<div dir="ltr">Do you have samtools installed or loaded in your HPC environment?</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Il giorno gio 17 ott 2019 alle ore 16:00 <<a href="mailto:miso-users-request@mit.edu">miso-users-request@mit.edu</a>> ha scritto:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send miso-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Installing misopy (Rayhaan Ali)<br>
<br>
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Message: 1<br>
Date: Thu, 17 Oct 2019 14:00:19 +0000<br>
From: Rayhaan Ali <<a href="mailto:rali03@qub.ac.uk" target="_blank">rali03@qub.ac.uk</a>><br>
Subject: [miso-users] Installing misopy<br>
To: "<a href="mailto:miso-users@mit.edu" target="_blank">miso-users@mit.edu</a>" <<a href="mailto:miso-users@mit.edu" target="_blank">miso-users@mit.edu</a>><br>
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Hi All,<br>
<br>
I have been attempting to install misopy (<a href="https://miso.readthedocs.io/en/fastmiso/#" rel="noreferrer" target="_blank">https://miso.readthedocs.io/en/fastmiso/#</a>) but have so far been unsuccessful. Recently, I contacted the HPC Support group at the institution I work at.<br>
<br>
The steps we both performed for installing misopy are:<br>
<br>
Adding the module: apps/pip/9.0.1/python-2.7.8<br>
Then running: pip install misopy<br>
I then checked that the following directory was in my pythonpath: /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages<br>
<br>
This all worked fine.<br>
<br>
To then test the installation, in Python I did:<br>
<br>
import misopy<br>
import pysplicing<br>
<br>
This all worked without outputting an error (previously, when I was first installing misopy I was creating a virtual env etc. but getting an error with 'import pysplicing'. HPC Support then suggested the above method for installing).<br>
<br>
I then ran the below to test if MISO could be run:<br>
<br>
python -m unittest discover misopy<br>
<br>
However, I get a failure:<br>
<br>
Testing fr-unstranded...<br>
Checking read f_read against +<br>
Checking read f_read against -<br>
Checking read r_read against +<br>
Checking read r_read against -<br>
Testing fr-firststrand...<br>
.Testing conversion of SAM to BAM...<br>
Executing: sam_to_bam --convert /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-data/sam-data/c2c12.Atp2b1.sam /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output<br>
sh: sam_to_bam: command not found<br>
FTesting gene-level Psi...<br>
Testing GFF indexing of: /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff<br>
Executing: index_gff --index /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed<br>
sh: index_gff: command not found<br>
Executing: miso --run /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1/indexed /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36<br>
sh: miso: command not found<br>
.Testing gene-level Psi...<br>
Executing: python /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py --index /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/genes/Atp2b1.mm9.gff /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed<br>
Traceback (most recent call last):<br>
File "/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py", line 199, in module<br>
main()<br>
File "/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/index_gff.py", line 188, in main<br>
os.makedirs(output_dir)<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/os.py", line 157, in makedirs<br>
mkdir(name, mode)<br>
OSError: [Errno 13] Permission denied: '/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed'<br>
Executing: python /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-genes-psi /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/gff-events/mm9/indexed /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/sam-output/c2c12.Atp2b1.sorted.bam --output-dir /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/gene-psi-output --read-len 36 --paired-end 250 30 --use-cluster<br>
MISO (Mixture of Isoforms model)<br>
To run MISO, please use "miso" instead.<br>
.Testing single-end SE event interface...<br>
Executing: python /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/run_events_analysis.py --compute-events-psi se-sample /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-data/se-counts/se_test.counts --output-dir /users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test-output/SE-output --read-len 35 --overhang-len 4 --event-type SE --use-cluster<br>
MISO (Mixture of Isoforms model)<br>
To run MISO, please use "miso" instead.<br>
.<br>
======================================================================<br>
FAIL: test_a_sam_to_bam (misopy.test_miso.TestMISO)<br>
----------------------------------------------------------------------<br>
Traceback (most recent call last):<br>
File "/users/122345678/gridware/share/python/2.7.8/lib/python2.7/site-packages/misopy/test_miso.py", line 51, in test_a_sam_to_bam<br>
"c2c12.Atp2b1.sorted.bam")))<br>
AssertionError<br>
<br>
----------------------------------------------------------------------<br>
Ran 5 tests in 2.761s<br>
<br>
FAILED (failures=1)<br>
<br>
<br>
When I do:<br>
python -m unittest discover miso<br>
<br>
I get:<br>
<br>
Traceback (most recent call last):<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/runpy.py", line 162, in _run_module_as_main<br>
"__main__", fname, loader, pkg_name)<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/runpy.py", line 72, in _run_code<br>
exec code in run_globals<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/__main__.py", line 12, in <module><br>
main(module=None)<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/main.py", line 94, in __init__<br>
self.parseArgs(argv)<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/main.py", line 113, in parseArgs<br>
self._do_discovery(argv[2:])<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/main.py", line 214, in _do_discovery<br>
self.test = loader.discover(start_dir, pattern, top_level_dir)<br>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/python/2.7.8/gcc-4.8.5/lib/python2.7/unittest/loader.py", line 204, in discover<br>
raise ImportError('Start directory is not importable: %r' % start_dir)<br>
ImportError: Start directory is not importable: 'miso'<br>
<br>
<br>
<br>
It looks like the commands for running Miso are not being recognised? I've checked the dependancy packages needed for Miso to run without a failure, and they satisfy the requirements in terms of versions. miso/misopy are not recognised either in Python or outside of python.<br>
<br>
Is anyone able to help with this? I would be grateful for any advice.<br>
<br>
Thanks,<br>
Ali.<br>
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