Question: Error when running Miso
gravatar for Ram
5.0 years ago by
Ram130 wrote:

Dear all,

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 :

Is anybody know what it causing for this error.

Thanks a lot.

"MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data for detecting differential isoforms
Use --help argument to view options.

Using MISO settings file: /home/aarora1/Tool/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
Computing Psi values...
  - GFF index: /home/aarora1/hg19/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/lib/python2.7/site-packages/misopy/", line 591, in main
  File "/home/aarora1/Tool/lib/python2.7/site-packages/misopy/", line 372, in compute_all_genes_psi
  File "/home/aarora1/Tool/lib/python2.7/site-packages/misopy/", 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 "


rna-seq splicing • 2.5k views
ADD COMMENTlink written 5.0 years ago by Ram130

Hi !

Shall we know if your GFF annotation and you BAM file have any matching chromosome names ? If not, the run always fails with an error. The truncated error message is about that.

ADD REPLYlink written 5.0 years ago by Thibault D.690
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