[miso-users] MISO aborts with error *** glibc detected *** python: free(): invalid pointer

[Anke Busch]

Hello Yarden,

I have installed MISO release 0.4.1 recently. I did all the steps you 
explain on your website. The setup worked fine, importing misopy and 
pysplicing works in python. When checking for availability of modules by 
using module_availability.py, everything is fine.

I work with an Ubuntu 10.04 system which has python release 2.6 
installed. When running the MISO test (test_miso.py) the following error 
message appears and the run crashes:


python /home/hertel/Software/src/misopy-0.4.1/misopy/test_miso.py

Testing conversion of SAM to BAM...
Executing: python 
/home/hertel/Software/src/misopy-0.4.1/misopy/sam_to_bam.py --convert 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-data/sam-data/c2c12.Atp2b1.sam 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-output/sam-output
Converting SAM to BAM...
   - Executing: samtools view -Sbh 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-data/sam-data/c2c12.Atp2b1.sam 
 > 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-output/sam-output/c2c12.Atp2b1.bam
[samopen] SAM header is present: 35 sequences.
Sorting BAM file...
.......
........
Loading settings from: 
/usr/local/lib/python2.6/dist-packages/misopy/settings/miso_settings.txt
Settings:
    short_queue_name quick
    long_queue_name long
    cluster_command qsub
    filter_results True
    min_event_reads 20
    lag 10
    burn_in 500
    num_iters 5000
Computing Psi for 1 genes...
   - ENSMUSG00000019943
   - GFF filename: 
/home/hertel/Software/src/misopy-0.4.1/misopy/gff-events/mm9/genes/Atp2b1/indexed/chr10/ENSMUSG00000019943.pickle
   - BAM: 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
   - Outputting to: 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-output/gene-psi-output
Loading BAM filename from: 
/home/hertel/Software/src/misopy-0.4.1/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam
Loading took 0.00 seconds
*** glibc detected *** python: free(): invalid pointer: 0x099e8c20 ***



samtools is installed properly and can be run. I don't know what else 
could cause the problem here. Do you have any idea, what could go wrong 
here?

Thanks a lot for your help.
Anke.


-- 
******************************************
   Dr. Anke Busch
   Postdoctoral Researcher
   Department of Microbiology and Molecular Genetics
   Medical Sciences I, C290
   University of California, Irvine, USA

   Email: abusch at uci.edu
   Phone: +1-949-824-2128
******************************************