SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 13 of 13
Search took 0.00 seconds.
Search: Posts Made By: Bob-Harris
Forum: Bioinformatics 12-14-2015, 10:38 AM
Replies: 6
Views: 7,512
Posted By Bob-Harris
FYI, bwa aln can generate the same "fail to...

FYI, bwa aln can generate the same "fail to locate the index" error message if it can't figure out how to parse the command line.

In my case, this happened because, trying to reproduce the methods...
Forum: Bioinformatics 08-24-2015, 11:25 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
Longer answer (assuming SeqAnswers doesn't throw...

Longer answer (assuming SeqAnswers doesn't throw it away again).

I've been lax in christening any of the newer releases over the last 5.5 years as "official". That should change soon, and the...
Forum: Bioinformatics 08-24-2015, 11:18 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
(SeqAnswers seems to have rejected my first...

(SeqAnswers seems to have rejected my first reply)

Short answer is use version 1.03.73 from here http://www.bx.psu.edu/~rsharris/lastz/newer

Bob H (lastz author)
Forum: Bioinformatics 08-24-2015, 09:36 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
Howdy, ereaye, This indicates some sort of...

Howdy, ereaye,

This indicates some sort of internal error in lastz. Internally it concatenates all the target sequences into one, is trying to convert a position in that concatenated sequence...
Forum: Bioinformatics 07-30-2015, 03:52 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
re: Lastz output problem

This is apparently a message from your shell. The string "no match" isn't something lastz ever outputs.

I've seen this reported a couple times before, but I've never found a machine that does it....
Forum: Bioinformatics 04-10-2015, 08:43 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
I'm expanding on my earlier answer, since other...

I'm expanding on my earlier answer, since other users may encounter this problem and google leads them to this page.

My best guess when this happens is that the input sequences contain a lot of...
Forum: Bioinformatics 05-15-2014, 07:28 AM
Replies: 14
Views: 6,203
Posted By Bob-Harris
I have found the prior report of this, from 2011....

I have found the prior report of this, from 2011. I was never able to determine the cause. We came up with a workaround which I will describe below.

First, though, can you run the following...
Forum: Bioinformatics 05-15-2014, 06:41 AM
Replies: 14
Views: 6,203
Posted By Bob-Harris
Sorry for not replying sooner. I've been out of...

Sorry for not replying sooner. I've been out of town and I did not have my account info for seqanswers.

The "no match" report is not from lastz (that text doesn't appear anywhere in the program)....
Forum: Bioinformatics 03-28-2014, 05:35 AM
Replies: 14
Views: 6,203
Posted By Bob-Harris
Agreed. The problem has been that the text...

Agreed.

The problem has been that the text of the readme file has lagged the new features added over the past 4 years. As features have been added, they've been added to the readme, but I haven't...
Forum: Bioinformatics 03-28-2014, 05:24 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
Howdy, David, I'm very surprised this could...

Howdy, David,

I'm very surprised this could be happening with such a small problem. Could you email me directly (my address is in the lastz readme)? I'd like to run the same sequences here so I...
Forum: Bioinformatics 03-28-2014, 05:20 AM
Replies: 23
Views: 6,189
Posted By Bob-Harris
Howdy, Ester, Sorry for this late reply. I...

Howdy, Ester,

Sorry for this late reply. I am new to seqanswers today.

Are you still having this problem? If so, please email me so I can figure out why this is happening (you can find my...
Forum: Bioinformatics 03-28-2014, 05:11 AM
Replies: 14
Views: 6,203
Posted By Bob-Harris
Sorry for this very late reply. I haven't been...

Sorry for this very late reply. I haven't been on seqanswers until today.

Werror tells the compiler to treat all warnings as errors. Turning this off is the easiest solution, but then you are...
Forum: Bioinformatics 03-28-2014, 04:56 AM
Replies: 4
Views: 2,273
Posted By Bob-Harris
The short answer is you need to use lastz_32...

The short answer is you need to use lastz_32 instead of lastz.

The long answer… the default lastz build can only handle a target up to 2Gbp combined length. This was a conscious design choice...
Showing results 1 to 13 of 13

 


All times are GMT -8. The time now is 12:54 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO