Error while running miso
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9.3 years ago

Hello,

I am running Miso for single end and paried end reads, while I am trying to run miso, I am getting an following error:

miso --run data/human/splicing_project/indexed_A3_events/ GM_sorted.bam --output-dir data/human/splicing_project/my_output1/ --read-len 100 --paired-end 294 75.4

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: /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
Computing Psi values...
  - GFF index: /home/priyanka/data/human/splicing_project/indexed_A3_events
  - BAM: /home/priyanka/GM_sorted.bam
  - Read length: 100
  - Output directory: /home/priyanka/data/human/splicing_project/my_output1
Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
Found reads of length 100 in BAM.
Mapping genes to their indexed GFF representation, using /home/priyanka/data/human/splicing_project/indexed_A3_events
Searching for /home/priyanka/data/human/splicing_project/indexed_A3_events/genes_to_filenames.shelve..
  - Found shelved file.
Preparing to run 1 batches of jobs...
Running batch of 2107 genes..
  - Executing: python /usr/local/lib/python2.7/site-packages/misopy/run_miso.py --compute-genes-from-file "/home/priyanka/data/human/splicing_project/my_output1/batch-genes/batch-0_genes.txt" /home/priyanka/GM_sorted.bam /home/priyanka/data/human/splicing_project/my_output1 --read-len 100  --paired-end 294.0 75.4 --settings-filename /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-0
Waiting on 1 threads...
08/17/2015 11:45:54 AM - miso_main - WARNING - Thread batch-0 might have failed...

Thanx in advance
RNA-Seq splicing • 7.3k views
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Execute the following command and see if you get any specific error:

python /usr/local/lib/python2.7/site-packages/misopy/run_miso.py \
  --compute-genes-from-file "/home/priyanka/data/human/splicing_project/my_output1/batch-genes/batch-0_genes.txt" \
  /home/priyanka/GM_sorted.bam \
  /home/priyanka/data/human/splicing_project/my_output1 \
  --read-len 100 \
  --paired-end 294.0 75.4 \
  --settings-filename /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt​
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I also experienced the same problem, but I was not able to run this line. The following error appears (even running from myenv)

python: can't open file '/usr/local/lib/python2.7/site-packages/misopy/run_miso.py': [Errno 2] No such file or directory

Any insight on what the problem might be?

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Where is misopy installed? It might not be in the directory shown. Hence, it shows the no directory error.

Is your BAM file indexed? It worked for me when I indexed my BAM file and regenerated indexed events. Hope this helps...

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Yes, now I reinstalled globally (and I always run sudo), but I still got the error.

This is my code:

miso --run /path/to/hsa_80_indexed /path/to/accepted_hits.bam --output-dir /path/to/output_dir --read-len 51 --paired-end 137 24 > BaP12.txt

...and this is the output

Using MISO settings file: /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
Computing Psi values...
  - GFF index: /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/hsa_80_indexed
  - BAM: /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/BAP_pilot/BaP_12h_1_thout/accepted_hits.bam
  - Read length: 51
  - Output directory: /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso
Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
Found reads of length 51 in BAM.
Mapping genes to their indexed GFF representation, using /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/hsa_80_indexed
Searching for /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/hsa_80_indexed/genes_to_filenames.shelve..
  - Found shelved file.
Preparing to run 3 batches of jobs...
Running batch of 21739 genes..
  - Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso/batch-genes/batch-0_genes.txt" /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/BAP_pilot/BaP_12h_1_thout/accepted_hits.bam /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso --read-len 51  --paired-end 137.0 24.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-0
Running batch of 21739 genes..
  - Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso/batch-genes/batch-1_genes.txt" /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/BAP_pilot/BaP_12h_1_thout/accepted_hits.bam /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso --read-len 51  --paired-end 137.0 24.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-1
Running batch of 21739 genes..
  - Executing: python /usr/local/lib/python2.7/dist-packages/misopy/run_miso.py --compute-genes-from-file "/home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso/batch-genes/batch-2_genes.txt" /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/BAP_pilot/BaP_12h_1_thout/accepted_hits.bam /home/terezinha/Dropbox/HCC_isoforms_splicing/de_novo/MISO/BaP_12h_1/miso --read-len 51  --paired-end 137.0 24.0 --settings-filename /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-2
Waiting on 3 threads...
09/01/2015 03:26:27 PM - miso_main - WARNING - Thread batch-0 might have failed...
09/01/2015 03:26:27 PM - miso_main - WARNING - Thread batch-1 might have failed...
09/01/2015 03:26:27 PM - miso_main - WARNING - Thread batch-2 might have failed...

I tried to change the miso settings to 3 threads and it still does not work.

If by indexed .BAM you mean a .bam.bai file in the same folder, yes, I also have that. Is that what you did?

Thanks in advance!

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I tried to run this and I got the error

Error: Settings file /usr/local/lib/python2.7/dist-packages/misopy/settings/miso_settings.txt​ does not exist.

But the file is there o.o

terezinha:/usr/local/lib/python2.7/dist-packages/misopy/settings$ ls
miso_settings.txt  sashimi_plot_settings.txt
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I guess it's an installation problem. In the MISO document, there is "Testing MISO" which ensures that you can run miso properly. I suggest you to go through it and run the following lines:

python -m unittest discover misopy

Try this and let me know.

Hope this helps...

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I am trying to test MISO using the command you provided. I get the following error:

Checking your GFF annotation and BAM for mismatches...

Error: BAM /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam cannot be found.

05/26/2016 12:03:13 PM - miso_main - ERROR - BAM file /usr/local/lib/python2.7/dist-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam not found.
.

FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam
    "c2c12.Atp2b1.sorted.bam")))
AssertionError

----------------------------------------------------------------------
Ran 5 tests in 1.185s

FAILED (failures=1)

I assume this is an installation problem, but uninstalling and installing again won't help. I have the newest versions of samtools and bedtools. I installed using root.

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Turns out it was a non-issue. Apparently the script test_miso.py looks for c2c12.Atp2b1.sorted.bam, but the file is named c2c12.Atp2b1.bam. Fixing the script (or renaming the bam file) solved it.

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Hi. I'm also have this problem with batch-0, and all of previous solutions wasn't helpful, all the commands for testing MISO returns OK. Did you solved it?

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Hi,

To debug:

First check your-output-dir/A5SS/batch-logs/*.log

My problem was that I indexed my pickle files from another directory, then moved them. The .shelves file links to the absolute path of where you initially indexed the files, which was why it couldn't find them when I ran miso. To solve this, I had to re-index all my annotation files with:

index_gff --index SE.gff3 indexed_SE_events/
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After running this command - python -m unittest discover misopy, I got this error:

Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "/usr/lib/python2.7/unittest/__main__.py", line 12, in <module>
    main(module=None)
  File "/usr/lib/python2.7/unittest/main.py", line 94, in __init__
    self.parseArgs(argv)
  File "/usr/lib/python2.7/unittest/main.py", line 113, in parseArgs
    self._do_discovery(argv[2:])
  File "/usr/lib/python2.7/unittest/main.py", line 214, in _do_discovery
    self.test = loader.discover(start_dir, pattern, top_level_dir)
  File "/usr/lib/python2.7/unittest/loader.py", line 204, in discover
    raise ImportError('Start directory is not importable: %r' % start_dir)
ImportError: Start directory is not importable: 'misopy'

I installed misopy by conda install -c bioconda misopy

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