Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Interesting. This certainly is not happening for most people.
Could you go to the bug reporting site and describe the error there:
Please include any program output and command-line parameters as well.
The best chance for me to fix the bug you are experiencing is if I can reproduce the error in question.
Thanks for testing the software!
// Michael
Comment
-
Firstly, thanks for making Mosaik available.
I have been trying the OS X build under OS X 10.4 ("Tiger") I too experienced segmentation faults (and bus errors) when running all Mosaik components. I managed to get them to run by compiling from source with the following modified macosx.inc
Code:# define our processor specific flags export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Dstat64=stat -Dfstat64=fstat export LDFLAGS = -Wl
Comment
-
@Nick: Thanks for the updated Mac OS X compilation options. These will be used when the MOSAIK update is pushed out this weekend.
@csffq: I'll take a look at why MOSAIK didn't like the '+' and '-' characters in the reference sequence names. Theoretically, it shouldn't matter, but I'll look into it either way.
Thanks again for the feedback,
// Michael
Comment
-
How can make gigaBayes a little fast?
Currently I am using mosaic package to align my solexa reads to reference of transcriptome. It works well as producing snp and coverage information.
Here I write to ask for help as some problems happen to me. When I used mosaikassemble to produce assemble files, it produce more than ten thousands files because the reference is more than 20000 contigs. When I tried to use gigabayes to get snp information from those .gig files produced by mosaikassemble, I have to run the command one by one, it really costs a lot of time.
Is there any way to get only one resulting file from mosaikassemble command, so that I could run gigabayes only once to get all the snp information from transcriptome?
Or is there some way to ran gigabayes with those more than ten thousand files just faster?
Comment
-
Re: about gigaBayes
I have merged the 20000 contigs into one whole sequence as you have said. with MosaikAssemble it produce only one .gig file. When using gigaBayes it still runs slowly, probably need 4-5 whole days to finish the task.
Fortunately I can just wait for the computer to finish the job, and then with perl scirpt to extract the useful information, thank you a lot!
Comment
Latest Articles
Collapse
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
-
by seqadmin
The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.
Avian Conservation
Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...-
Channel: Articles
03-08-2024, 10:41 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 03-27-2024, 06:37 PM
|
0 responses
13 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:37 PM
|
||
Started by seqadmin, 03-27-2024, 06:07 PM
|
0 responses
12 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
69 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment