[miso-users] errors??

[Katharine Abruzzi]

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.