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jdidion / atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)
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No module named lzma #54

Closed pkMyt1 closed 6 years ago

pkMyt1 commented 6 years ago

I downloaded this and tried a local install using python3 setup.py install --user. Now when I run it I get an error that I have been unable to trace. The full error stack is

[dsimpson@localhost atropos]$ atropos Traceback (most recent call last): File "/home/dsimpson/.local/bin/atropos", line 4, in import('pkg_resources').run_script('atropos==0+unknown', 'atropos') File "/usr/lib/python3.5/site-packages/pkg_resources/init.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3.5/site-packages/pkg_resources/init.py", line 1527, in run_script exec(code, namespace, namespace) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 26, in main() File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 23, in main sys.exit(execute_cli(args)) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 189, in execute_cli print_subcommands() File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 232, in print_subcommands command.get_help() for command in iter_commands()))) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 232, in command.get_help() for command in iter_commands()))) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 101, in get_help name=self.name, description=self.description.strip()) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 95, in description return self.get_command_parser_class().description File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 82, in get_command_parser_class mod = import_module(self.cli_module) File "/usr/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 986, in _gcd_import File "", line 969, in _find_and_load File "", line 944, in _find_and_load_unlocked File "", line 222, in _call_with_frames_removed File "", line 986, in _gcd_import File "", line 969, in _find_and_load File "", line 958, in _find_and_load_unlocked File "", line 673, in _load_unlocked File "", line 665, in exec_module File "", line 222, in _call_with_frames_removed File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/detect/init.py", line 8, in from atropos.commands.base import ( File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/base.py", line 8, in from atropos.adapters import AdapterCache File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/adapters/init.py", line 15, in from atropos.io.seqio import ColorspaceSequence, FastaReader File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/io/init.py", line 8, in from atropos.io.compression import get_file_opener File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/io/compression.py", line 6, in import lzma File "/usr/lib/python3.5/lzma.py", line 26, in from _lzma import * ImportError: No module named '_lzma'

I am assuming I did something wrong here, any ideas? Thank you.

jdidion commented 6 years ago

This is quite strange. Your python installation is missing the lzma library, which was added in python 3.3. Are you using a binary installation of cpython, or did you build from source, or are you using something else (e.g. IronPython or PyPy)?

On Dec 20, 2017, at 3:38 PM, Dennis Simpson notifications@github.com wrote:

I downloaded this and tried a local install using python3 setup.py install --user. Now when I run it I get an error that I have been unable to trace. The full error stack is

[dsimpson@localhost atropos]$ atropos Traceback (most recent call last): File "/home/dsimpson/.local/bin/atropos", line 4, in import('pkg_resources').run_script('atropos==0+unknown', 'atropos') File "/usr/lib/python3.5/site-packages/pkg_resources/init.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3.5/site-packages/pkg_resources/init.py", line 1527, in run_script exec(code, namespace, namespace) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 26, in main() File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 23, in main sys.exit(execute_cli(args)) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 189, in execute_cli print_subcommands() File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 232, in print_subcommands command.get_help() for command in iter_commands()))) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 232, in command.get_help() for command in iter_commands()))) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 101, in get_help name=self.name, description=self.description.strip()) File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 95, in description return self.get_command_parser_class().description File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 82, in get_command_parser_class mod = import_module(self.cli_module) File "/usr/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 986, in _gcd_import File "", line 969, in _find_and_load File "", line 944, in _find_and_load_unlocked File "", line 222, in _call_with_frames_removed File "", line 986, in _gcd_import File "", line 969, in _find_and_load File "", line 958, in _find_and_load_unlocked File "", line 673, in _load_unlocked File "", line 665, in exec_module File "", line 222, in _call_with_frames_removed File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/detect/init.py", line 8, in from atropos.commands.base import ( File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/base.py", line 8, in from atropos.adapters import AdapterCache File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/adapters/init.py", line 15, in from atropos.io.seqio import ColorspaceSequence, FastaReader File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/io/init.py", line 8, in from atropos.io.compression import get_file_opener File "/home/dsimpson/.local/lib/python3.5/site-packages/atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/io/compression.py", line 6, in import lzma File "/usr/lib/python3.5/lzma.py", line 26, in from _lzma import * ImportError: No module named '_lzma'

I am assuming I did something wrong here, any ideas? Thank you.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jdidion/atropos/issues/54, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHrns1Hkpr2YuMlUWJFt_ePE-awBlJwks5tCXAqgaJpZM4RI7nE.

pkMyt1 commented 6 years ago

The lzma module is there. To make doubly certain I just reinstalled everything. I get the error above from pip or setup install. Running atropos from GitHub or after a build but no install I get

[dsimpson@localhost atropos]$ bin/atropos --help Traceback (most recent call last): File "bin/atropos", line 6, in from atropos import check_importability ImportError: No module named atropos

I had it working two weeks ago but wanted a clean set of files so I downloaded a fresh copy. I will chase this some more.

pkMyt1 commented 6 years ago

I need to answer your other questions. Python 3.5 on Scientific Linux.

On Dec 20, 2017 3:47 PM, "John Didion" notifications@github.com wrote:

This is quite strange. Your python installation is missing the lzma library, which was added in python 3.3. Are you using a binary installation of cpython, or did you build from source, or are you using something else (e.g. IronPython or PyPy)?

On Dec 20, 2017, at 3:38 PM, Dennis Simpson notifications@github.com wrote:

I downloaded this and tried a local install using python3 setup.py install --user. Now when I run it I get an error that I have been unable to trace. The full error stack is

[dsimpson@localhost atropos]$ atropos Traceback (most recent call last): File "/home/dsimpson/.local/bin/atropos", line 4, in import('pkg_resources').run_script('atropos==0+unknown', 'atropos') File "/usr/lib/python3.5/site-packages/pkg_resources/init.py", line 750, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3.5/site-packages/pkg_resources/init.py", line 1527, in run_script exec(code, namespace, namespace) File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 26, in main() File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/EGG-INFO/scripts/atropos", line 23, in main sys.exit(execute_cli(args)) File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 189, in execute_cli print_subcommands() File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 232, in print_subcommands command.get_help() for command in iter_commands()))) File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 232, in command.get_help() for command in iter_commands()))) File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 101, in get_help name=self.name, description=self.description.strip()) File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 95, in description return self.get_command_parser_class().description File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/init.py", line 82, in get_command_parser_class mod = import_module(self.cli_module) File "/usr/lib/python3.5/importlib/init.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 986, in _gcd_import File "", line 969, in _find_and_load File "", line 944, in _find_and_load_unlocked File "", line 222, in _call_with_frames_removed File "", line 986, in _gcd_import File "", line 969, in _find_and_load File "", line 958, in _find_and_load_unlocked File "", line 673, in _load_unlocked File "", line 665, in exec_module File "", line 222, in _call_with_frames_removed File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/detect/init.py", line 8, in from atropos.commands.base import ( File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/commands/base.py", line 8, in from atropos.adapters import AdapterCache File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/adapters/init.py", line 15, in from atropos.io.seqio import ColorspaceSequence, FastaReader File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/io/init.py", line 8, in from atropos.io.compression import get_file_opener File "/home/dsimpson/.local/lib/python3.5/site-packages/ atropos-0+unknown-py3.5-linux-x86_64.egg/atropos/io/compression.py", line 6, in import lzma File "/usr/lib/python3.5/lzma.py", line 26, in from _lzma import * ImportError: No module named '_lzma'

I am assuming I did something wrong here, any ideas? Thank you.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub < https://github.com/jdidion/atropos/issues/54>, or mute the thread < https://github.com/notifications/unsubscribe-auth/AAHrns1Hkpr2YuMlUWJFt_ ePE-awBlJwks5tCXAqgaJpZM4RI7nE>.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jdidion/atropos/issues/54#issuecomment-353178044, or mute the thread https://github.com/notifications/unsubscribe-auth/AIEPaw7S7goRza4gea5Qcf8GIHNWQ9Yhks5tCXJJgaJpZM4RI7nE .

pkMyt1 commented 6 years ago

This turns out to be my problem. Somehow I damaged part of the lzma module during an update. I rebuilt Python and all is back to working as expected.