Hi, I am getting this error with around half my scRNA samples.
2023-12-13 16:14:49,603|[UCD]|INFO: Starting UCDeconvolveBASE Run. | Timer Started.
Preprocessing Dataset | 100% (5 of 5) |##| Elapsed Time: 0:00:00 Time: 0:00:00
2023-12-13 16:14:51,526|[UCD]|INFO: Uploading Data | Timer Started.
2023-12-13 16:14:53,916|[UCD]|INFO: Upload Complete | Elapsed Time: 2.389 (s)
Waiting For Submission : RUNNING | Queue Size : 1 | | |#| 1 Elapsed Time: 0:00:02
Waiting For Completion | 100% (1118 of 1118) || Elapsed Time: 0:00:16 Time: 0:00:16
2023-12-13 16:15:14,875|[UCD]|INFO: Download Results | Timer Started.
2023-12-13 16:15:16,578|[UCD]|INFO: Download Complete | Elapsed Time: 1.703 (s)
2023-12-13 16:15:16,579|[UCD]|INFO: Run Complete | Elapsed Time: 26.974 (s)
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
Cell In[38], line 1
----> 1 samples["1956A"] = scRNA_pipeline(samples["1956A"])
Cell In[3], line 22, in scRNA_pipeline(adata)
19 sc.tl.rank_genes_groups(adata, 'leiden', method='t-test')
20 sc.pl.rank_genes_groups(adata, n_genes=10, sharey=False)
---> 22 ucd.tl.base(adata)
23 ucd.pl.base_clustermap(adata, groupby = 'leiden', category = 'raw', n_top_celltypes = 75)
24 ucd.utils.assign_top_celltypes(adata, category = "raw", groupby = "leiden")
File ~/.local/lib/python3.9/site-packages/ucdeconvolve/_tools/_base.py:160, in deconvolve_base(data, token, split, sort, propagate, return_results, key_added, use_raw, verbosity)
154 with ucdutils.timer(ucdlogger, "Download Results", "Download Complete", logging.INFO):
155
156 # Include method
157 params['method'] = 'base'
159 adata_mixture_orig = \
--> 160 ucdapiutils.download_and_attach_results(
161 adata_mixture_orig,
162 results['download_url'],
163 metadata['runtype'],
164 key_added,
165 params)
167 # Remove and clean up run
168 ucdapi.remove_run(metadata['run_id'], token)
File ~/.local/lib/python3.9/site-packages/ucdeconvolve/_api/_apiutils.py:274, in download_and_attach_results(adata, download_url, runtype, key_added, additional_runinfo)
270 # Save function for base
271 if runtype == 'base':
272
273 # Get keys from file
--> 274 with h5py.File(temp_file.name) as hfile:
275 keys = list(hfile.keys())
277 # Iterate each results key and load
File ~/.local/lib/python3.9/site-packages/h5py/_hl/files.py:567, in File.__init__(self, name, mode, driver, libver, userblock_size, swmr, rdcc_nslots, rdcc_nbytes, rdcc_w0, track_order, fs_strategy, fs_persist, fs_threshold, fs_page_size, page_buf_size, min_meta_keep, min_raw_keep, locking, alignment_threshold, alignment_interval, meta_block_size, **kwds)
558 fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,
559 locking, page_buf_size, min_meta_keep, min_raw_keep,
560 alignment_threshold=alignment_threshold,
561 alignment_interval=alignment_interval,
562 meta_block_size=meta_block_size,
563 **kwds)
564 fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy,
565 fs_persist=fs_persist, fs_threshold=fs_threshold,
566 fs_page_size=fs_page_size)
--> 567 fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
569 if isinstance(libver, tuple):
570 self._libver = libver
File ~/.local/lib/python3.9/site-packages/h5py/_hl/files.py:231, in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
229 if swmr and swmr_support:
230 flags |= h5f.ACC_SWMR_READ
--> 231 fid = h5f.open(name, flags, fapl=fapl)
232 elif mode == 'r+':
233 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()
File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()
File h5py/h5f.pyx:106, in h5py.h5f.open()
OSError: Unable to open file (file signature not found)
Hi, I am getting this error with around half my scRNA samples.