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Flipajs / FERDA

MIT License
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database disk image is malformed #7

Closed bcasillas closed 6 years ago

bcasillas commented 6 years ago

While loading project, after parallelization run in cluster, part 19_rm.sqlite3 was corrupted (loading stops with error pasted below). Workaround: copy file again from cluster.

Initializing db at /home/casillas/Documents/FNWD/HH1_PRE_cluster/temp/part19_rm.sqlite3 Traceback (most recent call last): File "/home/casillas/ferda/FERDA/core/background_computer.py", line 135, in check_parallelization assembly_after_parallelization(self) File "/home/casillas/ferda/FERDA/core/bg_computer_assembling.py", line 74, in assembly_after_parallelization mergeparts(bgcomp.project.gm, g, relevant_vertices, bgcomp.project, rmold, chm) File "/home/casillas/ferda/FERDA/core/bg_computer_assembling.py", line 293, in merge_parts old_regions = old_rm[old_rids] File "/home/casillas/ferda/FERDA/core/region/region_manager.py", line 256, in getitem self.dbsearch(result, sql_ids) File "/home/casillas/ferda/FERDA/core/region/region_manager.py", line 321, in dbsearch rows = self.cur.fetchall() sqlite3.DatabaseError: database disk image is malformed

Flipajs commented 6 years ago

It happens when some files are not copied properly (e. g. copied from cluster while some error occurred).