[rhall]

The reference uploader job does not appear in the web-based jobs monitor

It will not appear as a job in Portal, but is a job in the sense that it has a directory in the jobs folder. Finding the job folder for the upload (the jobs in portal will skip a number) and checking the logs should tell you why the upload failed.
When mapping back to an assembly it is always worth considering the unmapped data. Epilogue and prologue sequence that is of significant length and does not map could be the result of the HQ region of the trace not being very accurate, and will likely occur in overloaded data. If a ZMW initially has two polymerases loaded the initial part of the trace can include cross talk from the two sequences, it is possible for one of the polymerases to stop sequencing and the trace will start to produce good sequence, if this point is not found accurately then a read can have 'junk' none mapping sequence in the epilogue or prologue. While you should be aware of this it is generally not a problem, and is accounted for in the HGAP assembly process. The bigger issue when aligning back to an assembly is the % of none mapping subreads, this can give an indication if the assembly accounts for all the underlying data. You should be looking for a mapping % of ~80-90% if this value is much lower then I would take a look at the unmapped_subreads file, and see if the unmapped data can be accounted for by the degenerage contigs, from CA, that are not included in the resequencing.

[pag]

looks like some of my problems were partially due to the overzealousness of Ubuntu's garbage cleaning.

[DEBUG] 2014-01-03 11:37:34,125 [pbpy.smrtpipe.SmrtPipeContext createTemporaryDir 593] Attempting to create temp directory with dir prefix '/opt/smrtanalysis/tmpdir'
[ERROR] 2014-01-03 11:37:34,137 [pbpy.smrtpipe.SmrtPipeMain run 581] [Errno 2] No such file or directory: '/opt/smrtanalysis/tmpdir/tmpDpLq3C'

/opt/smrtanalysis/tmpdir -> /tmp/smrtanalysis (broken link)

The smrtanalysis directory is wiped out upon reboot of my computer, as the entire contents of /tmp are cleaned out (I cannot recall if this is during system shutdown or startup). Perhaps the start script (smrtportal's kodosd + smrtview's smrtanalysis?) should recreate this directory? For now, I'll create an /opt/tmp which will be a temporary directory that will be more persistent

Edit:
as smrtanalysis
sudo chmod 777 /opt/tmp
sudo chmod o+t /opt/tmp
mkdir /opt/tmp/smrtanalysis
chmod o+w /opt/tmp/smrtanalysis/
sudo ln -s /opt/tmp/ /opt/smrtanalysis/tmpdir
sudo chown -h smrtanalysis:smrtanalysis /opt/smrtanalysis/tmpdir
ls -la /

...
drwxrwxrwt 22 www-data www-data 12288 Jan 3 12:17 tmp
...

ls -la /opt/

drwxrwxrwt 2 root root 4096 Jan 3 12:09 tmp

ls -la /opt/tmp

drwxrwxrwx 2 smrtanalysis smrtanalysis 4096 Jan 3 12:14 smrtanalysis

ls -la /opt/smrtanalysis

...
lrwxrwxrwx 1 smrtanalysis smrtanalysis 9 Jan 3 12:24 tmpdir -> /opt/tmp/
...

my issues with not being able to see individual read data with bridgemapper data loaded are still persisting; however, reference uploader now works and I've started a BM job with apparent success

[pag]

5 screenshots of the bug - had to tar/gz them and do 2 per file in order to meet file size limits here.

[pag]

Wishlist

SMRTView

• Go to: keep zoom level (or add "jump to")
  I have a coordinate that I want to go to directly with centered view. I can copy-paste into the details panel my coord^* twice as both start and finish (and click the arrow icon, not "close" or enter). This centers the view at the coord. However, this defaults to a view that is quite zoomed out. To get to maximum zoom-in, I have to click the "A" magnifier and then click the + magnifier a few times. It would be nice if there was a way to either keep the zoom level when jumping to a single coordinate or add two more zoom icons - maximum zoom and minimum/no zoom. If there was a "jump to" button that just had a single coord for input (in addition to the current "go to" option) that would be great.
  
• View insertions from allow panning or show more positions (with insertions) at once
  I'd like to see indels on BOTH sides of a homopolymer run often (to see if my scaffold/consensus sequence is correct) or sometimes I would like to see indels that are in close proximity to others. Initially a cmp.h5 file involved in a quiver-based (SMRT pipeline 2.0.1) comparison to my 454-generated sequences would place additional bases congruent (agreeing) with the homopolymer run on a single side or the other (may have had to do with read direction). Using a bridgemapper (SMRT portal 2.1.1) generated comparison, some congruent bases may even be "inserted" into the middle of a homopolymer run (without other inserted bases of a non-congruent type) or be present on both "ends" of the homopolymer.
  
• Make GUI obey system file manager style
  Currently uses MSwindows-positioned minimize/maximize/restore/close buttons (right side), rather than my system style (left side). Does not populate global (file, etc) menu
  
• Use better-contrasting colors for insertions and substitutions.
  T against the insertion background or A against the substitution background can render the base unreadable depending on the quality score of the site in question and/or your monitor's contrast level. Use of a black or white text color for currently same-colored bases or the use of a novel color for the background (e.g. cyan, pink, purple) instead of green/blue/red/yellow may be warranted.
  

* oocalc/msoffice copy of a cell copies also a carriage return. This means that control-V doesn't quite work visually within the box. A simple middle click doesn't work, but that's office's issue (as neither highlighting a cell nor control-C copy to the xclipboard). Control-V seems to function properly though. I have a shortcut on my system to paste minus the CR using control+middle click. I believe this was achieved with the xbindkeys package with xvkbd and xclip.
.xbindkeysrc file:

"sh -c 'xclip -o -selection clipboard | xvkbd -xsendevent -file -'"
control + b:2

This is a non-critical issue related to SMRTView - it IS a problem in consed, where control-V doesn't work

[pag]

I added more things above to the features requested list

Bugs (or other unexpected things)
SMRTView

• Change of color for base quality annotation type
  Under Variants annotation any change of color results in the box registering as gray (rather than the selected color). Clicking on a second annotation type color swatch does not allow you to select and modify that color (without going to another tab first). On the QV annotations tab, the qualities get screwed up in the sense that the 50 quality level appears to take the color from the 3 (or 0?) quality. Prior to selection of a different color high quality is on a "light" background and low quality on a "dark" background, after change of a color on Variants tab HQ is "dark", moderate is "mid tone" and LQ is also "dark" for all variant types (not just the one specifically altered). Additionally, the LQ color is not altered from the previous value (so replacing the green with cyan still retains green for LQ). These issues seem to be fixed on a settings save and then a reload of the application (the new color selection is used appropriately).
  
• Impossible to unload a bridgemapper track
  Loading the Bridgemapper track makes the view of the individual sequence reads impossible and precludes restoring the non-bridgemapper view by unloading the track. It is necessary to either exit the application or at the very least re "load data from server".
  
• Sometimes data does not load and display
  This seems to often occur for the first attempt to load something in SMRTView - I don't know if I'm launching too soon after tomcatd and kodosd start or what, but the status bar suggests that all data is loaded, but no sequences show in the details window and you cannot select a subrange in the "region" window. Also the close/minimize/restore buttons are missing from the window (and I don't believe the menus work either). I typically have to close from the system-wide window manager and relaunch.
  
• A right-click on the consensus sequence in the details panel with lateral mouse movement causes the sequence to scroll unexpectedly
  This often accidentally jumps my sequence "window" when the lateral mouse movement was unintentional and slight. I had intended to see the context menu allowing me to see insertions at the position.
  
• At various times the "Go to location" dialogue doesn't pop up when the button is pushed
  I can't seem to repeat the circumstances reliably, but I think this occurs when the dialogue is already open and the application is minimized. This may be related to my "sloppy focus" mouse settings (see http://askubuntu.com/questions/64605...-follows-mouse; settings: "focus_mode" sloppy, "focus_new_windows" smart, "raise_on_click" checked, "auto_raise" not checked; note also "button_layout" value "close,minimize,maximize:" re: one of my feature suggestions)

Forum moderators: feel free to split the last two posts here to a new topic "PacBio SMRTView Bugs and Feature Suggestions" (I cannot find the option myself)

[allison12]

Viewing BridgeMapper results in SMRT View

Thanks for your detailed installation post pag, it was very helpful.

I am having difficulty loading the results from BridgeMapper into SMRT View and noticed that I am having a similar problem that had been mentioned in this thread previously. In SMRT View, if I try to add the BridgeMapper split_reads.bridgemapper.gz file via the Add Tracks from Server, no tracks are added. If I try to add the file from the Add Tracks option rather than the Add Tracks from Server, I get an error box that reads 'Error reading BridgeMapperReads file split_reads.bridgemapper.gz'. BridgeMapper was run through the command line and seemed to complete without problems and if I take a look at the split_reads.bridgemapper file, it appears to have the correct tab delimited format.

I was wondering if there is a step that I am missing for being able to view BridgeMapper results in SMRT View? The assembly has 1 contig (sequenced with PacBio) and the reference.info.xml and aligned_reads.cmp.h5 files load into SMRT View without problems.

Thanks,
Allison