Re: [galaxy-dev] bwa failure preparing job
Branden, Sorry for the delay in response. Have you gotten things working yet? If not, what changeset are you on now? The data tables issue is what's going on here. But it's odd that you're still seeing from_file in BWA and Bowtie, because they (plus all NGS tools except the samtools ones) have been using data tables for some time. Let us know if you are still having problems with this. Thanks, Kelly On Tue Apr 26, at 5:11 PM, Branden Timm wrote: Vipin, thanks for the tip. I was not aware of data tables at all. I checked bwa_wrapper.xml and it is still using the from_file attribute for the reference genome parameter, not from_data_table. It would appear then that BWA is not using data tables? Additionally, I have now noticed that our bowtie runs are failing as well with the error: AssertionError: Requested 'path' column missing from column def I looked at bowtie_wrapper.xml, and it too seems to still be using from_file instead of from_data_table for the reference genome drop- down. There is a line there using data tables, but it is commented out: !--options from_data_table=bowtie_indexes/-- I'm really confused as to what is going on here, but it seems like when I updated recently (first time since January probably) it broke all of my location files and I'm not sure how to fix them. I'm also confused because it seems that even using data tables, the format of my .loc files shouldn't need to change because they both use four columns separated by tabs. As always, any help is greatly appreciated. -- Branden Timm bt...@glbrc.wisc.edu On 4/26/2011 12:29 PM, Vipin TS wrote: Hi Branden, I find a wiki documentation here, https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables Hope this will help you to experiment a bit around. regards, Vipin Does anybody have any idea why I would be getting this error before the tool runs? -- Branden Timm Great Lakes Bioenergy Research Center bt...@wisc.edu On 4/19/2011 10:45 AM, Branden Timm wrote: Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/ local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux- x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/ galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] bwa failure preparing job
Hi Branden, Vipin, thanks for the tip. I was not aware of data tables at all. I checked bwa_wrapper.xml and it is still using the from_file attribute for the reference genome parameter, not from_data_table. It would appear then that BWA is not using data tables? Additionally, I have now noticed that our bowtie runs are failing as well with the error: I am not sure about the below error message, based on the previous mail error message it is cleat that it is looking for a data_table type value instead of from_file. I hope something will be broken at your end when you pulled at last time. AssertionError: Requested 'path' column missing from column def I looked at bowtie_wrapper.xml, and it too seems to still be using from_file instead of from_data_table for the reference genome drop-down. There is a line there using data tables, but it is commented out: !--options from_data_table=bowtie_indexes/-- I'm really confused as to what is going on here, but it seems like when I updated recently (first time since January probably) it broke all of my location files and I'm not sure how to fix them. I'm also confused because it seems that even using data tables, the format of my .loc files shouldn't need to change because they both use four columns separated by tabs. As always, any help is greatly appreciated. I think probably the best idea to move everything to data_table based on the documentation available in the Wiki page. Galaxy also recommending the same. If I found something useful, I will share with you. regards, Vipin ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] bwa failure preparing job
Does anybody have any idea why I would be getting this error before the tool runs? -- Branden Timm Great Lakes Bioenergy Research Center bt...@wisc.edu On 4/19/2011 10:45 AM, Branden Timm wrote: Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] bwa failure preparing job
Hi Branden, I find a wiki documentation here, https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables Hope this will help you to experiment a bit around. regards, Vipin Does anybody have any idea why I would be getting this error before the tool runs? -- Branden Timm Great Lakes Bioenergy Research Center bt...@wisc.edu On 4/19/2011 10:45 AM, Branden Timm wrote: Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] bwa failure preparing job
Vipin, thanks for the tip. I was not aware of data tables at all. I checked bwa_wrapper.xml and it is still using the from_file attribute for the reference genome parameter, not from_data_table. It would appear then that BWA is not using data tables? Additionally, I have now noticed that our bowtie runs are failing as well with the error: AssertionError: Requested 'path' column missing from column def I looked at bowtie_wrapper.xml, and it too seems to still be using from_file instead of from_data_table for the reference genome drop-down. There is a line there using data tables, but it is commented out: !--options from_data_table=bowtie_indexes/-- I'm really confused as to what is going on here, but it seems like when I updated recently (first time since January probably) it broke all of my location files and I'm not sure how to fix them. I'm also confused because it seems that even using data tables, the format of my .loc files shouldn't need to change because they both use four columns separated by tabs. As always, any help is greatly appreciated. -- Branden Timm bt...@glbrc.wisc.edu On 4/26/2011 12:29 PM, Vipin TS wrote: Hi Branden, I find a wiki documentation here, https://bitbucket.org/galaxy/galaxy-central/wiki/DataTables Hope this will help you to experiment a bit around. regards, Vipin Does anybody have any idea why I would be getting this error before the tool runs? -- Branden Timm Great Lakes Bioenergy Research Center bt...@wisc.edu mailto:bt...@wisc.edu On 4/19/2011 10:45 AM, Branden Timm wrote: Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.edu mailto:bt...@glbrc.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] bwa failure preparing job
Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a). It seems that the error is a python list error while preparing the job: Traceback (most recent call last): File /home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py, line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /home/galaxy/galaxy-central/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002 I'm not sure what the next troubleshooting step is, any ideas? -- Branden Timm bt...@glbrc.wisc.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
