[miso-users] Syntax error with MISO

Tue Mar 5 21:35:49 EST 2013

Dear Yarden,

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?

katschi at 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.

Loading settings from:
/programs/apps/python/python-2.7/lib/python2.7/misopy/settings/miso_settings
.txt

Computing gene-level Psi for genes...

  - GFF index:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events

  - BAM:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_a
ccepted_hits.sorted.bam

  - Read length: 50

  - Output directory:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons

Mapping genes to their indexed GFF representation, using
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr6

  - Loading 1762 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr7

  - Loading 2059 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr5

  - Loading 1595 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr19

  - Loading 2343 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr1

  - Loading 4035 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr4

  - Loading 1466 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr8

  - Loading 1386 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr2

  - Loading 2781 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chrY

  - Loading 45 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr18

  - Loading 574 genes

Skipping:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/genes_to_filenames.shelve

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr15

  - Loading 1366 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr10

  - Loading 1774 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chrX

  - Loading 1146 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr11

  - Loading 2287 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr16

  - Loading 1709 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr12

  - Loading 2301 genes

Skipping:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/compressed_ids_to_genes.shelve

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr13

  - Loading 715 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr17

  - Loading 2146 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr21

  - Loading 438 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr14

  - Loading 1280 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr3

  - Loading 2397 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr9

  - Loading 1524 genes

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr22

  - Loading 1002 genes

Skipping:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/genes.gff

Loading indexed gene filenames from:
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/hg19_indexed_SE
_events/chr20

  - Loading 1101 genes

Preparing to run 4 batches of jobs...

Running batch of 9808 genes..

  - 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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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

  - Submitted thread batch-0

Running batch of 9808 genes..

  - 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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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

  - Submitted thread batch-1

Running batch of 9808 genes..

  - 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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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

  - Submitted thread batch-2

Running batch of 9808 genes..

  - 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_a
ccepted_hits.sorted.bam
/scratch_nmr/katschi/HEK293_KD_analysis/all_samples_complete/10L_thout/10L_e
xons --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

  - Submitted thread batch-3

Waiting on 4 threads...

  File "/programs/apps/miso/bin/run_miso.py", line 238

    with open(genes_filename) as genes_in:

            ^

SyntaxError: invalid syntax

  File "/programs/apps/miso/bin/run_miso.py", line 238

    with open(genes_filename) as genes_in:

            ^

SyntaxError: invalid syntax

WARNING: Thread batch-0 might have failed...

  File "/programs/apps/miso/bin/run_miso.py", line 238

    with open(genes_filename) as genes_in:

            ^

SyntaxError: invalid syntax

  File "/programs/apps/miso/bin/run_miso.py", line 238

    with open(genes_filename) as genes_in:

            ^

SyntaxError: invalid syntax

WARNING: Thread batch-1 might have failed...

WARNING: Thread batch-2 might have failed...

WARNING: Thread batch-3 might have failed...

  - Threads completed in 0.00 hours.

Kind regards,

Katerina

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