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<div class="moz-cite-prefix"><font face="Helvetica, Arial,
sans-serif">Hi Yarden,<br>
I ended up deleting up to <br>
</font>
<pre wrap=""><font face="Helvetica, Arial, sans-serif">/home/mkreitzman/.local/lib/python2.7/</font></pre>
<font face="Helvetica, Arial, sans-serif">
for it to work, seems good now. <br>
thanks!<br>
</font>Maayan<br>
<br>
<br>
<br>
On 04/08/2013 08:12 AM, Yarden Katz wrote:<br>
</div>
<blockquote
cite="mid:D271C31B-8D12-44CE-885A-8706F732C84B@csail.mit.edu"
type="cite">
<pre wrap="">Hi Maayan,
Looking at your log, i think the problem is that you're still running the old version of MISO and not the latest version from GitHub.
See the end of the log, where it says:
==
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]
==
So it's still using the old version (miso-0.4.7) which has that unfortunate bug.
I recommend deleting /home/mkreitzman/.local/lib/python2.7/site-packages/misopy-0.4.7*
and then installing your GitHub downloaded version in its place. You can do this ideally with a Python package manager like distribute or pip, but if you don't want to go that route you can just use:
(In "MISO-fastmiso" directory)
$ make Pythonpackage
$ python setup.py install --prefix=~/.local/
That should install your GitHub copy in the place where the stable release 0.4.7 was previously. Then if you have ~/.local/bin in your PATH you can run MISO as usual.
That should fix the error.
Best, --Yarden
On Apr 4, 2013, at 5:03 PM, Maayan Kreitzman wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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 [<a class="moz-txt-link-abbreviated" href="mailto:yardenny@gmail.com">yardenny@gmail.com</a>] On Behalf Of Yarden Katz [<a class="moz-txt-link-abbreviated" href="mailto:yarden@mit.edu">yarden@mit.edu</a>]
Sent: Monday, March 25, 2013 5:09 PM
To: Maayan Kreitzman
Cc: <a class="moz-txt-link-abbreviated" href="mailto:miso-users@mit.edu">miso-users@mit.edu</a>
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: <a class="moz-txt-link-freetext" href="http://genes.mit.edu/burgelab/miso/docs/#installing-the-latest-version-from-github-repository">http://genes.mit.edu/burgelab/miso/docs/#installing-the-latest-version-from-github-repository</a>). 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:
</pre>
<blockquote type="cite">
<pre wrap="">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
çâ ůîç!
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 [<a class="moz-txt-link-abbreviated" href="mailto:yardenny@gmail.com">yardenny@gmail.com</a>] On Behalf Of Yarden Katz [<a class="moz-txt-link-abbreviated" href="mailto:yarden@mit.edu">yarden@mit.edu</a>]
Sent: Friday, March 22, 2013 7:49 PM
To: Maayan Kreitzman
Cc: <a class="moz-txt-link-abbreviated" href="mailto:miso-users@mit.edu">miso-users@mit.edu</a>
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:
<a class="moz-txt-link-freetext" href="https://github.com/yarden/MISO">https://github.com/yarden/MISO</a>
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:
</pre>
<blockquote type="cite">
<pre wrap="">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 (<a class="moz-txt-link-freetext" href="http://genes.mit.edu/burgelab/miso/docs/#iso-centric">http://genes.mit.edu/burgelab/miso/docs/#iso-centric</a>)
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: <a class="moz-txt-link-freetext" href="https://www.dropbox.com/s/eljbpt1d6vjhuww/A08586_test.bam">https://www.dropbox.com/s/eljbpt1d6vjhuww/A08586_test.bam</a>
maayan
________________________________________
From: Yarden Katz [<a class="moz-txt-link-abbreviated" href="mailto:yardenny@gmail.com">yardenny@gmail.com</a>] On Behalf Of Yarden Katz [<a class="moz-txt-link-abbreviated" href="mailto:yarden@mit.edu">yarden@mit.edu</a>]
Sent: Thursday, March 21, 2013 3:45 PM
To: Maayan Kreitzman
Cc: <a class="moz-txt-link-abbreviated" href="mailto:miso-users@mit.edu">miso-users@mit.edu</a>
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:
</pre>
<blockquote type="cite">
<pre wrap="">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 [<a class="moz-txt-link-abbreviated" href="mailto:yardenny@gmail.com">yardenny@gmail.com</a>] On Behalf Of Yarden Katz [<a class="moz-txt-link-abbreviated" href="mailto:yarden@mit.edu">yarden@mit.edu</a>]
Sent: Wednesday, March 20, 2013 5:50 PM
To: Maayan Kreitzman
Cc: <a class="moz-txt-link-abbreviated" href="mailto:miso-users@mit.edu">miso-users@mit.edu</a>
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:
</pre>
<blockquote type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">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>_______________________________________________
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<pre wrap="">
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