TypeError: Database A_xenica_combined.fastq_screed is not a proper screed database

[johnsolk]

I'm using screed 1.0 to convert a fastq file to a fasta file, but it appears that the db file is being written over in the second step.

First:

screed db A_xenica_combined.fastq

With this result:

-rw-r--r-- 1 ljcohen ljcohen 86451998720 Aug 15 20:17 A_xenica_combined.fastq_screed

Second, this command:

(ONT) ljcohen@c11-71:~/A_xenica_promethION$ python -m screed dump_fasta A_xenica_combined.fastq_screed A_xenica_combined.fasta

With this result:

Traceback (most recent call last):
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/openscreed.py", line 147, in __init__
    admin_table, = res.fetchone()
TypeError: 'NoneType' object is not iterable

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/__main__.py", line 52, in <module>
    main()
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/__main__.py", line 48, in main
    ScreedCommands()
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/__main__.py", line 44, in __init__
    cmd(sys.argv[2:])
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/dump_fasta.py", line 27, in main
    n = ToFasta(args.dbfile, args.outputfile)
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/conversion.py", line 75, in ToFasta
    db = ScreedDB(dbFile)
  File "/home/ljcohen/miniconda3/envs/ONT/lib/python3.6/site-packages/screed/openscreed.py", line 157, in __init__
    % self._filepath)
TypeError: Database A_xenica_combined.fastq_screed is not a proper screed database

And now my file is only 8K:

-rw-r--r-- 1 ljcohen ljcohen        8192 Aug 16 09:25 A_xenica_combined.fastq_screed

Contents of file:

(ONT) ljcohen@c11-71:~/A_xenica_promethION$ cat A_xenica_combined.fastq_screed
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ LE SCREEDADMIN (id INTEGER PRIMARY KEY, FIELDNAME TEXT, ROLE TEXT)

Screed was installed with khmer 3.0.0a1 from the bioconda channel in a Python 3 conda 4.5.4 environment running on Ubuntu 16.04.4 LTS on the UCD farm cluster.

(ONT) ljcohen@c11-71:~/A_xenica_promethION$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.4 LTS
Release:	16.04
Codename:	xenial
(ONT) ljcohen@c11-71:~/A_xenica_promethION$ python
Python 3.6.6 | packaged by conda-forge | (default, Jul 26 2018, 09:53:17) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux
>>>