I am trying to decipher why I am getting a segmentation fault when trying to use SIFT.
I am using the test fasta file, and substituion file they provide. I am using the swissport database which I can successfully BLAST against on my system.
Here is what I get when trying to use SIFT:
arron#arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b $ bin/SIFT_for_submitting_fasta_seq.csh test/lacI.fasta db/swissprot.fa test/lacI.subst 2.75
tail is lacI.fasta
query is /home/arron/Phd/programs/sift4.0.3b/tmp/lacI.fasta.query
query length 360
entered read_psiblastuntillat
Segmentation fault
tell me i've entered
info_on_seqs
fawegwa
cannot open file /home/arron/Phd/programs/sift4.0.3b/tmp/lacI.alignedfasta
Output in /home/arron/Phd/programs/sift4.0.3b/tmp/lacI.SIFTprediction
I've been trying for the last two hours to find some source code where the error is handled, but I have been unsuccessful. Does anybody have any experience with SIFT segmentation faults, or are able to point me to the source code so that I can see what is going wrong?
Thanks very much.
Is there a reason you are using such an old version of SIFT? I think the latest version is 5.2.1 where you appear to be using 4.0.3b
My guess is you are using a newer version of Blast that is not compatible with the old version of SIFT.
The release notes for sift 5.2 say:
SIFT 5.2.0 released. Code has been updated to be compatible with later versions of BLAST (tested on 2.2.28+)
So I either suggest using the new version of SIFT or an old version of blast and see if that fixes things.
Related
I am looking into openmodelica and therefore I am recreating examples from the standard library.
Under Modelica > Fluid > Examples there is the HeatingSystem model which I recreated and the simulation fails due to division by zero. The original one from the library also fails.
I have two questions:
is it just me, or is it a buggy example?
If it is not me: Can somebody help me resolve the issue using the debugger, which confuses me very much?
I am running the latest nighly (since the fedora repo only offers nightlies..) with MSL 4.0.0
We have latest Xcode(7.2) having Swift(2.1.1) installed in few mac systems. Here developer didn't find any errors in his code which was checked in, but the same code used at other end were observing errors(most of them related unwrapping variables).
verified all settings and version details not able to find any difference. Any help or suggestions will be appreciated. Thanks
Most likely the machine "at the other end" is not running Xcode 7.2. There is a tool for converting Swift 1.x to 2.x, but not the other direction. But without code sample illustrating the problem, we can't help you much. In addition to shifting unwrapping conventions, there is new syntax later versions of Swift (e.g. guard, error throwing, etc.).
But, if you're going to share a Swift project amongst multiple developers, you probably just want to make sure everyone is using the same version of Xcode. And with Swift progressing as quickly as it is, you might want to encourage everyone to use the latest production version of Xcode.
I have an old MSDOS software realized in magic 5.6 with an btrieve 5.10a database, that should be modernized(completely redone using a modern DB).
For this I would love to just get the table structures and some understanding in the structure of the magic program.
But unfortunately I was not able to find any documentation on magic nor was I able to get the structure with column names from the tables(.btr but no ddf files).
Any idea on how to get a step further?
Not enough rep to comment, so I'm forced to post this as an answer.
If you can't get hold of any info regarding the data structure you might try:
A. Download and install a try-out version of a more recent Pervasive version and see if that enables you to read the data. In (still more or less current) server versions like V11 there is a DDF Builder utility, which does what the name implies. However, this is no automatic process, but relies on your ability to link the data shown in the application to the hex values on disk.
B. Try to find a BUTIL.EXE version that works with 5.x Btrieve files, run BUTIL -RECOVER and see what that gets you. You might get to parse the data with scripting tools this way - I've done it in the past on 6.x files, but nothing as old as you are dealing with.
The main issue here is whether you'll be able to find compatible tools for a version that old. But then again, maybe 6.x tools might just work.
I got an error when I am running the Labview, please see the attached picture.
It seems the bitfile is not matching with the system version, since I just updated the software, maybe I should download a new bitfile?
Where can I download one?
This means that the LabVIEW-Software you are trying to use is dynamically loading a bitfile to the FPGA. Whoever compiled the bitfile was using a different version of NI-RIO so you will need to recompile the bitfile from source / ask the original author to send you an updated version, or downgrade your installation of NI-RIO.
I have been tasked with fixing a bug found in a legacy app written in version 2.4.0 or 2.6.0 of STS.
After spending the better part of 2 days trying to port it to 3.6.2 without success I need to get my hands on either of these older releases to see if this even works or if there is something wrong with the app code base. I have spent the better part of an hour searching STS Spring for previous versions but can't find anything on the site. Where are previous versions of STS or why have they been stashed away?
OS Target: Window 7 - 64 bit
Thanks
Having a look at this post and the filename of the current version, you come up with: http://download.springsource.com/release/STS/2.6.0.SR1/dist/e3.6/springsource-tool-suite-2.6.0.SR1-e3.6.2-win32-x86_64.zip
Very strange that they are not linking the old versions even though they are still available.