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General Use Scripts and Helper functions
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Error Running make_trackhubs.py #69

Closed shassathe closed 9 years ago

shassathe commented 9 years ago

make_trackhubs.py errors out with a ValueError:

Traceback (most recent call last):
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/bin/make_trackhubs.py", line 4, in <module>
    __import__('pkg_resources').run_script('gscripts==0.1.6', 'make_trackhubs.py')
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/lib/python2.7/site-packages/setuptools-12.0.4-py2.7.egg/pkg_resources/__init__.py", line 696, in run_script
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/lib/python2.7/site-packages/setuptools-12.0.4-py2.7.egg/pkg_resources/__init__.py", line 1614, in run_script
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/EGG-INFO/scripts/make_trackhubs.py", line 102, in <module>
    visibility="full"
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/lib/python2.7/site-packages/trackhub/track.py", line 580, in __init__
    super(AggregateTrack, self).__init__(*args, **kwargs)
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/lib/python2.7/site-packages/trackhub/track.py", line 129, in __init__
    _check_name(name)
  File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ssathe_env/lib/python2.7/site-packages/trackhub/track.py", line 24, in _check_name
    raise ValueError('Non-alphanumeric character in name "%s"' % name)
ValueError: Non-alphanumeric character in name "CV-B_MN_ARS_NHS_1_CCGTCC_L002_R1.polyATrim"
olgabot commented 9 years ago

edited to add fenced code blocks

olgabot commented 9 years ago

what happens if you replace the - with a _ ?

ecwheele commented 9 years ago

Still not working. There is no "-" in my filename. Here is the error message I get.

(ecwheele)[ecwheele@tscc-login1 mds_splicing]$ make_trackhubs.py --genome hg19 --hub mds_splicing_rnaseq --server sauron.ucsd.edu --user ecwheeler --no_s3 Bejar09_CGATGT_R1.polyATrim.adapterTrim.rmRep.sorted.rg.norm.neg.bw /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/Crypto/Util/number.py:57: PowmInsecureWarning: Not using mpz_powm_sec. You should rebuild using libgmp >= 5 to avoid timing attack vulnerability. _warn("Not using mpz_powm_sec. You should rebuild using libgmp >= 5 to avoid timing attack vulnerability.", PowmInsecureWarning) ['Bejar09_CGATGT_R1', 'polyATrim'] ['Bejar09_CGATGT_R1.polyATrim.adapterTrim.rmRep.sorted.rg.norm.neg.bw'] Traceback (most recent call last): File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/bin/make_trackhubs.py", line 4, in import('pkg_resources').run_script('gscripts==0.1.6', 'make_trackhubs.py') File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/setuptools-12.0.4-py2.7.egg/pkg_resources/init.py", line 696, in run_script File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/setuptools-12.0.4-py2.7.egg/pkg_resources/init.py", line 1614, in run_script File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/EGG-INFO/scripts/make_trackhubs.py", line 102, in visibility="full" File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/trackhub/track.py", line 580, in init super(AggregateTrack, self).init(_args, *_kwargs) File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/trackhub/track.py", line 129, in init _check_name(name) File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/trackhub/track.py", line 24, in _check_name raise ValueError('Non-alphanumeric character in name "%s"' % name) ValueError: Non-alphanumeric character in name "Bejar09_CGATGT_R1.polyATrim"

gpratt commented 9 years ago

I think they are overly strict about non-alphanumeric chars in trackhub making.

Try my version of trackhub, I've fixed the bug but haven't pushed upstream because that feature may be by design.

https://github.com/gpratt/trackhub

Install it and see if it works.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Thu, Apr 16, 2015 at 5:03 PM, ecwheele notifications@github.com wrote:

Still not working. There is no "-" in my filename. Here is the error message I get.

(ecwheele)[ecwheele@tscc-login1 mds_splicing]$ make_trackhubs.py --genome hg19 --hub mds_splicing_rnaseq --server sauron.ucsd.edu --user ecwheeler --no_s3 Bejar09_CGATGT_R1.polyATrim.adapterTrim.rmRep.sorted.rg.norm.neg.bw /projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/Crypto/Util/number.py:57: PowmInsecureWarning: Not using mpz_powm_sec. You should rebuild using libgmp >= 5 to avoid timing attack vulnerability.

_warn("Not using mpz_powm_sec. You should rebuild using libgmp >= 5 to avoid timing attack vulnerability.", PowmInsecureWarning) ['Bejar09_CGATGT_R1', 'polyATrim'] ['Bejar09_CGATGT_R1.polyATrim.adapterTrim.rmRep.sorted.rg.norm.neg.bw http://Bejar09_CGATGT_R1.polyATrim.adapterTrim.rmRep.sorted.rg.norm.neg.bw'] Traceback (most recent call last): File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/bin/make_trackhubs.py", line 4, in import('pkg_resources').run_script('gscripts==0.1.6', 'make_trackhubs.py') File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/setuptools-12.0.4-py2.7.egg/pkg_resources/ init.py", line 696, in run_script File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/setuptools-12.0.4-py2.7.egg/pkg_resources/ init.py", line 1614, in run_script File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/gscripts-0.1.6-py2.7.egg/EGG-INFO/scripts/make_trackhubs.py", line 102, in visibility="full" File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/trackhub/track.py", line 580, in init super(AggregateTrack, self).init(_args, *_kwargs) File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/trackhub/track.py", line 129, in init _check_name(name) File "/projects/ps-yeolab/software/anaconda-2.1.0_2015-01-20/envs/ecwheele/lib/python2.7/site-packages/trackhub/track.py", line 24, in _check_name raise ValueError('Non-alphanumeric character in name "%s"' % name) ValueError: Non-alphanumeric character in name "Bejar09_CGATGT_R1.polyATrim"

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/69#issuecomment-93865134.

gpratt commented 9 years ago

Think this works now

shassathe commented 9 years ago

Yes. It does thanks!

Shashank

On Tue, Jun 2, 2015 at 9:37 AM, Gabriel Pratt notifications@github.com wrote:

Think this works now

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/69#issuecomment-108008857.