[miso-users] Miso error

[Yarden Katz]

Hi Ankit,

It looks like you have more than one miso version installed, one quite old (misopy-0.5.0) and they are conflicting.  Can you make sure you're using 0.5.3 and remove the older versions from your path?  

Best, Yarden

On Mar 30, 2015, at 5:54 AM, Ankit Arora <arora at atlas-biolabs.com> wrote:

> Respected Sir/madam,
> 
> I am running Miso for single end and paried end reads, while I am trying 
> to run miso for paired end reads. I am getting an following error :
> 
> Computing Psi values...
>   - GFF index: 
> /home/aarora1/Tool/misopy-0.5.0/virtualenv-develop/myVE/bin/indexed
>   - BAM: /projects/aarora1/Result/C/accepted_hits_sorted.bam
>   - Read length: 60
>   - Output directory: /projects/aarora1/Miso
> Checking your GFF annotation and BAM for mismatches...
> Checking if BAM has mixed read lengths...
> Found reads of length 60 in BAM.
> Traceback (most recent call last):
>   File "./miso", line 9, in <module>
>     load_entry_point('misopy==0.5.3', 'console_scripts', 'miso')()
>   File 
> "/home/aarora1/Tool/misopy-0.5.0/virtualenv-develop/myVE/lib/python2.6/site-packages/misopy/miso.py", 
> line 591, in main
>     wait_on_jobs=wait_on_jobs)
>   File 
> "/home/aarora1/Tool/misopy-0.5.0/virtualenv-develop/myVE/lib/python2.6/site-packages/misopy/miso.py", 
> line 372, in compute_all_genes_psi
>     given_read_len=read_len)
>   File 
> "/home/aarora1/Tool/misopy-0.5.0/virtualenv-develop/myVE/lib/python2.6/site-packages/misopy/run_events_analysis.py", 
> line 171, in check_gff_and_bam
>     miso_logger.warning("It looks like your GFF annotation file and 
> your BAM " \
> NameError: global name 'miso_logger' is not defined
> 
> 
> Can you please help me out. I look forward to hear back from you soon.
> 
> Regards
> Ankit
> 
> -- 
> Ankit Arora
> Bioinformatics / Research
> T +49 30 3 19 89 66 25 | F -19
> arora at atlas-biolabs.com
> 
> ATLAS Biolabs GmbH
> Friedrichstraße  147 | 10117 Berlin
> www.atlas-biolabs.com
> 
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