First want validating original assemblies
LazyFosmid_datacapture.mov

#fail. 

Not all carried out using consistent parameters.
----

Fosmids to date
17  
18
19
21
22
24
25
26
29





--

New conversions 
20
23 (no 23 found)
27 (no 27)
28 (no 28)
30 (no 30)
26 (redo- orginal parameters wrong)
31 
32
33



code

./fastq-dump -A SR327420 /Volumes/Bay3/OysterGenomeBGI/SRX089207/SRX089207/SRR327420/SRR327420.sra -O /Volumes/Bay4\ scratch/BGIfastaOUTPUT

--
drive full changing up disks to NGS Drive.

./fastq-dump -A SR327431 /Volumes/NGS\ Drive/OtherData/OysterGenomeBGI/SRX089214/SRR327431/SRR327431.sra -O /Volumes/NGS\ Drive/OtherData/OysterGenomeBGI/Oyster_SRAconverts

./fastq-dump -A SR327433 /Volumes/NGS\ Drive/OtherData/OysterGenomeBGI/SRX089216/SRR327433/SRR327433.sra -O /Volumes/NGS\ Drive/OtherData/OysterGenomeBGI/Oyster_SRAconverts


--
Going to take 26 through server AND v5.0 to check flow.
*interesting 5.0 asks for paired end info. - server did not.

Going with 150-250 paired end.

AND maybe Galaxy too. 
Note file size of raw data is 80 GB

---
Hard drive greenbird (SDD filled)
need to find way to assign tmp


Server import #failed twice.

Local import on v5 is working.



Assembling Reads in v5

selected simple (fast) consensus genera





Move most other fosmids to disk so can convert on different machine.

./fastq-dump -A SR327431 /Volumes/NGS\ Drive/OtherData/OysterGenomeBGI/SRX089214/SRR327431/SRR327431.sra -O /Volumes/NGS\ Drive/OtherData/OysterGenomeBGI/Oyster_SRAconverts


PROBLEM / ISSUE 

On mini, only one output file (fastq) is generated, on green bird two files are generated. 

adding --split-files to ./fastq-dump command

March 9
Uploading raw data to server
20
33
33 _1
31
37 _1 _2 (1.5) no "paired"
37 _1 _2 (1.4) ok
37 _1 _2 (1.2) ok
39 _1
49




*issue, 37 up as _1 and _2 but appear as single end.
33 and 39 are coming up 2 files  with "paired" many more. seem correct. (only _1 evident)





Assembly


IGNORE non specifics



Going in to fosmid folder, then specific once assembly starts.



Checking original consensus files (temp/BGI)

17 - corrupt
21 - ok (conflict annotations)
22 - corrupt
24 - ok (ca)
29 - ok
18 - corrupt
19 - ok (ca)
25 - ok

March 12
39
33
49
40
42
47
43
52
53
55