[miso-users] errors??

[Yarden Katz]

Hi,

Could you please send me a subset of your BAM file so I can try to reproduce it here?  Are you using our own posted modENCODE SE annotations from MISO website?  

Also, please check the MISO logs, they should have more information about what failed and that might be helpful.

Best, --Yarden

On Dec 9, 2013, at 4:47 PM, Katharine Abruzzi wrote:

> Dear Yarden,
> 
> I've just started working with Miso.  I installed the github version (which I am now thinking might have been a mistake?).  It seems to run okay and then I get thread-bath-1,2, and 3 might have failed?
> 
> Any ideas?
> 
> Thanks,
> Kate Abruzzi
> 
> Katharine Abruzzi, PhD
> Rosbash Lab
> Department of Biology
> Brandeis University
> 415 South Street
> Waltham, MA 02454
> 
> 
> python /usr/local/bin/anaconda/bin/miso --run /home/katea/analysis/modENCODE/indexed_SE_events/ /data/sequence3/katea_analysis/Evening_2/ESAT/KA_SEQ_61_sort.bam --output-dir /data/sequence3/katea_analysis/MISO/my_sample_output/ --read-len 51
> 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/bin/anaconda/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
> Computing Psi values...
>  - GFF index: /home/katea/analysis/modENCODE/indexed_SE_events
>  - BAM: /data/sequence3/katea_analysis/Evening_2/ESAT/KA_SEQ_61_sort.bam
>  - Read length: 51
>  - Output directory: /data/sequence3/katea_analysis/MISO/my_sample_output
> 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/katea/analysis/modENCODE/indexed_SE_events
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr2R
>  - Loading 534 genes
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/compressed_ids_to_genes.shelve.dir
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr4
>  - Loading 124 genes
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr3R
>  - Loading 507 genes
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/compressed_ids_to_genes.shelve.bak
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr2RHet
>  - Loading 28 genes
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/genes.gff
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/genes_to_filenames.shelve.dat
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/genes_to_filenames.shelve.bak
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chrX
>  - Loading 344 genes
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chrU
>  - Loading 4 genes
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr2L
>  - Loading 381 genes
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chrXHet
>  - Loading 3 genes
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/genes_to_filenames.shelve.dir
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr3L
>  - Loading 436 genes
> Skipping: /home/katea/analysis/modENCODE/indexed_SE_events/compressed_ids_to_genes.shelve.dat
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr3RHet
>  - Loading 5 genes
> Loading indexed gene filenames from: /home/katea/analysis/modENCODE/indexed_SE_events/chr3LHet
>  - Loading 4 genes
> Preparing to run 4 batches of jobs...
> Running batch of 592 genes..
>  - Executing: python /usr/local/bin/anaconda/bin/run_miso.py --compute-genes-from-file "/data/sequence3/katea_analysis/MISO/my_sample_output/batch-genes/batch-0_genes.txt" /data/sequence3/katea_analysis/Evening_2/ESAT/KA_SEQ_61_sort.bam /data/sequence3/katea_analysis/MISO/my_sample_output --read-len 51  --overhang-len 1 --settings-filename /usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
>  - Submitted thread batch-0
> Running batch of 593 genes..
>  - Executing: python /usr/local/bin/anaconda/bin/run_miso.py --compute-genes-from-file "/data/sequence3/katea_analysis/MISO/my_sample_output/batch-genes/batch-1_genes.txt" /data/sequence3/katea_analysis/Evening_2/ESAT/KA_SEQ_61_sort.bam /data/sequence3/katea_analysis/MISO/my_sample_output --read-len 51  --overhang-len 1 --settings-filename /usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
>  - Submitted thread batch-1
> Running batch of 592 genes..
>  - Executing: python /usr/local/bin/anaconda/bin/run_miso.py --compute-genes-from-file "/data/sequence3/katea_analysis/MISO/my_sample_output/batch-genes/batch-2_genes.txt" /data/sequence3/katea_analysis/Evening_2/ESAT/KA_SEQ_61_sort.bam /data/sequence3/katea_analysis/MISO/my_sample_output --read-len 51  --overhang-len 1 --settings-filename /usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
>  - Submitted thread batch-2
> Traceback (most recent call last):
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 490, in <module>
>    main()
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 434, in main
>    run_compute_genes_from_file(options)
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 254, in run_compute_genes_from_file
>    event_type=options.event_type)
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 124, in compute_gene_psi
>    gff_utils.get_inclusive_txn_bounds(gene_info['hierarchy'][gene_id])
>  File "/usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/gff_utils.py", line 945, in get_inclusive_txn_bounds
>    assert(strand != None)
> AssertionError
> Running batch of 593 genes..
>  - Executing: python /usr/local/bin/anaconda/bin/run_miso.py --compute-genes-from-file "/data/sequence3/katea_analysis/MISO/my_sample_output/batch-genes/batch-3_genes.txt" /data/sequence3/katea_analysis/Evening_2/ESAT/KA_SEQ_61_sort.bam /data/sequence3/katea_analysis/MISO/my_sample_output --read-len 51  --overhang-len 1 --settings-filename /usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
>  - Submitted thread batch-3
> Waiting on local threads...
> Waiting on 4 threads...
> WARNING: Thread batch-0 might have failed...
> Traceback (most recent call last):
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 490, in <module>
>    main()
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 434, in main
>    run_compute_genes_from_file(options)
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 254, in run_compute_genes_from_file
>    event_type=options.event_type)
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 124, in compute_gene_psi
>    gff_utils.get_inclusive_txn_bounds(gene_info['hierarchy'][gene_id])
>  File "/usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/gff_utils.py", line 945, in get_inclusive_txn_bounds
>    assert(strand != None)
> AssertionError
> WARNING: Thread batch-2 might have failed...
> Traceback (most recent call last):
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 490, in <module>
>    main()
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 434, in main
>    run_compute_genes_from_file(options)
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 254, in run_compute_genes_from_file
>    event_type=options.event_type)
>  File "/usr/local/bin/anaconda/bin/run_miso.py", line 124, in compute_gene_psi
>    gff_utils.get_inclusive_txn_bounds(gene_info['hierarchy'][gene_id])
>  File "/usr/local/bin/anaconda/lib/python2.7/site-packages/misopy/gff_utils.py", line 945, in get_inclusive_txn_bounds
>    assert(strand != None)
> AssertionError
> WARNING: Thread batch-3 might have failed...
>  - Threads completed in 0.00 hours.
> _______________________________________________
> miso-users mailing list
> miso-users at mit.edu
> http://mailman.mit.edu/mailman/listinfo/miso-users