temporary file problem - Githubissues

dieterich-lab / DCC

DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.

https://dieterichlab.org/software/

GNU General Public License v3.0

36 stars 20 forks source link

temporary file problem #29

Closed CDieterich closed 7 years ago

CDieterich commented 8 years ago

Traceback (most recent call last): File "/beegfs/homes/cdieterich/software/DCC/DCC_env/bin/DCC", line 11, in load_entry_point('DCC==0.4.4', 'console_scripts', 'DCC')() File "build/bdist.linux-x86_64/egg/DCC/main.py", line 429, in main File "/biosw/python2/2.7.11/lib/python2.7/multiprocessing/pool.py", line 251, in map return self.map_async(func, iterable, chunksize).get() File "/biosw/python2/2.7.11/lib/python2.7/multiprocessing/pool.py", line 567, in get raise self._value OSError: [Errno 2] No such file or directory: '/tmp/tmpQIwWxY' srun: error: amalthea: task 0: Exited with exit code 1

tjakobi commented 8 years ago

The -temp flag has been changed in the 0.4.4 release to -k. See the "Notes" section of the latest release: https://github.com/dieterich-lab/DCC/releases/tag/v0.4.4

The use of the old flag now is read as "-t emp ", thus creating a folder "emp" as temporary directory which is probably not intended.

Strangely, the error message refers to the system /tmp/ folder, which should not be used at all. I'll investigate this error.

tjakobi commented 8 years ago

Tested with same CLI parameters and most recent build from GitHub (0.4.4 is 3 commits or so behind) and could not reproduce the error. Maybe fixed by one of the latest fixes (41d2fd17a6163df1ea22d277e2c82d5fa1d8f1a0)? Please try again with the latest stable GitHub version via git clone/pull.