[miso-users] errors with run_events_analysis
Maayan Kreitzman
mkreitzman at bcgsc.ca
Thu Apr 4 17:03:44 EDT 2013
Hi Yarden,
Sorry to be such a pest about this. I installed the latest version, and re-built the index but I'm still not able to run the program successfully the way you did. I'm using he same mini bam file that I sent to you.
I'm attaching the log.
Maayan
________________________________________
From: Yarden Katz [yardenny at gmail.com] On Behalf Of Yarden Katz [yarden at mit.edu]
Sent: Monday, March 25, 2013 5:09 PM
To: Maayan Kreitzman
Cc: miso-users at mit.edu
Subject: Re: [miso-users] errors with run_events_analysis
Hi Maayan,
When you install from Github, there's an additional step in the installation (described in detail here: http://genes.mit.edu/burgelab/miso/docs/#installing-the-latest-version-from-github-repository). Basically, before running setup.py install, you have to run:
$ make Pythonpackage
That will create the necessary files needed to compile the program. Then your call to setup.py install should run.
Also, I don't recommend installing packages with setup.py install in general (it's better to use pip or the distribute version of easy_install) but if it's working for you, stick to it. It should install the new MISO over your old version if you install it the same way.
Best, --Yarden
On Mar 25, 2013, at 6:24 PM, Maayan Kreitzman wrote:
> Hi Yarden,
>
> I can't seem to install the new version. I downloaded the zip file from the GitHub page.
>
> Before I was using misopy-0.4.7, which I installed using
> python setup.py install --prefix=~/
> and then adding the directory to the PYTHONPATH.
>
> Now I'm getting the messages copied below
>
> חג שמח!
>
> Maayan
>
>
> /gsc/software/linux-x86_64-centos5/python-science-2.7.1/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'install_requires'
> warnings.warn(msg)
> running install
> running build
> running build_py
> copying misopy/__init__.py -> build/lib.linux-x86_64-2.7/misopy
> running build_ext
> building 'pysplicing.pysplicing' extension
> gcc44 -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_RINTF=1 -DHAVE_FINITE=1 -DHAVE_EXPM1=1 -DHAVE_RINT=1 -DHAVE_LOG2=1 -DHAVE_LOGBL=1 -DHAVE_SNPRINTF=1 -DHAVE_LOG1P=1 -DHAVE_ROUND=1 -DHAVE_FMIN=1 -Ipysplicing/include -Ipysplicing/src/lapack -Ipysplicing/src/f2c -I/gsc/software/linux-x86_64-centos5/python-science-2.7.1/include/python2.7 -c pysplicing/src/pyconvert.c -o build/temp.linux-x86_64-2.7/pysplicing/src/pyconvert.o
> In file included from pysplicing/src/pyconvert.c:2:
> pysplicing/include/pysplicing.h:7:22: error: splicing.h: No such file or directory
> In file included from pysplicing/src/pyconvert.c:2:
> pysplicing/include/pysplicing.h:9: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:10: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_t’
> pysplicing/include/pysplicing.h:11: error: expected declaration specifiers or ‘...’ before ‘splicing_strvector_t’
> pysplicing/include/pysplicing.h:12: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:13: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:15: warning: type defaults to ‘int’ in declaration of ‘splicing_vector_t’
> pysplicing/include/pysplicing.h:15: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:16: warning: type defaults to ‘int’ in declaration of ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:16: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:17: warning: type defaults to ‘int’ in declaration of ‘splicing_matrix_t’
> pysplicing/include/pysplicing.h:17: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:18: warning: type defaults to ‘int’ in declaration of ‘splicing_strvector_t’
> pysplicing/include/pysplicing.h:18: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:19: warning: type defaults to ‘int’ in declaration of ‘splicing_vector_int_t’
> pysplicing/include/pysplicing.h:19: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/include/pysplicing.h:21: warning: type defaults to ‘int’ in declaration of ‘splicing_miso_rundata_t’
> pysplicing/include/pysplicing.h:21: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:4: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_vector_int’:
> pysplicing/src/pyconvert.c:13: warning: implicit declaration of function ‘splicing_vector_int_init’
> pysplicing/src/pyconvert.c:13: error: ‘v’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c:13: error: (Each undeclared identifier is reported only once
> pysplicing/src/pyconvert.c:13: error: for each function it appears in.)
> pysplicing/src/pyconvert.c:16: warning: implicit declaration of function ‘VECTOR’
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:22: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_vector’:
> pysplicing/src/pyconvert.c:31: warning: implicit declaration of function ‘splicing_vector_init’
> pysplicing/src/pyconvert.c:31: error: ‘v’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:40: error: expected declaration specifiers or ‘...’ before ‘splicing_strvector_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_strvector’:
> pysplicing/src/pyconvert.c:49: warning: implicit declaration of function ‘splicing_strvector_init’
> pysplicing/src/pyconvert.c:49: error: ‘v’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c:50: warning: implicit declaration of function ‘splicing_strvector_reserve’
> pysplicing/src/pyconvert.c:53: warning: implicit declaration of function ‘splicing_strvector_append’
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:59: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_exons’:
> pysplicing/src/pyconvert.c:61: error: ‘ex’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:70: error: expected declaration specifiers or ‘...’ before ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c: In function ‘pysplicing_to_isoforms’:
> pysplicing/src/pyconvert.c:77: error: ‘iso’ undeclared (first use in this function)
> pysplicing/src/pyconvert.c: At top level:
> pysplicing/src/pyconvert.c:91: warning: type defaults to ‘int’ in declaration of ‘splicing_vector_t’
> pysplicing/src/pyconvert.c:91: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:101: warning: type defaults to ‘int’ in declaration of ‘splicing_matrix_t’
> pysplicing/src/pyconvert.c:101: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:118: warning: type defaults to ‘int’ in declaration of ‘splicing_matrix_t’
> pysplicing/src/pyconvert.c:118: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:135: warning: type defaults to ‘int’ in declaration of ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c:135: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:146: warning: type defaults to ‘int’ in declaration of ‘splicing_strvector_t’
> pysplicing/src/pyconvert.c:146: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:156: warning: type defaults to ‘int’ in declaration of ‘splicing_vector_int_t’
> pysplicing/src/pyconvert.c:156: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> pysplicing/src/pyconvert.c:174: warning: type defaults to ‘int’ in declaration of ‘splicing_miso_rundata_t’
> pysplicing/src/pyconvert.c:174: error: expected ‘;’, ‘,’ or ‘)’ before ‘*’ token
> error: command 'gcc44' failed with exit status 1
>
>
> ________________________________________
> From: Yarden Katz [yardenny at gmail.com] On Behalf Of Yarden Katz [yarden at mit.edu]
> Sent: Friday, March 22, 2013 7:49 PM
> To: Maayan Kreitzman
> Cc: miso-users at mit.edu
> Subject: Re: [miso-users] errors with run_events_analysis
>
> Hi Maayan,
>
> It was an unfortunate bug with handling of non-UCSC style chromosomes that is now fixed in Github. I guess most people use Ensembl annotations from UCSC as opposed to Ensembl (which follow UCSC-style chromosome naming) so it was not reported. You can download the latest version here:
>
> https://github.com/yarden/MISO
>
> You can click on the "zip" button to download the latest version. Just install it in place of current and it should work. I was able to run it on your BAM with:
>
> $ run_events_analysis.py --compute-genes-psi ./indexed/ ./maayan.bam --output-dir ./miso_output/ --read-len 100 --prefilter -p 10
>
> I include the output I got below. You don't have to use the "--prefilter -p 10" options but they do speed things up considerably if you're running on a single multi-core machine and not a cluster (note that "--prefilter" requires bedtools/tagBam to be available.)
>
> If you confirm that it works for you, I'll make a new release stable with this issue fixed.
>
> Thanks. Best, --Yarden
>
>
>
> ========
> $ ./test_maayan.sh
> MISO (Mixture of Isoforms model)
> Probabilistic analysis of RNA-Seq data to detect differential isoforms
> Use --help argument to view options.
>
> Loading settings from: /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> Computing gene-level Psi for genes...
> - GFF index: /lab/solexa_data2/yarden/test-maayan/indexed
> - BAM: /lab/solexa_data2/yarden/test-maayan/maayan.bam
> - Read length: 100
> - Output directory: /lab/solexa_data2/yarden/test-maayan/miso_output
> - Prefilter: True
> - Prefiltering on
> Prefiltering reads...
> Generating coverage file...
> - BAM file: /lab/solexa_data2/yarden/test-maayan/maayan.bam
> - GFF file: /lab/solexa_data2/yarden/test-maayan/indexed/genes.gff
> - Output file: /lab/solexa_data2/yarden/test-maayan/miso_output/maayan.bed
> Executing: bedtools intersect -abam /lab/solexa_data2/yarden/test-maayan/maayan.bam -b /lab/solexa_data2/yarden/test-maayan/indexed/genes.gff -f 1 -ubam | bedtools coverage -abam - -b /lab/solexa_data2/yarden/test-maayan/indexed/genes.gff -counts > /lab/solexa_data2/yarden/test-maayan/miso_output/maayan.bed
> - Total of 166 events pass coverage filter.
> Using 10 processors
> Mapping genes to their indexed GFF representation, using /lab/solexa_data2/yarden/test-maayan/indexed
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr18
> - Loading 537 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000219.1
> - Loading 6 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_APD
> - Loading 185 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr3
> - Loading 2897 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr20
> - Loading 1273 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR4_1
> - Loading 9 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_MANN
> - Loading 322 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr17
> - Loading 2027 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr8
> - Loading 2297 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000193.1
> - Loading 5 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000230.1
> - Loading 3 genes
> Skipping: /lab/solexa_data2/yarden/test-maayan/indexed/compressed_ids_to_genes.shelve
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000192.1
> - Loading 7 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr19
> - Loading 1950 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr15
> - Loading 1797 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr10
> - Loading 2193 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr12
> - Loading 2740 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_DBB
> - Loading 333 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr16
> - Loading 1347 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000205.1
> - Loading 8 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000223.1
> - Loading 5 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_COX
> - Loading 362 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000240.1
> - Loading 3 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrX
> - Loading 2323 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_SSTO
> - Loading 326 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000224.1
> - Loading 4 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr14
> - Loading 2167 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr5
> - Loading 2720 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr22
> - Loading 1189 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000228.1
> - Loading 17 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr2
> - Loading 3856 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr6
> - Loading 2782 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr7
> - Loading 2754 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000213.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000201.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr1
> - Loading 5145 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000222.1
> - Loading 3 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000194.1
> - Loading 3 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr9
> - Loading 2336 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000209.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000212.1
> - Loading 4 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000199.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_MCF
> - Loading 286 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000233.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr13
> - Loading 1176 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000195.1
> - Loading 2 genes
> Skipping: /lab/solexa_data2/yarden/test-maayan/indexed/genes_to_filenames.shelve
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR6_MHC_QBL
> - Loading 344 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr21
> - Loading 695 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrMT
> - Loading 37 genes
> Skipping: /lab/solexa_data2/yarden/test-maayan/indexed/genes.gff
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000243.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000191.1
> - Loading 2 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrY
> - Loading 513 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr4
> - Loading 2477 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000220.1
> - Loading 18 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chr11
> - Loading 3107 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrHSCHR17_1
> - Loading 48 genes
> Loading indexed gene filenames from: /lab/solexa_data2/yarden/test-maayan/indexed/chrGL000247.1
> - Loading 3 genes
> Preparing to run 11 batches of jobs...
> Running batch of 16 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-0_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-0
> Running batch of 17 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-1_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-1
> Running batch of 16 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-2_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-2
> Running batch of 17 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-3_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-3
> Running batch of 17 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-4_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-4
> Running batch of 16 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-5_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-5
> Running batch of 17 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-6_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-6
> Running batch of 16 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-7_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-7
> Running batch of 17 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-8_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-8
> Running batch of 16 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-9_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-9
> Running batch of 1 genes..
> - Executing: python /lab/solexa_data2/yarden/MISO/misopy/run_miso.py --compute-genes-from-file "/lab/solexa_data2/yarden/test-maayan/miso_output/batch-genes/batch-10_genes.txt" /lab/solexa_data2/yarden/test-maayan/maayan.bam /lab/solexa_data2/yarden/test-maayan/miso_output --read-len 100 --overhang-len 1 --settings-filename /lab/solexa_data2/yarden/MISO/misopy/settings/miso_settings.txt
> - Submitted thread batch-10
> Waiting on 11 threads...
> - Threads completed in 0.17 hours.
>
>
>
> On Mar 21, 2013, at 7:23 PM, Maayan Kreitzman wrote:
>
>> Hi Yarden,
>>
>> I just downloaded the Homo_sapiens.GRCh37.65.gff you supply in the manual at the bottom of the "Human/mouse gene models for isoform-centric analysis" section (http://genes.mit.edu/burgelab/miso/docs/#iso-centric)
>> the folders in the indexed/ directory do have the chr prefix so it must be that. Was this the wrong gff3 to be using?
>> I put a piece f the bam file on dropbox: https://www.dropbox.com/s/eljbpt1d6vjhuww/A08586_test.bam
>>
>> maayan
>> ________________________________________
>> From: Yarden Katz [yardenny at gmail.com] On Behalf Of Yarden Katz [yarden at mit.edu]
>> Sent: Thursday, March 21, 2013 3:45 PM
>> To: Maayan Kreitzman
>> Cc: miso-users at mit.edu
>> Subject: Re: [miso-users] errors with run_events_analysis
>>
>> Hi Maayan,
>>
>> I think it's a bug with chromosome naming of the index files that was introduced a while ago and was fixed. The newest version of MISO (in github) should have better error handling. But to be sure, could you please tell me how your indexed chromosome directories are named, i.e. what is:
>>
>> $ ls /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/
>>
>> Finally, the easiest way to get to the bottom of it is if you send me the GFF you used (I assume it's from an Ensembl annotaton) and any small portion of the BAM. I don't need the whole BAM, you can simply take out any segment of it that has the headers, e.g. one chromosome's worth of reads or even less, such as:
>>
>> # pulls out all of chromosome 1
>> $ samtools view -bh yourbam.bam 1 -o test.bam
>>
>> # pulls out a segment of chromosome 1, bases 1-10000000
>> $ samtools view -bh yourbam.bam 1:1-10000000 -o test.bam
>>
>> A small BAM segment reveals nothing of anything and I assure you I will delete it once I get to the bottom of this bug. I'm sure that this will be trivial to fix (if it isn't already fixed in the latest GitHub version).
>>
>> --Yarden
>>
>>
>>
>>
>> On Mar 21, 2013, at 1:10 PM, Maayan Kreitzman wrote:
>>
>>> Hi Yarden,
>>>
>>> As far as I can tell, there are no prefixes in the bam file.
>>>
>>> I attached the results from the three commands so you can take a look.
>>>
>>> thanks for you help!
>>>
>>> Maayan
>>> ________________________________________
>>> From: Yarden Katz [yardenny at gmail.com] On Behalf Of Yarden Katz [yarden at mit.edu]
>>> Sent: Wednesday, March 20, 2013 5:50 PM
>>> To: Maayan Kreitzman
>>> Cc: miso-users at mit.edu
>>> Subject: Re: [miso-users] errors with run_events_analysis
>>>
>>> It would also be useful to see:
>>>
>>> $ head /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/genes.gff
>>>
>>>
>>> --Yarden
>>>
>>>
>>>
>>> On Mar 20, 2013, at 8:46 PM, Yarden Katz wrote:
>>>
>>>> Hi Maayan,
>>>>
>>>> Can you confirm that your BAM file does not have chr prefixes? I.e. can you please let me know what the output of these commands are:
>>>>
>>>> $ samtools view /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam | head
>>>>
>>>> and
>>>>
>>>> $ samtools view -H /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam
>>>>
>>>> Best, --Yarden
>>>>
>>>>
>>>>
>>>>
>>>> On Mar 20, 2013, at 8:35 PM, Maayan Kreitzman wrote:
>>>>
>>>>> Hi everyone,
>>>>>
>>>>> I'm new to MISO, and would like some help. I've successfully installed misopy-0.4.7.
>>>>>
>>>>> I also downloaded and indexed the ensembl gff3 (no "chr" in the chromosome names).
>>>>> The next step isn't working though. My library is a paired-end strand specific library.
>>>>>
>>>>> The command I ran is this:
>>>>>
>>>>> python misopy/run_events_analysis.py --paired-end 75 8 --compute-genes-psi /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/indexed/ /projects/mkreitzman_prj/expression_quantification_testing/testing/test_data/strand_specific/JAGuaR_rev_87647/A08586_gr3.neg.bam --output-dir /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results --read-len 100 &> /projects/mkreitzman_prj/expression_quantification_testing/testing/MISO/results/A08586.log
>>>>>
>>>>> the errors I get look like this (I've attached the full std out + stderr):
>>>>> Traceback (most recent call last):
>>>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 488, in <module>
>>>>> main()
>>>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 432, in main
>>>>> run_compute_genes_from_file(options)
>>>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 247, in run_compute_genes_from_file
>>>>> event_type=options.event_type)
>>>>> File "/projects/mkreitzman_prj/expression_quantification_testing/misopy-0.4.7/misopy/run_miso.py", line 128, in compute_gene_psi
>>>>> gene_obj)
>>>>> File "/home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7-py2.7-linux-x86_64.egg/misopy/sam_utils.py", line 191, in fetch_bam_reads_in_gene
>>>>> chrom = chrom_parts[1]
>>>>> IndexError: list index out of range
>>>>>
>>>>> The bam file is position sorted and has a .bai in the same folder. The parameters for the --paired-end are just off the top of my head, but I tried without this option at all and the same thing happens.
>>>>>
>>>>> Thanks in advance for any ideas you may have.
>>>>>
>>>>> Maayan<A08586.log>_______________________________________________
>>>>> miso-users mailing list
>>>>> miso-users at mit.edu
>>>>> http://mailman.mit.edu/mailman/listinfo/miso-users
>>>>
>>>>
>>>> _______________________________________________
>>>> miso-users mailing list
>>>> miso-users at mit.edu
>>>> http://mailman.mit.edu/mailman/listinfo/miso-users
>>>
>>
>
>
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