Continuing aborted run

[zwuckl]

Hey Bao,

I'm running AlignGraph for reference guided improvement of a ~400MBp plant genome assembly on a compute cluster as a single job with 8 cores for 6 days - the maximum allowed walltime for any job on the cluster.
Unfortunately, when reaching the walltime limit AlignGraph is still in the Bowtie alignment phase and the job is killed. Is there any chance of continuing the pipeline from a given point or maybe even perform the alignment as a seperate job with more resources?
If I understood correctly, Bowite is executed with 8 cores by default from within AlignGraph. Is there maybe a way to freely define Bowtie's (and BLAT's) resources?

Thanks in advance,
Nico

[baoe]

Hello, Nico,

I'm afraid AlignGraph does not have checkpoints within the alignment step.
However, you could change all the "-p 8" in the source file to for example "-p 16" and recompile AlignGraph to accelerate the Bowtie alignment.

Best,
Bao

---

From: zwuckl [notifications@github.com]
Sent: Wednesday, July 15, 2015 2:02 AM
To: baoe/AlignGraph
Subject: [AlignGraph] Continuing aborted run (#12)

Hey Bao,

I'm running AlignGraph for reference guided improvement of a ~400MBp plant genome assembly on a compute cluster as a single job with 8 cores for 6 days - the maximum allowed walltime for any job on the cluster.
Unfortunately, when reaching the walltime limit AlignGraph is still in the Bowtie alignment phase and the job is killed. Is there any chance of continuing the pipeline from a given point or maybe even perform the alignment as a seperate job with more resources?
If I understood correctly, Bowite is executed with 8 cores by default from within AlignGraph. Is there maybe a way to freely define Bowtie's (and BLAT's) resources?

Thanks in advance,
Nico

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/12.

[zwuckl]

Hey Bao,

thanks for your fast reply! I just edited and recompiled the source accordingly and will see if it suffices...

Best,
Nico