INFO X36_5459B Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:17] INFO X36_5459B Concatenating and compressing chunks logger.py:27 | ||
| [11:22:55] INFO Writing compressed chunks for Genes: 5357624 logger.py:27 | ||
| bytes | ||
| INFO X36_5459B Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X36_5459B Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| INFO X36_5459B Adding csv feature 'Domain of Cell' logger.py:27 | ||
| INFO X36_5459B Adding csv feature 'nCounts' logger.py:27 | ||
| [11:22:56] INFO X36_5459B Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X36_5459B Adding csv feature 'Cell Area' logger.py:27 | ||
| INFO X36_5459B Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X36_5459B' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X36_5459B | ||
| **** Job ends **** | ||
| Wed Nov 27 11:22:56 AM EST 2024 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935951 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 3 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X36_8667C' Executing queued functions logger.py:27 | ||
| INFO X36_8667C Adding coords 'coords' logger.py:27 | ||
| INFO X36_8667C Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:22] INFO X36_8667C Concatenating and compressing chunks logger.py:27 | ||
| [11:23:02] INFO Writing compressed chunks for Genes: 5884573 logger.py:27 | ||
| bytes | ||
| INFO X36_8667C Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X36_8667C Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| INFO X36_8667C Adding csv feature 'Domain of Cell' logger.py:27 | ||
| INFO X36_8667C Adding csv feature 'nCounts' logger.py:27 | ||
| INFO X36_8667C Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X36_8667C Adding csv feature 'Cell Area' logger.py:27 | ||
| [11:23:03] INFO X36_8667C Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X36_8667C' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X36_8667C | ||
| **** Job ends **** | ||
| Wed Nov 27 11:23:03 AM EST 2024 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| date: Wed Nov 27 11:21:48 AM EST 2024 | ||
| **** JHPCE info **** | ||
| User: rmiller | ||
| Job id: 10935952 | ||
| Job name: 04samui | ||
| Hostname: | ||
| Task id: 4 | ||
| Loading LIBD SLURM module for samui/1.0.0-next.49 | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2: | ||
| * 'allow_mutation' has been removed | ||
| warnings.warn(message, UserWarning) | ||
| /jhpce/shared/libd/core/samui/1.0.0-next.49/samui_env/lib/python3.10/site-packages/anndata/__init__.py:55: FutureWarning: `anndata.read` is deprecated, use `anndata.read_h5ad` instead. `ad.read` will be removed in mid 2024. | ||
| warnings.warn( | ||
| Using 366 genes as features. | ||
| [11:21:54] INFO 'X86_reg1' Executing queued functions logger.py:27 | ||
| INFO X86_reg1 Adding coords 'coords' logger.py:27 | ||
| INFO X86_reg1 Adding chunked feature 'Genes' logger.py:27 | ||
| [11:22:22] INFO X86_reg1 Concatenating and compressing chunks logger.py:27 | ||
| [11:23:09] INFO Writing compressed chunks for Genes: 6956514 logger.py:27 | ||
| bytes | ||
| INFO X86_reg1 Adding csv feature 'Banksy-Cluster' logger.py:27 | ||
| INFO X86_reg1 Adding csv feature 'Banksy Cluster logger.py:27 | ||
| Grouped' | ||
| INFO X86_reg1 Adding csv feature 'Domain of Cell' logger.py:27 | ||
| INFO X86_reg1 Adding csv feature 'nCounts' logger.py:27 | ||
| INFO X86_reg1 Adding csv feature 'nGenes' logger.py:27 | ||
| INFO X86_reg1 Adding csv feature 'Cell Area' logger.py:27 | ||
| [11:23:10] INFO X86_reg1 Adding csv feature 'Nucleus Area' logger.py:27 | ||
| INFO 'X86_reg1' written to logger.py:27 | ||
| /dcs04/lieber/marmaypag/spatialHYP_LIBD4195/spa | ||
| tial_HYP/xenium_HYP/code/13-samui/../../../xeni | ||
| um_HYP/processed-data/12-samui/X86_reg1 | ||
| **** Job ends **** | ||
| Wed Nov 27 11:23:10 AM EST 2024 |
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