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yarden / MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation
http://genes.mit.edu/burgelab/miso/index.html
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IndexError: too many indices for array #117

Open limeng12 opened 6 years ago

limeng12 commented 6 years ago

I installed MISO locally, and run many times, but seems one bam file seems have some problems when running MISO on it, others worked very well. The problem is:

Traceback (most recent call last): File "/N/u/liulab/Karst/limeng/myenv/bin/summarize_miso", line 9, in load_entry_point('misopy==0.5.4', 'console_scripts', 'summarize_miso')() File "/gpfs/home/l/i/liulab/Karst/limeng/myenv/lib/python2.7/site-packages/misopy/summarize_miso.py", line 93, in main use_compressed=use_compressed) File "/gpfs/home/l/i/liulab/Karst/limeng/myenv/lib/python2.7/site-packages/misopy/samples_utils.py", line 285, in summarize_sampler_results samples_results = samples_obj.get_event_samples(event_name) File "/gpfs/home/l/i/liulab/Karst/limeng/myenv/lib/python2.7/site-packages/misopy/samples_utils.py", line 109, in get_event_samples samples = load_samples(f) File "/gpfs/home/l/i/liulab/Karst/limeng/myenv/lib/python2.7/site-packages/misopy/samples_utils.py", line 137, in load_samples data, h = csv2array(samples_in, skiprows=1, raw_header=True) File "/gpfs/home/l/i/liulab/Karst/limeng/myenv/lib/python2.7/site-packages/misopy/parse_csv.py", line 81, in csv2array cols = data_array[0,:] IndexError: too many indices for array

ibmuller commented 6 years ago

I have the same problem. Did you solve it already?

ajones-lab commented 4 years ago

Hi,

Were either of you able to find a solution to this?

ibmuller commented 4 years ago

Yeah in my case it was that i had a very old version of samtools running. Thanks.

From: ajones-lab notifications@github.com Sent: Friday, October 16, 2020 21:28 To: yarden/MISO MISO@noreply.github.com Cc: Muller, I.B. (Ittai) i.muller@amsterdamumc.nl; Comment comment@noreply.github.com Subject: Re: [yarden/MISO] IndexError: too many indices for array (#117)

Hi,

Were either of you able to find a solution to this?

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ajones-lab commented 4 years ago

Thank you! As in you sorted the bam file that you fed to miso with an old version of samtools? Its my understanding that the summarize_miso function isn't calling samtools?