implementing parallelized blat? about aligngraph HOT 3 OPEN

Hi, Kevin,

That's a perfect suggestion! I will try to incorporate pblat asap.

Best,
Bao

From: kpboh [[email protected]]
Sent: Thursday, September 17, 2015 9:39 AM
To: baoe/AlignGraph
Subject: [AlignGraph] implementing parallelized blat? (#13)

Like others have mentioned here, I've been struggling with some exceptionally long runtimes, which seem to be occurring due to a bottleneck at the blat alignment stage. I was wondering how difficult would it be to incorporate a parallelized version of blat (e.g., pblat) into the AlignGraph source? Evidently pblat requires only a single additional command ("-threads" option).

Thanks in advance,
Kevin

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/13.

from aligngraph.

Hi Bao, Thanks for the response and incorporating pblat. However, the new version returned an error of "BLAT CALLED FAILED!" when I tried to run it (on 2 different machines). In looking at the source code, it looks like it's supposed to call 'blat' if calling 'pblat' returns an error. I have both blat and pblat in my path environmental variable. Thanks for any suggestions! -Kevin

from aligngraph.

Hi, Kevin,

My guess is there should be some problem with blat/pblat in your path, since AlignGraph checks bowtie2 in the same way with blat and it looks like there is no problem for bowtie2. Can you check if you could run the command line "blat" to make sure blat is in the path?

Best,
Bao

From: kpboh [[email protected]]
Sent: Friday, September 25, 2015 8:29 AM
To: baoe/AlignGraph
Cc: Bao
Subject: Re: [AlignGraph] implementing parallelized blat? (#13)

Hi Bao, Thanks for the response and incorporating pblat. However, the new version returned an error of "BLAT CALLED FAILED!" when I tried to run it (on 2 different machines). In looking at the source code, it looks like it's supposed to call 'blat' if calling 'pblat' returns an error. I have both blat and pblat in my path environmental variable. Thanks for any suggestions! -Kevin

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/13#issuecomment-143252598.

from aligngraph.