error"Exception: No submit queue specified"

[zypiner]

Hello，

I met one problem when I ran remix, the command I executed is that
"
remixt run ref_data_dir result_remix breakpoit/bp.hg19.txt --normal_sample_id oec --normal_bam_file bam/OEC130618.rlg.bam --tumour_sample_ids lm130227 --tumour_bam_files bam/LM130227.rlg.bam --results_files lm130227.hd --tmpdir temp
",

and the error is that:
"
/home/yuzh/miniconda2/lib/python2.7/site-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
from pandas.core import datetools
Traceback (most recent call last):
File "/home/yuzh/miniconda2/bin/remixt", line 11, in
load_entry_point('remixt==0.5.5', 'console_scripts', 'remixt')()
File "/home/yuzh/miniconda2/lib/python2.7/site-packages/remixt/ui/main.py", line 24, in main
func(**args)
File "/home/yuzh/miniconda2/lib/python2.7/site-packages/remixt/ui/run.py", line 32, in run
pyp = pypeliner.app.Pypeline([remixt], pypeliner_config)
File "/home/yuzh/miniconda2/lib/python2.7/site-packages/pypeliner/app.py", line 195, in init
config_filename=self.config['submit_config'])
File "/home/yuzh/miniconda2/lib/python2.7/site-packages/pypeliner/execqueue/factory.py", line 6, in create
raise Exception('No submit queue specified')
Exception: No submit queue specified
“

By the way, the reference genome I used is hg19 instead of GRCh37, I was wondering whether it will have an effect on the result.

I have no idea about how to solve this problem. I will appreciate it very much if you could help me.

Thank you!

[amcpherson]

Try adding --submit local

…

On Thu, May 24, 2018 at 10:49 PM, zypiner ***@***.***> wrote: Hello， I met one problem when I ran remix, the command I executed is that " remixt run ref_data_dir result_remix breakpoit/bp.hg19.txt --normal_sample_id oec --normal_bam_file bam/OEC130618.rlg.bam --tumour_sample_ids lm130227 --tumour_bam_files bam/LM130227.rlg.bam --results_files lm130227.hd --tmpdir temp ", and the error is that: " /home/yuzh/miniconda2/lib/python2.7/site-packages/ statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead. from pandas.core import datetools Traceback (most recent call last): File "/home/yuzh/miniconda2/bin/remixt", line 11, in load_entry_point('remixt==0.5.5', 'console_scripts', 'remixt')() File "/home/yuzh/miniconda2/lib/python2.7/site-packages/remixt/ui/main.py", line 24, in main func(**args) File "/home/yuzh/miniconda2/lib/python2.7/site-packages/remixt/ui/run.py", line 32, in run pyp = pypeliner.app.Pypeline([remixt], pypeliner_config) File "/home/yuzh/miniconda2/lib/python2.7/site-packages/pypeliner/app.py", line 195, in *init* config_filename=self.config['submit_config']) File "/home/yuzh/miniconda2/lib/python2.7/site-packages/ pypeliner/execqueue/factory.py", line 6, in create raise Exception('No submit queue specified') Exception: No submit queue specified “ By the way, the reference genome I used is hg19 instead of GRCh37, I was wondering whether it will have an effect on the result. I have no idea about how to solve this problem. I will appreciate it very much if you could help me. Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABHbOtxanMqLh4yIeC-dxqUpGObhfGPIks5t15tngaJpZM4UNZvF> .

[simozacca]

I had the same issue and the solution worked when running on a local machine.

If the expected default behavior is indeed to run on a single multi-core machine, would be possible to make this value --submit local as the default one?