Open lhock17 opened 11 months ago
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.