Eukrhythmic command not working #76
Description
Hello,
I am trying out the Eukrhythmic pipeline for metatranscriptomic analysis. Initially I am just trying to run the test samples provided with the package.
Here is what I ran (and what I encountered):
- I cloned the Git repo, installed the conda environment and activated the conda env as per instructions (successfully).
- I did the "alias eukrhythmic='./bin/eukrhythmic.sh'" command (successfully)
- Running eukrhythmic -h prints the help file...so far so good
- I tried running the test samples by running eukrhythmic without any arguments
eukrhythmic
and this is what I got
$ eukrhythmic
__ __ _ __ _
[ | _ [ | / |[ | (_)
.---. __ _ | | / ] _ .--.| |--. _ _`| |-| |--. _ .--..--. __ .---.
/ /__\[ | | | | '' < [ `/'`\| .-. | [ \ [ | | | .-. |[ `.-. .-. |[ |/ /'`\]
| \__.,| \_/ |,| |`\ \ | | | | | | \ '/ /| |,| | | | | | | | | | | || \__.
'.__.''.__.'_[__| \_[___] [___]|__[\_: / \__[___]|__[___||__||__[___'.___.'
\__.'
******************************************************************************
******************************************************************************
Welcome to eukrhythmic! Visit the readthedocs for more information
on how to use the command line functionality. Note that not all options
will be implemented for the command line.
******************************************************************************
******************************************************************************
No arguments were given to eukrhythmic. Please provide arguments or run
eukrhythmic with the -h flag for more information.
- Next, I tried running the following command on the test data files provided, by explicitly stating where the input files were etc
eukrhythmic -o testOut -i input/testdata -s input/sampledata.txt -c scratch
and I got this error
$ eukrhythmic -o testOut -i input/testdata -s input/sampledata.txt -c scratch
__ __ _ __ _
[ | _ [ | / |[ | (_)
.---. __ _ | | / ] _ .--.| |--. _ _`| |-| |--. _ .--..--. __ .---.
/ /__\[ | | | | '' < [ `/'`\| .-. | [ \ [ | | | .-. |[ `.-. .-. |[ |/ /'`\]
| \__.,| \_/ |,| |`\ \ | | | | | | \ '/ /| |,| | | | | | | | | | | || \__.
'.__.''.__.'_[__| \_[___] [___]|__[\_: / \__[___]|__[___||__||__[___'.___.'
\__.'
******************************************************************************
******************************************************************************
Welcome to eukrhythmic! Visit the readthedocs for more information
on how to use the command line functionality. Note that not all options
will be implemented for the command line.
******************************************************************************
******************************************************************************
Reading in variables from configuration file...
Reading in variables from cluster configuration file...
Checking directory formatting...
Setting appropriate cluster.yaml entries if specified...
Checking that appropriate input files exist...
Traceback (most recent call last):
File "/home/dhwani/MyGit/eukrhythmic/scripts/importworkspace.py", line 211, in <module>
foundnames.extend(os.listdir(search_dir))
^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'input/testdata/HN008'
Running locally.
Reading in variables from configuration file...
Reading in variables from cluster configuration file...
Checking directory formatting...
Setting appropriate cluster.yaml entries if specified...
Checking that appropriate input files exist...
FileNotFoundError in file /home/dhwani/MyGit/eukrhythmic/eukrhythmic, line 17:
[Errno 2] No such file or directory: 'input/testdata/HN008'
File "/home/dhwani/MyGit/eukrhythmic/eukrhythmic", line 17, in <module>
File "/home/dhwani/MyGit/eukrhythmic/scripts/importworkspace.py", line 211, in <module>
- So I checked the input/sampledata.txt file and there was an extra entry corresponding to HN008 sample, the corresponding fastq file for which, was not present in the input/testdata folder. So I removed that entry from the input/sampledata.txt and reran
$ eukrhythmic -o testOut -i input/testdata -s input/sampledata.txt -c scratch
__ __ _ __ _
[ | _ [ | / |[ | (_)
.---. __ _ | | / ] _ .--.| |--. _ _`| |-| |--. _ .--..--. __ .---.
/ /__\[ | | | | '' < [ `/'`\| .-. | [ \ [ | | | .-. |[ `.-. .-. |[ |/ /'`\]
| \__.,| \_/ |,| |`\ \ | | | | | | \ '/ /| |,| | | | | | | | | | | || \__.
'.__.''.__.'_[__| \_[___] [___]|__[\_: / \__[___]|__[___||__||__[___'.___.'
\__.'
******************************************************************************
******************************************************************************
Welcome to eukrhythmic! Visit the readthedocs for more information
on how to use the command line functionality. Note that not all options
will be implemented for the command line.
******************************************************************************
******************************************************************************
Reading in variables from configuration file...
Reading in variables from cluster configuration file...
Checking directory formatting...
Setting appropriate cluster.yaml entries if specified...
Checking that appropriate input files exist...
Running locally.
Reading in variables from configuration file...
Reading in variables from cluster configuration file...
Checking directory formatting...
Setting appropriate cluster.yaml entries if specified...
Checking that appropriate input files exist...
Reading in variables from configuration file...
Reading in variables from cluster configuration file...
Checking directory formatting...
Setting appropriate cluster.yaml entries if specified...
Checking that appropriate input files exist...
Checking that configuration file entries are valid...
All initial checks complete.
Traceback (most recent call last):
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 137, in consume
for t, orig in self.state(token):
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 230, in block
yield from self.block_content(token)
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 804, in block_content
for t in self.subautomaton(
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 134, in consume
for token in self.snakefile:
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 1269, in __next__
return next(self.tokens)
^^^^^^^^^^^^^^^^^
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/tokenize.py", line 543, in _generate_tokens_from_c_tokenizer
raise TokenError(msg, (e.lineno, e.offset)) from None
tokenize.TokenError: ('unexpected character after line continuation character', (74, 48))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/cli.py", line 1978, in args_to_api
dag_api = workflow_api.dag(
^^^^^^^^^^^^^^^^^
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/api.py", line 328, in dag
return DAGApi(
^^^^^^^
File "<string>", line 6, in __init__
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/api.py", line 438, in __post_init__
self.workflow_api._workflow.dag_settings = self.dag_settings
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/api.py", line 386, in _workflow
workflow.include(
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/workflow.py", line 1398, in include
exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
File "/home/dhwani/MyGit/eukrhythmic/eukrhythmic", line 32, in <module>
include: "rules/05-assembly/megahit-snake.smk"
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/workflow.py", line 1378, in include
code, rulecount = parse(
^^^^^^
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 1295, in parse
for t, orig_token in automaton.consume():
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 137, in consume
for t, orig in self.state(token):
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 1243, in python
for t in self.subautomaton(token.string, token=token).consume():
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 146, in consume
self.error(
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/parser.py", line 157, in error
raise SyntaxError(msg, (self.snakefile.path, lineno(token), None, None))
File "/home/dhwani/MyGit/eukrhythmic/rules/02-trim.smk", line 73
SyntaxError: unexpected character after line continuation character
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/cli.py", line 2136, in main
success = args_to_api(args, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/cli.py", line 2110, in args_to_api
snakemake_api.print_exception(e)
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/api.py", line 241, in print_exception
print_exception(ex, linemaps)
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/exceptions.py", line 96, in print_exception
format_error(
File "/home/dhwani/anaconda3/envs/eukrhythmic/lib/python3.12/site-packages/snakemake/exceptions.py", line 20, in format_error
lineno = linemaps[snakefile][lineno]
~~~~~~~~~~~~~~~~~~~^^^^^^^^
KeyError: 73
- So this is it. This time it seems to have read and checked the input files properly, but I can't go beyond this point, and don't know how to get rid of this error.
Any help regarding this issue will be greatly appreciated. I eventually plan to run this with my own samples.
I am running this on a Linux workstation with Ubuntu 20.04 LTS. Please let me know if any more info is needed from my side.
regards,
Dhwani