Crashed for unknown reasons

[ggirelli]

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This issue affects

• GPSeq analysis of FISH data (gpseq_fromfish)

What did you do (e.g., steps to reproduce)

Ran as in iFISH-singLoc-snakemake.

What happened instead?

...........................................................................
.../pygpseq/fish/image.py in analyze_field_of_view(sid=4, data=               x            y          z ...   x...6723 ...  564   954  26

[1958 rows x 15 columns], im2fov={1: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_001_cmle.tif', 2: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_002_cmle.tif', 3: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_003_cmle.tif', 4: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_004_cmle.tif', 5: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_005_cmle.tif', 6: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_006_cmle.tif', 7: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_007_cmle.tif', 8: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_008_cmle.tif', 9: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_009_cmle.tif', 10: '/media/MiSo/iFISH-singleLocus-analysis/input/decon/iAM196_20180830_002//dapi_010_cmle.tif', ...}, dilate_factor=5, istruct=array([[[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
     ...[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]]], dtype=uint8), aspect=[300.0, 130.0, 130.0], mask_dir='/media/MiSo/iFISH-singleLocus-analysis/input/cmask/iAM196_20180830_002/', mask_prefix='cmask_', plotCompartments=True, pole_fraction=0.25, outdir='/media/MiSo/iFISH-singleLocus-DOTTER/output/iFIS...orrected-preFitting/fromfish/iAM196_20180830_002/', noplot=False, labeled=False, compressed=True, dist_type=1, nbins=200, discard_dilation_mode=False, an_type=2, seg_type=2, mask2d_dir=None, verbose=False, debug=False, debug_dir='')
    158 
    159     # Export mask as PNG
    160     if not noplot:
    161         # Create png masks output directory
    162         maskdir = os.path.join(outdir, 'masks/')
--> 163         if not os.path.isdir(maskdir): os.mkdir(maskdir)
        maskdir = '/media/MiSo/iFISH-singleLocus-DOTTER/output/iFIS...ed-preFitting/fromfish/iAM196_20180830_002/masks/'
    164         imbname = os.path.splitext(os.path.basename(im2fov[sid]))[0]
    165 
    166         # Save default mask
    167         msg += printout("Saving default binary mask...", 3, v)

FileExistsError: [Errno 17] File exists: '/media/MiSo/iFISH-singleLocus-DOTTER/output/iFISH-singLoc-snakemake-rootOutput-CAcorrected-preFitting/fromfish/iAM196_20180830_002/masks/'
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Additional information

[stale]

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