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

[Sol Katzman]

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