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<p class=MsoNormal>Dear Yarden,<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I have only just started using MISO and am not very
experienced with bioinformatics. I have mapped my RNA-seq data with TOPHAT and
am currently trying to detect differentially spliced exons with MISO. The
program unfortunately seems to run into a syntax error. I pasted everything
below. Maybe you have an idea what could be going wrong?<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoPlainText><span style='color:#215868'>katschi@rupertbear
all_samples_complete]$ run_events_analysis.py --compute-genes-psi
hg19_indexed_SE_events/ 10L_thout/10L_accepted_hits.sorted.bam --output-dir
10L_thout/10L_exons --read-len 50 --paired-end 120 23 MISO (Mixture of Isoforms
model) Probabilistic analysis of RNA-Seq data to detect differential isoforms
Use --help argument to view options.<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'><o:p> </o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading settings from:
/programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Computing gene-level Psi for
genes...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - GFF index:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - BAM:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Read length: 50<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Output directory:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Mapping genes to their
indexed GFF representation, using
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr6<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1762 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr7<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2059 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr5<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1595 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr19<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2343 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr1<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 4035 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr4<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1466 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr8<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1386 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr2<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2781 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chrY<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 45 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene filenames
from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr18<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 574 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Skipping:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/genes_to_filenames.shelve<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr15<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1366 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr10<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1774 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chrX<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1146 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr11<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2287 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr16<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1709 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr12<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2301 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Skipping:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/compressed_ids_to_genes.shelve<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr13<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 715 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr17<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2146 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr21<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 438 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr14<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1280 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr3<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 2397 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr9<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1524 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr22<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1002 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Skipping:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/genes.gff<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Loading indexed gene
filenames from: /scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE_events/chr20<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Loading 1101 genes<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Preparing to run 4 batches of
jobs...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Running batch of 9808 genes..<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Executing: python
/programs/apps/miso/bin/run_miso.py --compute-genes-from-file
"/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-0_genes.txt"
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons
--read-len 50 --paired-end 120.0 23.0 --settings-filename
/programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Submitted thread batch-0<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Running batch of 9808 genes..<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Executing: python
/programs/apps/miso/bin/run_miso.py --compute-genes-from-file
"/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-1_genes.txt"
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons
--read-len 50 --paired-end 120.0 23.0 --settings-filename
/programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Submitted thread batch-1<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Running batch of 9808 genes..<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Executing: python
/programs/apps/miso/bin/run_miso.py --compute-genes-from-file
"/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-2_genes.txt"
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons
--read-len 50 --paired-end 120.0 23.0 --settings-filename
/programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Submitted thread batch-2<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Running batch of 9808 genes..<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Executing: python
/programs/apps/miso/bin/run_miso.py --compute-genes-from-file
"/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons/batch-genes/batch-3_genes.txt"
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_accepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_exons
--read-len 50 --paired-end 120.0 23.0 --settings-filename
/programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings.txt<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Submitted thread batch-3<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>Waiting on 4 threads...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> File
"/programs/apps/miso/bin/run_miso.py", line 238<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> with open(genes_filename)
as genes_in:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> ^<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>SyntaxError: invalid syntax<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> File
"/programs/apps/miso/bin/run_miso.py", line 238<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> with open(genes_filename)
as genes_in:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> ^<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>SyntaxError: invalid syntax<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>WARNING: Thread batch-0 might
have failed...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> File
"/programs/apps/miso/bin/run_miso.py", line 238<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> with open(genes_filename)
as genes_in:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> ^<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>SyntaxError: invalid syntax<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> File
"/programs/apps/miso/bin/run_miso.py", line 238<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> with open(genes_filename)
as genes_in:<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> ^<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>SyntaxError: invalid syntax<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>WARNING: Thread batch-1 might
have failed...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>WARNING: Thread batch-2 might
have failed...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'>WARNING: Thread batch-3 might
have failed...<o:p></o:p></span></p>
<p class=MsoPlainText><span style='color:#215868'> - Threads completed in 0.00
hours.<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Kind regards,<o:p></o:p></p>
<p class=MsoNormal>Katerina<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
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