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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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blobtools create: [ERROR:27] nodesDB ("--db") could not be read #95

Closed etvedte closed 4 years ago

etvedte commented 4 years ago

I ran blobtools create and it returned an error message stating nodes.dmp could not be read. Thinking this was related to the read only nature of the area of the filesystem where this was installed, I copied nodes.dmp to a different area and gave it read write and execute permissions. When I ran the following: blobtools create --db nodes.dmp -i reference.fasta -b sorted.bam -t blast.out -o my_first_blobplot

I saw the same error message: [ERROR:27] : nodesDB ("--db") /local/projects-t3/RDBKO/dana.quickmerge/pb.sqII+minion.LIG.3X.polished/blobtools/nodes.dmp could not be read.

When I ran with --names and --nodes instead, I got this:

Traceback (most recent call last): File "/usr/local/packages/blobtools/blobtools", line 7, in main() File "/usr/local/packages/blobtools-1.1/lib/interface.py", line 62, in main create.main() File "/usr/local/packages/blobtools-1.1/lib/create.py", line 103, in main nodesDB, nodesDB_f = BtIO.parseNodesDB(nodes=nodes_f, names=names_f, nodesDB=nodesDB_f, nodesDBdefault=nodesDB_default) File "/usr/local/packages/blobtools-1.1/lib/BtIO.py", line 619, in parseNodesDB writeNodesDB(nodesDB, nodesDB_f) File "/usr/local/packages/blobtools-1.1/lib/BtIO.py", line 660, in writeNodesDB with open(nodesDB_f, 'w') as fh: OSError: [Errno 30] Read-only file system: '/usr/local/packages/blobtools-1.1/lib/../data/nodesDB.txt'

Any idea how I can resolve this issue?

etvedte commented 4 years ago

If blobtools is installed in a filesystem area that is read-only, the user can use the --names /path/to/names.dmp --nodes /path/to/nodes.dmp and --db /path/to/nodesDB.txt parameters together, with the nodesDB.txt file in an area that has write permissions.