IMP issueshttps://git-r3lab.uni.lu/IMP/IMP/-/issues2019-08-27T08:50:26+02:00https://git-r3lab.uni.lu/IMP/IMP/-/issues/92IncompleteFilesException error2019-08-27T08:50:26+02:00Federico BaldiniIncompleteFilesException errorFollowing error:
```bash
$ impy init --index ~/hg38.fa
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4.1
IMP image found
Executing IMP command:
docker run --rm --name home_federico_impyinstall_imp_db -v /home/federico/impyinstall/imp-...Following error:
```bash
$ impy init --index ~/hg38.fa
[x] Found IMP docker-r3lab.uni.lu/imp/imp 1.4.1
IMP image found
Executing IMP command:
docker run --rm --name home_federico_impyinstall_imp_db -v /home/federico/impyinstall/imp-db:/home/imp/databases -e "LOCAL_USER_ID=`id -u $USER`" -e "LOCAL_GROUP_ID=`id -g $USER`" -e FILTER="hg38" docker-r3lab.uni.lu/imp/imp:1.4.1 snakemake -s /home/imp/code/rules/ini/init
IncompleteFilesException:
The files below seem to be incomplete. If you are sure that certain files are not incomplete, mark them as complete with
snakemake --cleanup-metadata <filenames>
To re-generate the files rerun your command with the --rerun-incomplete flag.
Incomplete files:
filtering/hg38.fa
```
I downloaded the file `hg38.fa` using:
```bash
$ wget http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
```
and then unzipped it using:
```bash
$ gunzip hg38.fa.gz
```
Running the following command:
```bash
$ snakemake --cleanup-metadata ./imp-db/filtering/hg38.fa
```
yields:
```bash
Error: Snakefile "Snakefile" not present.
```
Can you help me out please? Thanks.Yohan Jaroszyohan.jarosz@uni.luYohan Jaroszyohan.jarosz@uni.luhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/150IMP image not installed. Please run `impy install_imp_container` first.2019-01-16T15:05:22+01:00TANKENGUOIMP image not installed. Please run `impy install_imp_container` first.$impy init
IMP image not installed. Please run `impy install_imp_container` first.
how to solve this problem?$impy init
IMP image not installed. Please run `impy install_imp_container` first.
how to solve this problem?https://git-r3lab.uni.lu/IMP/IMP/-/issues/142impy init errors2018-10-19T19:33:27+02:00Billy Tajimpy init errorsHi.
I'm running into this issue while trying to get IMPY to work.
Running Docker CE, as my windows 10 is home-edition, and won't take to regular Docker.
Using Anaconda3
ran:
> pip install impy
this exited just fine
tried to run:
> impy...Hi.
I'm running into this issue while trying to get IMPY to work.
Running Docker CE, as my windows 10 is home-edition, and won't take to regular Docker.
Using Anaconda3
ran:
> pip install impy
this exited just fine
tried to run:
> impy init
and failed, resulting in the error below.
```
Traceback (most recent call last):
File "c:\programdata\anaconda3\lib\runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "c:\programdata\anaconda3\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\ProgramData\Anaconda3\Scripts\impy.exe\__main__.py", line 9, in <module>
File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 697, in main
rv = self.invoke(ctx)
File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 535, in invoke
return callback(*args, **kwargs)
File "c:\programdata\anaconda3\lib\site-packages\click\decorators.py", line 17, in new_func
return f(get_current_context(), *args, **kwargs)
File "c:\programdata\anaconda3\lib\site-packages\impy.py", line 380, in init
if not is_imp_container_installed(ctx.obj['image-name'], ctx.obj['image-tag']):
File "c:\programdata\anaconda3\lib\site-packages\impy.py", line 154, in is_imp_container_installed
if not requirements():
File "c:\programdata\anaconda3\lib\site-packages\impy.py", line 112, in requirements
subprocess.check_output(['which', 'docker'])
File "c:\programdata\anaconda3\lib\subprocess.py", line 336, in check_output
**kwargs).stdout
File "c:\programdata\anaconda3\lib\subprocess.py", line 403, in run
with Popen(*popenargs, **kwargs) as process:
File "c:\programdata\anaconda3\lib\subprocess.py", line 709, in __init__
restore_signals, start_new_session)
File "c:\programdata\anaconda3\lib\subprocess.py", line 997, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
```
Help please?Yohan Jaroszyohan.jarosz@uni.luYohan Jaroszyohan.jarosz@uni.luhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/76IMP does not complain when path to config file leads into Nirvana2017-05-31T09:51:20+02:00Anna BuschartIMP does not complain when path to config file leads into NirvanaHi guys-
I came across a suboptimal behaviour of IMP: I started IMP giving a path to a config file which was not actually there. Unfortunately, IMP just silently ran with the default config file. I would prefer IMP to complain that there...Hi guys-
I came across a suboptimal behaviour of IMP: I started IMP giving a path to a config file which was not actually there. Unfortunately, IMP just silently ran with the default config file. I would prefer IMP to complain that there is no such file, because this sort of error can happen and is a bit sad to notice after the run (if ever). I have to add, this is not the latest version, so ignore me, if this has been changed already.
thanks-
AYohan Jaroszyohan.jarosz@uni.luYohan Jaroszyohan.jarosz@uni.luhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/78(How) can I turn binning of?2017-05-31T09:51:20+02:00Anna Buschart(How) can I turn binning of?Hi guys -
I have run IMP on a few data sets which don't result in contigs with a bacterial marker gene for Maxbin. Maxbin then throws an error message: "Marker gene search reveals that the dataset cannot be binned (the medium of marker g...Hi guys -
I have run IMP on a few data sets which don't result in contigs with a bacterial marker gene for Maxbin. Maxbin then throws an error message: "Marker gene search reveals that the dataset cannot be binned (the medium of marker gene number <= 1)" and I can live with that (I didn't expect bacteria). But IMP also dies and does not finish all the other nice things it does. Can I run IMP without Maxbin, and if yes what's the magic word?
For the longer term, I guess it would be good if IMP could ignore this kind of error and report that binning wasn't possible but finish?
Thanks -
Anna