Exception: No submit queue specified

[EmilyWesel]

I have tried running destruct with the following command:

./destruct run /u/flashscratch/e/emilyewe/testData/chr19_new.fa break break2 break3 --bam_files /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.bam /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.header.bam --lib_ids tumour normal --tmpdir tempdir

I receive the following error: raise Exception('No submit queue specified')
Exception: No submit queue specified

I would like to run destruct for deletions only.

How do I fix this so that destruct can run?

Thanks,
Emily

[amcpherson]

You need to specify how jobs are submitted, easiest is —submit local

…

On Thu, Jul 19, 2018 at 5:39 PM Emily Wesel ***@***.***> wrote: I have tried running destruct with the following command: ./destruct run /u/flashscratch/e/emilyewe/testData/chr19_new.fa break break2 break3 --bam_files /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.bam /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.header.bam --lib_ids tumour normal --tmpdir tempdir I receive the following error: raise Exception('No submit queue specified') Exception: No submit queue specified I would like to run destruct for deletions only. How do I fix this so that destruct can run? Thanks, Emily — 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/ABHbOq548jSIhzkM4bnpyDcd3AsN9qBWks5uISbNgaJpZM4VXSdF> .

[EmilyWesel]

Hello,

Thanks for your helpful response!

I added --submit local, so my command is now ./destruct run /u/flashscratch/e/emilyewe/testData/chr19_new.fa break break2 break3 --bam_files /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.bam /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.header.bam --lib_ids tumour normal --tmpdir tempdir --submit local

Although --submit local has solved the submit queue error, I am now receiving a pipeline failed error even after installing pytables.

Here's the complete output:
2018-07-20 13:52:59,283 - pypeliner.execqueue - ERROR - /bylibrary:normal/bamdisc submit failed
---------- delegator command ----------
pypeliner_delegate /u/home/e/emilyewe/.conda/envs/my_pymc_env/bin/tempdir/log/20180720-135249/bylibrary/normal/bamdisc/exc0/job.dgt.before /u/home/e/emilyewe/.conda/envs/my_pymc_env/bin/tempdir/log/20180720-135249/bylibrary/normal/bamdisc/exc0/job.dgt.after /u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/destruct-0.4.9-py2.7.egg/destruct
[Errno 2] No such file or directory
---------- job stderr ----------
---------- job stdout ----------
2018-07-20 13:52:59,298 - pypeliner.scheduler - ERROR - exception
Traceback (most recent call last):
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 76, in run
self._add_jobs(exec_queue, workflow, runskip)
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 130, in _add_jobs
self._add_job(exec_queue, job)
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 112, in _add_job
exec_queue.send(job.ctx, job.displayname, sent, exc_dir)
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/execqueue/subproc.py", line 28, in send
submitted = self.create(ctx, name, sent, temps_dir)
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/execqueue/local.py", line 56, in create
return LocalJob(ctx, name, sent, temps_dir, self.modules)
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/execqueue/local.py", line 34, in init
raise pypeliner.execqueue.base.SubmitError()
SubmitError
2018-07-20 13:52:59,298 - pypeliner.scheduler - ERROR - pipeline failed
log file: tempdir/log/20180720-135249/pipeline.log
Traceback (most recent call last):
File "./destruct", line 11, in
load_entry_point('destruct==0.4.9', 'console_scripts', 'destruct')()
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/destruct-0.4.9-py2.7.egg/destruct/ui/main.py", line 16, in main
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/destruct-0.4.9-py2.7.egg/destruct/ui/run.py", line 31, in run
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/app.py", line 221, in run
self.sch.run(workflow, self.exec_queue, self.file_storage, self.runskip)
File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 97, in run
raise PipelineException('pipeline failed')
pypeliner.scheduler.PipelineException: pipeline failed

Thanks,
Emily

[amcpherson]

Somethings wrong with your installation. Try running the delegator command, if that doesn’t work figure out why Pypeliner isn’t installed correctly

…

On Fri, Jul 20, 2018 at 5:03 PM Emily Wesel ***@***.***> wrote: Hello, Thanks for your helpful response! I added --submit local, so my command is now ./destruct run /u/flashscratch/e/emilyewe/testData/chr19_new.fa break break2 break3 --bam_files /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.bam /u/flashscratch/e/emilyewe/testData/LP_J.chr19.1.25p.5_sorted.header.bam --lib_ids tumour normal --tmpdir tempdir --submit local Although --submit local has solved the submit queue error, I am now receiving a pipeline failed error even after install pytables. Here's the complete output: 2018-07-20 13:52:59,283 - pypeliner.execqueue - ERROR - /bylibrary:normal/bamdisc submit failed ---------- delegator command ---------- pypeliner_delegate /u/home/e/emilyewe/.conda/envs/my_pymc_env/bin/tempdir/log/20180720-135249/bylibrary/normal/bamdisc/exc0/job.dgt.before /u/home/e/emilyewe/.conda/envs/my_pymc_env/bin/tempdir/log/20180720-135249/bylibrary/normal/bamdisc/exc0/job.dgt.after /u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/destruct-0.4.9-py2.7.egg/destruct [Errno 2] No such file or directory ---------- job stderr ---------- ---------- job stdout ---------- 2018-07-20 13:52:59,298 - pypeliner.scheduler - ERROR - exception Traceback (most recent call last): File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 76, in run self._add_jobs(exec_queue, workflow, runskip) File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 130, in _add_jobs self._add_job(exec_queue, job) File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 112, in _add_job exec_queue.send(job.ctx, job.displayname, sent, exc_dir) File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/execqueue/subproc.py", line 28, in send submitted = self.create(ctx, name, sent, temps_dir) File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/execqueue/local.py", line 56, in create return LocalJob(ctx, name, sent, temps_dir, self.modules) File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/execqueue/local.py", line 34, in *init* raise pypeliner.execqueue.base.SubmitError() SubmitError 2018-07-20 13:52:59,298 - pypeliner.scheduler - ERROR - pipeline failed log file: tempdir/log/20180720-135249/pipeline.log Traceback (most recent call last): File "./destruct", line 11, in load_entry_point('destruct==0.4.9', 'console_scripts', 'destruct')() File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/destruct-0.4.9-py2.7.egg/destruct/ui/main.py", line 16, in main File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/destruct-0.4.9-py2.7.egg/destruct/ui/run.py", line 31, in run File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/app.py", line 221, in run self.sch.run(workflow, self.exec_queue, self.file_storage, self.runskip) File "/u/home/e/emilyewe/.conda/envs/my_pymc_env/lib/python2.7/site-packages/pypeliner/scheduler.py", line 97, in run raise PipelineException('pipeline failed') pypeliner.scheduler.PipelineException: pipeline failed Thanks, Emily — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABHbOvDvMcaTN3jZ2KPLf42jxZk-jkxTks5uIkW7gaJpZM4VXSdF> .