Does anybody have any idea why I would be getting this error before the tool runs?

-- Branden Timm Great Lakes Bioenergy Research Center btimm@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 btimm@glbrc.wisc.edu

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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 btimm@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
btimm@wisc.edu <mailto:btimm@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
btimm@glbrc.wisc.edu <mailto:btimm@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:

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___________________________________________________________
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:

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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 btimm@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 btimm@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 btimm@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/