Clipper runtime?

[Elisabeth R]

Hi,

I'm running through the eCLIP analysis pipeline v. 2.0 on an existing ENCODE dataset, ENCSR534YOI, and Clipper has been running for about 6 hours on an HPC cluster with the following command:

clipper -b read1.merged.r2.bam -s hg19 -o read1.merged.r2.peaks.bed --save-pickle

Is this a normal runtime or is something broken? clipper -h works fine.

Thanks,

Liz

[Gabriel Pratt]

Clipper with 8 threads takes about 8 hours to run (highly variable depending on dataset, it could take up to 24).

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[Sol Katzman]

Dear Elisabeth,

See my new post about the default timeout setting.

Check your logs for timeouts. Could be your problem.

/Sol.

On Tuesday, May 21, 2019 at 4:00:42 PM UTC-7, Gabriel Pratt wrote:

Clipper with 8 threads takes about 8 hours to run (highly variable depending on dataset, it could take up to 24).

On Tue, May 21, 2019, 3:56 PM Elisabeth R <ereb...@gmail.com> wrote:

Hi,

I'm running through the eCLIP analysis pipeline v. 2.0 on an existing ENCODE dataset, ENCSR534YOI, and Clipper has been running for about 6 hours on an HPC cluster with the following command:

clipper -b read1.merged.r2.bam -s hg19 -o read1.merged.r2.peaks.bed --save-pickle

Is this a normal runtime or is something broken? clipper -h works fine.

Thanks,

Liz

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