1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
|
Running Test Bathches:
1. Download TestReferences and TestFiles from XXX and put in same location as mothur executable
2. Download TestBatches and put in same location as mothur's executable
3. Download mothur's external programs: vsearch, uchime, prefetch and fasterq-dump. Available with mothur's executable versions
4. Run an individual batch test:
sarahwestcott$ cd mothur_test_batches
mothur_test_batches sarahwestcott$ ls
TestBatches TestReferences fasterq-dump prefetch vsearch
TestFiles mothur uchime
mothur_test_batches sarahwestcott$ ./mothur "./TestBatches/align.seqs/batch"
Output to screen will look like:
mothur > set.dir(input=./TestFiles, output=./TestResults/align.seqs, tempdefault=./TestReferences)
Mothur's directories:
outputDir=/Users/sarahwestcott/Desktop/mothur_test_batches/align.seqs/
inputDir=/Users/sarahwestcott/Desktop/mothur_test_batches/TestFiles/
tempDefault=/Users/sarahwestcott/Desktop/mothur_test_batches/TestReferences/
mothur > set.logfile(name=alignseqs.logfile)
...
5. Run all test batches:
sarahwestcott$ cd mothur_test_batches
mothur_test_batches sarahwestcott$ ls
TestBatches TestReferences fasterq-dump prefetch vsearch
TestFiles mothur uchime
mothur_test_batches sarahwestcott$ ./mothur "./TestBatches/master_batch"
Output to screen will look like:
...
Batch Mode
/*****************************************************************************/
mothur > set.dir(input=./TestFiles, output=./TestResults/align.seqs, tempdefault=./TestReferences)
Mothur's directories:
outputDir=/Users/swestcott/Desktop/batchTest/TestResults/align.seqs/
inputDir=/Users/swestcott/Desktop/batchTest/TestFiles/
tempDefault=/Users/swestcott/Desktop/batchTest/TestReferences/
mothur > set.logfile(name=alignseqs.logfile)
Setting logfile name to /Users/swestcott/Desktop/batchTest/TestFiles/alignseqs.logfile
...
|
