Yabish returning results inconsistently

[GoogleCodeExporter]

When running this command:

./yabish blast -p blastn -d nt -o myoutput.bls -i ../../test_data/a

which stages in a directory which looks like this:

├── a
│   ├── b
│   │   ├── aa123456.fa
│   │   └── f3
│   ├── f1
│   ├── f2
│   └── some.fa

... yabish does not always fetch the resulting files. The jobs run and the 
results are visible through yabife. This causes the tests to fail as they call 
this to test the blast tools.

Of five test runs the results looked like this (only run3 was successful):

run1
├── 1
│   └── STDERR.txt
└── 2
    ├── some.fa.bls
    ├── STDERR.txt
    └── STDOUT.txt
run2
├── 1
│   ├── STDERR.txt
│   └── STDOUT.txt
└── 2
    ├── some.fa.bls
    ├── STDERR.txt
    └── STDOUT.txt
run3
├── 1
│   ├── some.fa.bls
│   ├── STDERR.txt
│   └── STDOUT.txt
└── 2
    ├── aa123456.fa.bls
    ├── STDERR.txt
    └── STDOUT.txt
run4
└── 2
    ├── aa123456.fa.bls
    ├── STDERR.txt
    └── STDOUT.txt
run5
└── 1
    ├── some.fa.bls
    ├── STDERR.txt
    └── STDOUT.txt

Original issue reported on code.google.com by amacgregor on 30 Jan 2012 at 3:21

• Merged into: #118

[GoogleCodeExporter]

It is because the complete status is set prior to stageout.

See #118

Original comment by aahun...@gmail.com on 1 Feb 2012 at 6:19

• Changed state: Invalid

[GoogleCodeExporter]

Original comment by amacgregor on 1 Mar 2012 at 2:05

• Changed state: Duplicate