search

weberlab-hhu / Helixer

Using Deep Learning to predict gene annotations
GNU General Public License v3.0
165 stars 28 forks source link

error message = 'No space left on device" #139

Closed AlonsoLongoria23 closed 1 month ago

AlonsoLongoria23 commented 3 months ago

Hello, I'm running helixer and I encounter this error

starting to load test data into memory.. For h5 starting with species = b'': x shape: (17374, 213840, 4) Data loading of 17374 (total so far 17374) samples of data/X into memory took 140.20 secs Compressed data size of data/X is at least 1.5990 GB

setting self.n_seqs to 17374, bc that is len of data/X Traceback (most recent call last): File "/usr/local/bin/Helixer.py", line 248, in main() File "/usr/local/bin/Helixer.py", line 228, in main model.run() File "/usr/local/lib/python3.8/dist-packages/helixer/prediction/HelixerModel.py", line 1031, in run self._make_predictions(model) File "/usr/local/lib/python3.8/dist-packages/helixer/prediction/HelixerModel.py", line 892, in _make_predictions pred_out[dset_name][old_len:] = pred_dset File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "/usr/local/lib/python3.8/dist-packages/h5py/_hl/dataset.py", line 999, in setitem self.id.write(mspace, fspace, val, mtype, dxpl=self._dxpl) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5d.pyx", line 282, in h5py.h5d.DatasetID.write File "h5py/_proxy.pyx", line 115, in h5py._proxy.dset_rw OSError: [Errno 28] Can't synchronously write data (file write failed: time = Wed Aug 7 21:49:41 2024 , filename = '/tmp/tmpx_8rm915/tmppredictions.h5', file descriptor = 5, errno = 28, error message = 'No space left on device', buf = 0x797bc7e5, total write size = 992670, bytes this sub-write = 992670, bytes actually written = 18446744073709551615, offset = 0) INFO: Cleaning up image...

the command I used was

singularity run --nv helixer-docker_helixer_v0.3.3_cuda_11.8.0-cudnn8.sif Helixer.py --fasta-path GCA_023634145.1_fThyThy.pri.20220222_genomic.fna.gz --lineage vertebrate --gff-output-path thymallus_thymallus_complete_helixer.gff3 --subsequence-length 213840 --overlap-offset 106920 --overlap-core-length 160380

Environment OS: Ubuntu Container: Singularity version 3.8.0 Web tool: Not used

felicitas215 commented 3 months ago

Hello, it looks like your /tmp directory is running out of disk space. Try using --temporary-dir to specify a different location where the temporary files created by Helixer can be stored.