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Search took 0.02 seconds. Search: Posts Made By: pag
Forum: Pacific Biosciences 02-05-2014, 12:46 PM
Replies: 20
Views: 11,405
Posted By pag
I added more things above to the features...

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...
Forum: Pacific Biosciences 01-29-2014, 06:44 PM
Replies: 20
Views: 11,405
Posted By pag
Wishlist SMRTView Go to: keep zoom...

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...
Forum: Pacific Biosciences 01-24-2014, 11:44 AM
Replies: 2
Views: 2,388
Posted By pag
My notes to get 8.1 to work within the SMRT...

My notes to get 8.1 to work within the SMRT analysis pipeline are on this forum. Obviously if running on command-line outside of SMRT analysis, you won't need all of these.

Here are the relevant...
Forum: Pacific Biosciences 01-06-2014, 05:13 PM
Replies: 20
Views: 11,405
Posted By pag
5 screenshots of the bug - had to tar/gz them and...

5 screenshots of the bug - had to tar/gz them and do 2 per file in order to meet file size limits here.
Forum: Pacific Biosciences 01-03-2014, 12:08 PM
Replies: 20
Views: 11,405
Posted By pag
looks like some of my problems were partially due...

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]...
Forum: Pacific Biosciences 01-03-2014, 11:36 AM
Replies: 20
Views: 11,405
Posted By pag
I understand completely. Thanks for getting back...

I understand completely. Thanks for getting back to me at all!


Thanks for the BLASR tip. I'll probably look into that soon.


It looks like it generated 47 contigs. The reference uploader...
Forum: Pacific Biosciences 01-03-2014, 11:18 AM
Replies: 20
Views: 11,405
Posted By pag
a few minor, minor issues: the linux_configure...

a few minor, minor issues: the linux_configure script in smartview-2.1.0/bin does not functionally run a second time. e.g. @HTTPPORT has already been replaced with the value of $S_PORT from the...
Forum: Pacific Biosciences 01-02-2014, 01:24 PM
Replies: 20
Views: 11,405
Posted By pag
currently hitting a problem with displaying the...

currently hitting a problem with displaying the BridgeMapper job that I did Dec 18th. I don't know if this is an issue with the permissions of the smrtanalysis user, my standard user, or something...
Forum: Pacific Biosciences 01-02-2014, 11:48 AM
Replies: 20
Views: 11,405
Posted By pag
based on assembly time, it seems that it used the...

based on assembly time, it seems that it used the 454 data, but SMRTView doesn't appear to display non-PB data. Is there a recommended viewer for the mapping of all data (PB+454 in this case). My...
Forum: Pacific Biosciences 12-23-2013, 10:31 AM
Replies: 20
Views: 11,405
Posted By pag
Edited post above to contain more specific...

Edited post above to contain more specific errors/info found in log files. However, using the SMRTportal/analysis default spec file ran without error. As indicated in other posts, I'm still...
Forum: Pacific Biosciences 12-23-2013, 10:04 AM
Replies: 20
Views: 11,405
Posted By pag
it looks like it didn't keep the setting for the...

it looks like it didn't keep the setting for the custom spec file itself. I had specified a path in the jobs_dropbox directory, but it seems that the SMRTPortal doesn't like that, and clears the...
Forum: Pacific Biosciences 12-23-2013, 09:41 AM
Replies: 20
Views: 11,405
Posted By pag
I was able to run it with the default settings,...

I was able to run it with the default settings, clearing the custom spec file field.
Then, I looked into the 016444 directory (most recent run), pulled out the spec file, changed the line that read...
Forum: Pacific Biosciences 12-22-2013, 02:43 PM
Replies: 20
Views: 11,405
Posted By pag
INFO] 2013-12-21 18:49:45,188 [smrtpipe.status...

INFO] 2013-12-21 18:49:45,188 [smrtpipe.status refreshTargets 419] Starting task://016443/P_CeleraAssembler/runCaHgap
[ERROR] 2013-12-22 13:03:29,981 [smrtpipe.status refreshTargets 413] *** Failed...
Forum: Pacific Biosciences 12-21-2013, 05:25 PM
Replies: 20
Views: 11,405
Posted By pag
unfortunately using a custom spec for hybrid...

unfortunately using a custom spec for hybrid assembly (RS_HGAP_ASSEMBLY.2) is not straightforward. I uploaded a spec file that had definitions of all EXCEPT my PB data, which would be generated...
Forum: Pacific Biosciences 12-20-2013, 07:37 PM
Replies: 20
Views: 11,405
Posted By pag
installation of wgs-8.1 added; pretty...

installation of wgs-8.1 added; pretty straightforward to use the precompiled package. building from source is a bit more painful (if I recall).
Forum: Pacific Biosciences 12-20-2013, 12:25 PM
Replies: 20
Views: 11,405
Posted By pag
Thanks rhall (richard?), It was suggested to...

Thanks rhall (richard?),

It was suggested to me during a previous stage of my assembly that I create a diary here on SeqAnswers (probably from the MIRA mailing list?). I didn't do so immediately,...
Forum: Pacific Biosciences 12-20-2013, 11:06 AM
Replies: 20
Views: 11,405
Posted By pag
Diary: Assembly in SMRT Portal 2.1.1 with HGAP+CA 8.1

Description of genome and assembly desires
SMRT Portal 2.1.1 was released within the last couple of months (packaged with Celera Assembler 7); the Celera Assembler has, in the last week, released...
Forum: Bioinformatics 06-25-2013, 01:59 PM
Replies: 12
Views: 9,861
Posted By pag
using version 3.9, the following "worked" on 454...

using version 3.9, the following "worked" on 454 data

This was a situation where I had already largely determined the sequence using a denovo assembly, using information also from newbler and...
Forum: Bioinformatics 06-24-2013, 08:16 AM
Replies: 19
Views: 7,369
Posted By pag
yes, according to MIRA's mapping assembly (after...

yes, according to MIRA's mapping assembly (after pacbio error-correction), I have 30x coverage. There are a couple of problem regions of course (chiefly involving the transposons)
Forum: Bioinformatics 06-23-2013, 05:49 PM
Replies: 19
Views: 7,369
Posted By pag
setting -m 2 is processing many more blocks. ...

setting -m 2 is processing many more blocks. However, even at m=5 it was near-instant.

I noticed a section "What happens when my sample is a mixture, or diploid?" in the Quiver FAQ

Does this...
Forum: Bioinformatics 06-23-2013, 05:12 PM
Replies: 19
Views: 7,369
Posted By pag
quiver -v -j4 cp6.cmp.h5 -r consensus.fasta -o...

quiver -v -j4 cp6.cmp.h5 -r consensus.fasta -o quiver-assembly.fasta
2013-06-23 17:03:40,711 [INFO] h5py version: 2.0.1
2013-06-23 17:03:40,711 [INFO] hdf5 version: 1.8.4
2013-06-23 17:03:40,714...
Forum: Bioinformatics 06-23-2013, 03:41 PM
Replies: 19
Views: 7,369
Posted By pag
looks like I can get quiver to run if I specify...

looks like I can get quiver to run if I specify every single track...I'm not sure which are the important ones other than the QV ones.

however, it runs in about 2 seconds flat, which seems like it...
Forum: Bioinformatics 06-23-2013, 01:25 PM
Replies: 19
Views: 7,369
Posted By pag
That didn't appear to generate a new cmp.h5, but...

That didn't appear to generate a new cmp.h5, but rather altered the existing one (aligned5; at least I think so based on the timestamp)

I then tried
loadPulses blah.bas.h5 aligned5.cmp.h5...
Forum: Bioinformatics 06-22-2013, 03:50 AM
Replies: 19
Views: 7,369
Posted By pag
after reconfiguring SWIG and several other items,...

after reconfiguring SWIG and several other items, I get
"Input CmpH5 file must be sorted." when running Quiver

I cannot seem to locate a sort script. Also, is it supposed to sort by quality,...
Forum: Bioinformatics 06-21-2013, 08:27 PM
Replies: 19
Views: 7,369
Posted By pag
running compareSequences.py --algorithm=blasr...

running compareSequences.py --algorithm=blasr --h5fn=aligned.cmp.h5 --debug --circularReference filtered_subreads.fasta reference_genome.fasta worked

Edit: running loadPulses on the reads...
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