Error Running make_trackhubs.py

[shassathe]

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]

edited to add fenced code blocks

[olgabot]

what happens if you replace the - with a _ ?

[ecwheele]

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]

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"

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Reply to this email directly or view it on GitHub
#69 (comment).

[gpratt]

Think this works now

[shassathe]

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
#69 (comment).