[miso-users] excessive runtimes for ALE and AFE events
Sol Katzman
solkatzman at sbcglobal.net
Mon Dec 3 01:16:35 EST 2012
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
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