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rmkoesterer / uga

Universal Genome Analyst (uga) is an open, flexible, and efficient tool for the distribution, management, and visualization of whole genome data analyses.
GNU General Public License v3.0
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error when running "snvgroupplot" #25

Closed shirley0818 closed 7 years ago

shirley0818 commented 7 years ago

When running "uga snvgroupplot --file wes.release3.high.enriched/wes.release3.high.enriched.ea.filtered.gz --color --qq --qq-strat --mht", I got the following permission error message which I have never got before. Thanks. Xiaoling from BU

(uga_python2.7)[zhangxl@scc4 uga_snvgroup]$ uga snvgroupplot --file wes.release3.high.enriched/wes.release3.high.enriched.meta.filtered.gz --color --qq --qq-strat --mht

uga v2.0b3 (c) 2015 Ryan Koesterer GNU General Public License v3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/

active module: snvgroupplot Traceback (most recent call last): File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/bin/uga", line 9, in load_entry_point('uga==2.0b3', 'console_scripts', 'uga')() File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/uga-2.0b3-py2.7-linux-x86_64.egg/uga/main.py", line 366, in main Process.interactive(qsub_wrapper, cmd, cfg['out'] + '.log') File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/uga-2.0b3-py2.7-linux-x86_64.egg/uga/Process.py", line 42, in interactive p = subprocess.Popen([submit,cmd], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, bufsize=1) File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/subprocess.py", line 710, in init errread, errwrite) File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 13] Permission denied

rmkoesterer commented 7 years ago

Hi Xiaoling,

Sorry about the delay, I haven't been working with UGA much lately, so haven't checked in. Your error is saying that you don't have appropriate permissions to read or execute a file. This is not a UGA error. It comes from the operating system. It appears that you are trying to include a file that you don't have permission to access, or it could be possible that your permissions have changed for the qsub wrapper script.

Ryan

shirley0818 commented 7 years ago

Thanks Ryan for your response. I just checked, I should have permission to access the file in the command as listed below: (uga_python2.7)[zhangxl@scc4 uga_snvgroup]$ uga snvgroupplot --file wes.release3.high.enriched/wes.release3.high.enriched.meta.filtered.gz --color --qq --qq-strat --mht [zhangxl@scc4 uga_snvgroup]$ ls -l wes.release3.high.enriched/*.gz -rw-r--r-- 1 zhangxl casa 68151 Jan 3 12:53 wes.release3.high.enriched/wes.release3.high.enriched.ea.filtered.gz -rw-r--r-- 1 zhangxl casa 379668 Jan 3 12:50 wes.release3.high.enriched/wes.release3.high.enriched.ea.gz -rw-r--r-- 1 zhangxl casa 10424 Jan 3 12:53 wes.release3.high.enriched/wes.release3.high.enriched.hi.filtered.gz -rw-r--r-- 1 zhangxl casa 283383 Jan 3 12:50 wes.release3.high.enriched/wes.release3.high.enriched.hi.gz -rw-r--r-- 1 zhangxl casa 56281 Jan 3 12:53 wes.release3.high.enriched/wes.release3.high.enriched.meta.filtered.gz -rw-r--r-- 1 zhangxl casa 296507 Jan 3 12:50 wes.release3.high.enriched/wes.release3.high.enriched.meta.gz

Many thanks, Xiaoling

From: Ryan Koesterer [mailto:notifications@github.com] Sent: Thursday, January 12, 2017 9:25 PM To: rmkoesterer/uga Cc: Zhang, Xiaoling; Author Subject: Re: [rmkoesterer/uga] error when running "snvgroupplot" (#25)

Hi Xiaoling,

Sorry about the delay, I haven't been working with UGA much lately, so haven't checked in. Your error is saying that you don't have appropriate permissions to read or execute a file. This is not a UGA error. It comes from the operating system. It appears that you are trying to include a file that you don't have permission to access, or it could be possible that your permissions have changed for the qsub wrapper script.

Ryan

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/rmkoesterer/uga/issues/25#issuecomment-272344381, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AUXD3NCkBJz3Ks_aHNBiAc0akU77XTtbks5rRuCUgaJpZM4LZ3fd.

rmkoesterer commented 7 years ago

In the error, it appears to have a problem with running the qsub_wrapper, which in your version (2.0b3) should be pointing to the file /usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/uga-2.0b3-py2.7-linux-x86_64.egg/uga/Qsub.py. You will need execute permissions on that file to run interactively. I would certainly recommend updating to the latest release, 2.0b5, since a number of issues were resolved and improvements have been made since 2.0b3. One improvement that was made moved the Qsub.py file to the outer directory of the install and made it user definable (using the 'uga settings' module). You would still need to make the file executable, however.

shirley0818 commented 7 years ago

Hi Ryan,

As you suggested, I updated uga to 2.0b5. However, after installing, to check whether uga is functional with “uga –h”, I got the following error: Do I need to remove the old version “2.0b3” before updating? Many thanks, Xiaoling

(uga_python2.7)[zhangxl@scc4 uga-2.0b5]$ uga -h Traceback (most recent call last): File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/bin/uga", line 9, in load_entry_point('uga==2.0b5', 'console_scripts', 'uga')() File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/setuptools-18.5-py2.7.egg/pkg_resources/init.py", line 565, in load_entry_point File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/setuptools-18.5-py2.7.egg/pkg_resources/init.py", line 2697, in load_entry_point File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/setuptools-18.5-py2.7.egg/pkg_resources/init.py", line 2370, in load File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/setuptools-18.5-py2.7.egg/pkg_resources/init.py", line 2376, in resolve File "/usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/uga-2.0b5-py2.7-linux-x86_64.egg/uga/main.py", line 18, in import demandimport; demandimport.enable(); demandimport.ignore('bottleneck'); demandimport.ignore('pathlib') ImportError: No module named demandimport

From: Ryan Koesterer [mailto:notifications@github.com] Sent: Friday, January 13, 2017 8:03 AM To: rmkoesterer/uga Cc: Zhang, Xiaoling; Author Subject: Re: [rmkoesterer/uga] error when running "snvgroupplot" (#25)

In the error, it appears to have a problem with running the qsub_wrapper, which in your version (2.0b3) should be pointing to the file /usr3/graduate/zhangxl/.conda/envs/uga_python2.7/lib/python2.7/site-packages/uga-2.0b3-py2.7-linux-x86_64.egg/uga/Qsub.py. You will need execute permissions on that file to run interactively. I would certainly recommend updating to the latest release, 2.0b5, since a number of issues were resolved and improvements have been made since 2.0b3. One improvement that was made moved the Qsub.py file to the outer directory of the install and made it user definable (using the 'uga settings' module). You would still need to make the file executable, however.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/rmkoesterer/uga/issues/25#issuecomment-272438311, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AUXD3DtqMMHdkVRLHBtFG01Q8hpoGvW-ks5rR3YPgaJpZM4LZ3fd.

rmkoesterer commented 7 years ago

Hi Xiaoling,

The new version has slightly different requirements. It needs a module named demandimport, which is not part of your existing conda environment. What I usually do is install a new conda environment under the name of the uga release that you are installing. The following commands should install it correctly.

tar -xvf uga-2.0b5.tar.gz cd uga_v2.0b5 conda env create -f environment.yml source activate uga_v2.0b5

shirley0818 commented 7 years ago

Thanks Ryan. By following your suggestion. I successfully installed uga-2.0b5, however, when running “uga snvgroup”, I got the following error. Please help me out. Thanks, Xiaoling

(uga_v2.0b5)[zhangxl@scc4 uga_snvgroup]$ ./high.enriched.sh

uga v2.0b5 (c) 2015 Ryan Koesterer GNU General Public License v3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/

active module: snvgroup

ERROR: uga qsub wrapper /usr3/bustaff/koesterr/uga/Qsub.py is not executable

From: Ryan Koesterer [mailto:notifications@github.com] Sent: Saturday, January 14, 2017 9:09 AM To: rmkoesterer/uga Cc: Zhang, Xiaoling; Author Subject: Re: [rmkoesterer/uga] error when running "snvgroupplot" (#25)

Hi Xiaoling,

The new version has slightly different requirements. It needs a module named demandimport, which is not part of your existing conda environment. What I usually do is install a new conda environment under the name of the uga release that you are installing. The following commands should install it correctly.

tar -xvf uga-2.0b5.tar.gz cd uga_v2.0b5 conda env create -f environment.yml source activate uga_v2.0b5

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/rmkoesterer/uga/issues/25#issuecomment-272626335, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AUXD3FAP_7tlbQP7PSfbW6TD5yKxbE5tks5rSNb-gaJpZM4LZ3fd.

rmkoesterer commented 7 years ago

Hi, You just need to update the settings using the 'uga settings' module. Enter 'uga settings -h' to get help. The current settings are the ones below. You can see that the 'wrapper' setting is for the file that caused the error, because it does not exist. You just need to update these file locations and you should be ok to run.

snpeff = /restricted/projectnb/addiction/annotation/snpEff/snpEff.jar snpsift = /restricted/projectnb/addiction/annotation/snpEff/SnpSift.jar dbnsfp = /restricted/projectnb/addiction/annotation/snpEff/data/dbNSFP_current locuszoom = /restricted/projectnb/addiction/programs/locuszoom/bin/locuszoom wrapper = /usr3/bustaff/koesterr/uga/Qsub.py

You need to change the location of Qsub.py to the one in your uga_v2.0b5 directory that you just installed from. Also, make sure that you have set the Qsub.py file as executable.

shirley0818 commented 7 years ago

Thank you very much. Now I am all set. Really appreciate your help.

I would like to say that the newest version uga_v2.0b5 is better than old versions. It’s great to see that you have been trying to update uga, which is a very very good tool. Thanks again for your response in a timely manner!

Best, Xiaoling

From: Ryan Koesterer [mailto:notifications@github.com] Sent: Saturday, January 14, 2017 1:59 PM To: rmkoesterer/uga Cc: Zhang, Xiaoling; Author Subject: Re: [rmkoesterer/uga] error when running "snvgroupplot" (#25)

Hi, You just need to update the settings using the 'uga settings' module. Enter 'uga settings -h' to get help. The current settings are the ones below. You can see that the 'wrapper' setting is for the file that caused the error, because it does not exist. You just need to update these file locations and you should be ok to run.

snpeff = /restricted/projectnb/addiction/annotation/snpEff/snpEff.jar snpsift = /restricted/projectnb/addiction/annotation/snpEff/SnpSift.jar dbnsfp = /restricted/projectnb/addiction/annotation/snpEff/data/dbNSFP_current locuszoom = /restricted/projectnb/addiction/programs/locuszoom/bin/locuszoom wrapper = /usr3/bustaff/koesterr/uga/Qsub.py

You need to change the location of Qsub.py to the one in your uga_v2.0b5 directory that you just installed from. Also, make sure that you have set the Qsub.py file as executable.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/rmkoesterer/uga/issues/25#issuecomment-272645100, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AUXD3DA1SUDHrnjdY_EBk74lb4XjEf4Jks5rSRr1gaJpZM4LZ3fd.