sourmash lca classify db error message isn't very friendly

[taylorreiter]

I recently ran sourmash lca classify with a corrupted database inside of a snakemake workflow, producing the following error message:

rule run_sourmash_LCA_sylv:
    input: inputs/genbank_lca/genbank-k31.lca.json, outputs/sylvestris/Olea_europaea_1kb_scaffolds-k31.fa.sig
    output: outputs/sourmash_lca/Olea_europaea_1kb_scaffolds-k31.lca.txt
    jobid: 1

Activating conda environment /home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7.
Traceback (most recent call last):k_lca/genbank-k31.lca.json
  File "/home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7/bin/sourmash", line 11, in <module>
    load_entry_point('sourmash', 'console_scripts', 'sourmash')()
  File "/home/ubuntu/olive_genome/dummy/src/sourmash/sourmash_lib/__main__.py", line 63, in main
    cmd(sys.argv[2:])
  File "/home/ubuntu/olive_genome/dummy/src/sourmash/sourmash_lib/lca/__main__.py", line 46, in main
    cmd(sysv_args[1:])
  File "/home/ubuntu/olive_genome/dummy/src/sourmash/sourmash_lib/lca/command_classify.py", line 111, in classify
    dblist, ksize, scaled = lca_utils.load_databases(args.db, args.scaled)
  File "/home/ubuntu/olive_genome/dummy/src/sourmash/sourmash_lib/lca/lca_utils.py", line 249, in load_databases
    lca_db.load(db_name)
  File "/home/ubuntu/olive_genome/dummy/src/sourmash/sourmash_lib/lca/lca_utils.py", line 139, in load
    load_d = json.load(fp)
  File "/home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7/lib/python3.6/json/__init__.py", line 299, in load
    parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
  File "/home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7/lib/python3.6/json/__init__.py", line 354, in loads
    return _default_decoder.decode(s)
  File "/home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7/lib/python3.6/json/decoder.py", line 339, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7/lib/python3.6/json/decoder.py", line 357, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
Error in rule run_sourmash_LCA_sylv:
    jobid: 1
    output: outputs/sourmash_lca/Olea_europaea_1kb_scaffolds-k31.lca.txt

RuleException:
CalledProcessError in line 59 of /home/ubuntu/olive_genome/dummy/sourmashlca.snakefile:
Command 'source activate /home/ubuntu/olive_genome/dummy/.snakemake/conda/54f9bee7; set -euo pipefail;  
    sourmash lca classify --db inputs/genbank_lca/genbank-k31.lca.json --query outputs/sylvestris/Olea_europaea_1kb_scaffolds-k31.fa.sig -o outputs/sourmash_lca/Olea_europaea_1kb_scaffolds-k31.lca.txt ' returned non-zero exit status 1.
  File "/home/ubuntu/olive_genome/dummy/sourmashlca.snakefile", line 59, in __rule_run_sourmash_LCA_sylv
  File "/home/ubuntu/miniconda3/envs/snakemake/lib/python3.6/concurrent/futures/thread.py", line 55, in run

As @titus indicated, this is from a corrupted database. However, this error message wasn't very friendly. A more informative/friendly error message would be helpful!

[ctb]

Fixed in #390 aae3c49