[miso-users] errors with run_events_analysis

Wed Apr 10 10:39:40 EDT 2013

Hi Yarden,

I'm having trouble with run_events_analysis.py on my Drosophila bam file and the modENCODE alternative event annotations. The MISO test scripts work fine, but my run seems to crash out of python. I'll post the run info below. Thanks for the help.

-Eric

$ python run_events_analysis.py --compute-genes-psi ../../modENCODE/indexed_a5ss_events/ ../../input_miso/EG003_slug_sorted.bam --output-dir ../../output_miso/output_a5ss_miso --read-len 48
MISO (Mixture of Isoforms model)
Probabilistic analysis of RNA-Seq data to detect differential isoforms
Use --help argument to view options.

Loading settings from: /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
Computing Psi values...
  - GFF index: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events
  - BAM: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam
  - Read length: 48
  - Output directory: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso
Checking your GFF annotation and BAM for mismatches...
Checking if BAM has mixed read lengths...
Found reads of length 48 in BAM.
Mapping genes to their indexed GFF representation, using /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr2L
  - Loading 715 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr2LHet
  - Loading 6 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr2R
  - Loading 868 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr2RHet
  - Loading 13 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr3L
  - Loading 777 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr3LHet
  - Loading 10 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr3R
  - Loading 1005 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr3RHet
  - Loading 6 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chr4
  - Loading 123 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chrU
  - Loading 12 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chrX
  - Loading 806 genes
Loading indexed gene filenames from: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/chrXHet
  - Loading 4 genes
Skipping: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/compressed_ids_to_genes.shelve
Skipping: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/genes.gff
Skipping: /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/modENCODE/indexed_a5ss_events/genes_to_filenames.shelve
Preparing to run 4 batches of jobs...
Running batch of 1086 genes..
  - Executing: python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-0_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48  --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-0
Running batch of 1086 genes..
  - Executing: python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-1_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48  --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-1
Running batch of 1086 genes..
  - Executing: python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-2_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48  --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-2
Running batch of 1087 genes..
  - Executing: python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-3_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48  --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt
  - Submitted thread batch-3
Waiting on 4 threads...
Python(32458) malloc: *** error for object 0x108895ef0: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
/bin/sh: line 1: 32458 Abort trap: 6           python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-0_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48 --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt >> "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-logs/batch-0-04-10-13_10:12:49.log"
WARNING: Thread batch-0 might have failed...
/bin/sh: line 1: 32459 Bus error: 10           python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-1_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48 --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt >> "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-logs/batch-1-04-10-13_10:12:49.log"
WARNING: Thread batch-1 might have failed...
/bin/sh: line 1: 32462 Bus error: 10           python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-2_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48 --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt >> "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-logs/batch-2-04-10-13_10:12:49.log"
WARNING: Thread batch-2 might have failed...
/bin/sh: line 1: 32463 Bus error: 10           python /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/yarden-MISO-84401f4/misopy/run_miso.py --compute-genes-from-file "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-genes/batch-3_genes.txt" /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/input_miso/EG003_slug_sorted.bam /Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso --read-len 48 --overhang-len 1 --settings-filename /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/misopy/settings/miso_settings.txt >> "/Users/gregmatera/Desktop/EG.RNAseq.Analysis/Python/output_miso/output_a5ss_miso/batch-logs/batch-3-04-10-13_10:12:49.log"
WARNING: Thread batch-3 might have failed...
  - Threads completed in 0.05 hours.

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