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

[Sol Katzman]

Dear Yarden,

I am still trying to determine the scope of this problem. In the meantime,

1) running sashimi on some of these events I get a "MemoryError" crash in getScaling().

    http://users.soe.ucsc.edu/~sol/MISO_info/miso_sashimi_AFE_MemoryErr_traceback

2) I have extracted the distributions of the lengths of the "gene" items in the gff3
    (hg19) event definitions. There are many (1100+/500+) AFE/ALE events over 1Mb in length.
    Only a handful (10) such SE events.

    http://users.soe.ucsc.edu/~sol/MISO_info/get_miso_event_gff_gene_lengths

I think that the events longer than 1Mb are pretty questionable.

/Sol.


On 12/3/2012 5:35 AM, Yarden Katz wrote:
> 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
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>