breons
commented
3 years ago Hi!
Thanks for trying ALLSorts, apologies for the hurdle at the very first step! Let's get it working.
I'd be really keen to see how you go! I would try using the automated pipelines to get the best out of ALLSorts:
- https://github.com/Oshlack/ALLSorts/wiki/2.1.-Automated-Pipeline---Starting-with-FASTQ-or-FASTA-files or
- https://github.com/Oshlack/ALLSorts/wiki/2.2.-Automated-Pipeline---Starting-with-BAM-files
It looks like it has something to do with the UMAP import. Could you please do a:
conda list
After you've entered the conda environment? i.e. conda activate allsorts
Cheers, Breon.
vipmak
Hi, thanks for you great work, we are also doing an ALL classifier but we are using very simple algorithms so I'm hoping to use your tool to make sure our models are not too far off from more sophisticated approaches. However, I have not been able to complete the test (I'm not familiar with Python + Anaconda). It looks like something fails in the Python code but I can't tell what.
Any help is greatly appreciated!
Here's as far as I got:
(base) [Linus ~]$ cd .vipmak/ALLSorts/ (base) [Linus ALLSorts]$ conda activate allsorts (allsorts) [Linus ALLSorts]$ mkdir test_results (allsorts) [Linus ALLSorts]$ ls ALLSorts counts Dockerfile env LICENSE MANIFEST.in README.md setup.py test_results tests tools (allsorts) [Linus ALLSorts]$ python ALLSorts -samples tests/counts/test_counts.csv -destination test_results Traceback (most recent call last): File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/errors.py", line 776, in new_error_context yield File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 235, in lower_block self.lower_inst(inst) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 380, in lower_inst val = self.lower_assign(ty, inst) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 556, in lower_assign return self.lower_expr(ty, value) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 1084, in lower_expr res = self.lower_call(resty, expr) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 815, in lower_call res = self._lower_call_normal(fnty, expr, signature) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 1055, in _lower_call_normal res = impl(self.builder, argvals, self.loc) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/base.py", line 1194, in call res = self._imp(self._context, builder, self._sig, args, loc=loc) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/base.py", line 1224, in wrapper return fn(*args, **kwargs) File "/home/vipmak/.local/lib/python3.8/site-packages/numba/cpython/rangeobj.py", line 40, in range1_impl state.stop = stop File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/cgutils.py", line 164, in setattr self[self._datamodel.get_field_position(field)] = value File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/cgutils.py", line 188, in setitem raise TypeError("Invalid store of {value.type} to " TypeError: Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x7f700734ca90> (trying to write member #1)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/vipmak/.conda/envs/allsorts/lib/python3.8/runpy.py", line 194, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/vipmak/.conda/envs/allsorts/lib/python3.8/runpy.py", line 87, in _run_code exec(code, run_globals) File "ALLSorts/main.py", line 13, in
import allsorts
File "ALLSorts/allsorts.py", line 32, in
from ALLSorts.operations.comparisons import rebuildcomparisons
File "/home/vipmak/.local/lib/python3.8/site-packages/ALLSorts/operations/comparisons.py", line 20, in
from umap import UMAP
File "/home/vipmak/.local/lib/python3.8/site-packages/umap/init.py", line 1, in
from .umap import UMAP
File "/home/vipmak/.local/lib/python3.8/site-packages/umap/umap_.py", line 54, in
from umap.layouts import (
File "/home/vipmak/.local/lib/python3.8/site-packages/umap/layouts.py", line 39, in
def rdist(x, y):
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/decorators.py", line 226, in wrapper
disp.compile(sig)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/dispatcher.py", line 979, in compile
cres = self._compiler.compile(args, return_type)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/dispatcher.py", line 141, in compile
status, retval = self._compile_cached(args, return_type)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/dispatcher.py", line 155, in _compile_cached
retval = self._compile_core(args, return_type)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/dispatcher.py", line 168, in _compile_core
cres = compiler.compile_extra(self.targetdescr.typing_context,
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler.py", line 686, in compile_extra
return pipeline.compile_extra(func)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler.py", line 428, in compile_extra
return self._compile_bytecode()
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler.py", line 492, in _compile_bytecode
return self._compile_core()
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler.py", line 471, in _compile_core
raise e
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler.py", line 462, in _compile_core
pm.run(self.state)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 343, in run
raise patched_exception
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 334, in run
self._runPass(idx, pass_inst, state)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler_lock.py", line 35, in _acquire_compile_lock
return func(*args, **kwargs)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 289, in _runPass
mutated |= check(pss.run_pass, internal_state)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/compiler_machinery.py", line 262, in check
mangled = func(compiler_state)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/typed_passes.py", line 396, in run_pass
lower.lower()
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 138, in lower
self.lower_normal_function(self.fndesc)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 192, in lower_normal_function
entry_block_tail = self.lower_function_body()
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 221, in lower_function_body
self.lower_block(block)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/lowering.py", line 235, in lower_block
self.lower_inst(inst)
File "/home/vipmak/.conda/envs/allsorts/lib/python3.8/contextlib.py", line 131, in exit
self.gen.throw(type, value, traceback)
File "/home/vipmak/.local/lib/python3.8/site-packages/numba/core/errors.py", line 786, in new_error_context
raise newerr.with_traceback(tb)
numba.core.errors.LoweringError: Failed in nopython mode pipeline (step: native lowering)
Invalid store of i64 to i32 in <numba.core.datamodel.models.RangeModel object at 0x7f700734ca90> (trying to write member #1)
File "../../.local/lib/python3.8/site-packages/umap/layouts.py", line 53: def rdist(x, y):
During: lowering "$20call_function.7 = call $16load_global.5(dim, func=$16load_global.5, args=[Var(dim, layouts.py:52)], kws=(), vararg=None, target=None)" at /home/vipmak/.local/lib/python3.8/site-packages/umap/layouts.py (53)
(allsorts) [Linus ALLSorts]$ uname -a Linux Linus 5.11.0-27-generic #29~20.04.1-Ubuntu SMP Wed Aug 11 15:58:17 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux