[miso-users] excessive runtimes for ALE and AFE events

[Yarden Katz]

Dear Sol,

Do you mind re-running this event with num_chains set to 1 (note below that you ran it with the new default settings of num chains = 6)?  Could you please let me know what the run time is for that?

Thanks, --Yarden





On Dec 3, 2012, at 1:16 AM, Sol Katzman wrote:

> Dear Yarden,
> 
> I am seeing some excessive run times for many ALE and AFE events.
> 
> Below is a log from one AFE event run. I will investigate further to
> get more detail, but the cause for the long run time is likely the
> extremely high number (over 2M in the case below) of reads that are
> being processed for the event.
> 
> I suspect that this is due to an extremely long genomic region defining
> the event. So either:
> 
> a) this is not a valid event
> b) perhaps MISO could do some additional filtering of the reads prior
>    to PSI estimation.
> 
> /Sol.
> ------------------------------------------------------
> The log from my script, including MISO output, indicates
>  the event: 51529 at uc002kbx.1@uc002kjr.1
>  number of reads used: 2220390
>  elapsed time: 3525.68 seconds
> 
> running miso run_miso.py with options:   --compute-gene-psi 51529 at uc002kbx.1@uc002kjr.1 
> 51529 at uc002kbx.1@uc002kjr.1.pickle temp.se1Filt.cyr_rn03_hg19.ih1.rd1.xpe.yc.chr17only.tophat.map.trk.bam 
> /scratch/sol-16071-1354482368/miso_results/AFE    --read-len 75         in scratch directory /scratch/sol-16071-1354482368
> /cluster/home/sol/.local/lib/python2.7/site-packages/misopy/miso_sampler.py:298: RuntimeWarning: Long inserted alignment 
> at pysplicing/src/solve.c:262
>   stop_cond)
> /cluster/home/sol/.local/lib/python2.7/site-packages/misopy/miso_sampler.py:298: RuntimeWarning: Long deleted alignment 
> at pysplicing/src/solve.c:252
>   stop_cond)
> Loading settings from: /cluster/home/sol/.local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
> Settings:
>    filter_results True
>    min_event_reads 20
>    cluster_command qsub
>    long_queue_name long
>    short_queue_name quick
>    burn_in 500
>    lag 10
>    num_iters 5000
>    num_chains 6
> Computing Psi for 1 genes...
>   - 51529 at uc002kbx.1@uc002kjr.1
>   - GFF filename: /scratch/sol-16071-1354482368/51529 at uc002kbx.1@uc002kjr.1.pickle
>   - BAM: /scratch/sol-16071-1354482368/temp.se1Filt.cyr_rn03_hg19.ih1.rd1.xpe.yc.chr17only.tophat.map.trk.bam
>   - Outputting to: /scratch/sol-16071-1354482368/miso_results/AFE
> Loading genes from indexed GFF...
>   - Loading took: 0.00 seconds
> Loading BAM filename from: 
> /scratch/sol-16071-1354482368/temp.se1Filt.cyr_rn03_hg19.ih1.rd1.xpe.yc.chr17only.tophat.map.trk.bam
> Loading took 0.00 seconds
> 2220390 raw reads in event
> no chains: 6
> Outputting samples to: /scratch/sol-16071-1354482368/miso_results/AFE/chr17/51529 at uc002kbx.1@uc002kjr.1.miso...
> Completed outputting.
> Event took 3525.68 seconds
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users