I am new to Pyspark and I am trying to do a simple count. However it is giving me this error. The text file is inside hdfs.
CODE:
>>> mydata = sc.textFile("hdfs://user/poem.txt")
>>> mydata.count()
ERROR:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/spark-2.0.1-bin-hadoop2.7/python/pyspark/rdd.py", line 1008, in count
return self.mapPartitions(lambda i: [sum(1 for _ in i)]).sum()
File "/usr/local/lib/spark-2.0.1-bin-hadoop2.7/python/pyspark/rdd.py", line 999, in sum
return self.mapPartitions(lambda x: [sum(x)]).fold(0, operator.add)
File "/usr/local/lib/spark-2.0.1-bin-hadoop2.7/python/pyspark/rdd.py", line 873, in fold
vals = self.mapPartitions(func).collect()
File "/usr/local/lib/spark-2.0.1-bin-hadoop2.7/python/pyspark/rdd.py", line 776, in collect
port = self.ctx._jvm.PythonRDD.collectAndServe(self._jrdd.rdd())
File "/usr/local/lib/spark-2.0.1-bin-hadoop2.7/python/lib/py4j-0.10.3-src.zip/py4j/java_gateway.py", line 1133, in __call__
File "/usr/local/lib/spark-2.0.1-bin-hadoop2.7/python/pyspark/sql/utils.py", line 79, in deco
raise IllegalArgumentException(s.split(': ', 1)[1], stackTrace)
pyspark.sql.utils.IllegalArgumentException: u'java.net.UnknownHostException: user'
You are missing a "/"
r = sc.textFile("hdfs://user/myFile")
r.count()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/opt/cloudera/parcels/CDH-5.7.0-1.cdh5.7.0.p1464.1349/lib/spark/python/pyspark/rdd.py", line 1004, in count
return self.mapPartitions(lambda i: [sum(1 for _ in i)]).sum()
File "/opt/cloudera/parcels/CDH-5.7.0-1.cdh5.7.0.p1464.1349/lib/spark/python/pyspark/rdd.py", line 995, in sum
return self.mapPartitions(lambda x: [sum(x)]).fold(0, operator.add)
File "/opt/cloudera/parcels/CDH-5.7.0-1.cdh5.7.0.p1464.1349/lib/spark/python/pyspark/rdd.py", line 869, in fold
vals = self.mapPartitions(func).collect()
File "/opt/cloudera/parcels/CDH-5.7.0-1.cdh5.7.0.p1464.1349/lib/spark/python/pyspark/rdd.py", line 771, in collect
port = self.ctx._jvm.PythonRDD.collectAndServe(self._jrdd.rdd())
File "/opt/cloudera/parcels/CDH-5.7.0-1.cdh5.7.0.p1464.1349/lib/spark/python/lib/py4j-0.9-src.zip/py4j/java_gateway.py", line 813, in __call__
File "/opt/cloudera/parcels/CDH-5.7.0-1.cdh5.7.0.p1464.1349/lib/spark/python/pyspark/sql/utils.py", line 53, in deco
raise IllegalArgumentException(s.split(': ', 1)[1], stackTrace)
pyspark.sql.utils.IllegalArgumentException: u'java.net.UnknownHostException: user'
However, if you do
>>> r = sc.textFile("hdfs:///user/myFile")
>>> r.count()
318199
it is because hdfs:// is the URI. And in Fullly qualified syntax, it should be hdfs:///. Hence, Spark is thinking the token "user" as NN-Host
Related
I installed python 3.10 then tried to install django but it just starts downloading by after it reaches a certain point it crashes and shows this error Exception:
Traceback (most recent call last):
File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 302, in _error_catcher
yield File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 384, in read
data = self._fp.read(amt) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\cachecontrol\filewrapper.py",
line 60, in read
data = self.__fp.read(amt) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\http\client.py",
line 447, in read
n = self.readinto(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\http\client.py",
line 491, in readinto
n = self.fp.readinto(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\socket.py",
line 589, in readinto
return self._sock.recv_into(b) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\ssl.py",
line 1049, in recv_into
return self.read(nbytes, buffer) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\ssl.py",
line 908, in read
return self._sslobj.read(len, buffer) socket.timeout: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\basecommand.py",
line 228, in main
status = self.run(options, args) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\commands\install.py",
line 291, in run
resolver.resolve(requirement_set) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 103, in resolve
self._resolve_one(requirement_set, req) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 257, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\resolve.py",
line 210, in _get_abstract_dist_for
self.require_hashes File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\operations\prepare.py",
line 310, in prepare_linked_requirement
progress_bar=self.progress_bar File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 837, in unpack_url
progress_bar=progress_bar File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 674, in unpack_http_url
progress_bar) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 898, in _download_http_url
_download_url(resp, link, content_file, hashes, progress_bar) File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 618, in _download_url
hashes.check_against_chunks(downloaded_chunks) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\hashes.py",
line 48, in check_against_chunks
for chunk in chunks: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 586, in written_chunks
for chunk in chunks: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\utils\ui.py",
line 159, in iter
for x in it: File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_internal\download.py",
line 575, in resp_read
decode_content=False): File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 436, in stream
data = self.read(amt=amt, decode_content=decode_content) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 401, in read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining) File
"c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\contextlib.py",
line 130, in exit
self.gen.throw(type, value, traceback) File "c:\users\gabraham.aecigroup\appdata\local\programs\python\python37\lib\site-packages\pip_vendor\urllib3\response.py",
line 307, in _error_catcher
raise ReadTimeoutError(self._pool, None, 'Read timed out.') pip._vendor.urllib3.exceptions.ReadTimeoutError:
HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read
timed out.
So I tried to replace python 3.10 with version 3.7.0 but I am still getting the same error. How do I avoid this error?
check here, probably you have bad connection to internet or the download takes too long...
I'm trying to do anything with my GeoDataFrame that I'm importing from the Census website, but when I try to dissolve or overlay with other data frames I get:
pygeos.GEOSException: IllegalArgumentException: Argument must be Polygonal or LinearRing
It won't every overlay itself which is weird. I've exploded it to get rid of the multi polygon and buffered the three invalid polygons, but I'm lost. New to geopandas but I can general feel my way around these things. Any help would be appreciated.
Is my installed package the issue?
Download this file
>>> import geopandas as gpd
>>> SHAPE_URL = 'https://www2.census.gov/geo/tiger/GENZ2018/shp/cb_2018_us_cd116_20m.zip'
>>> cd = gpd.read_file(SHAPE_URL)
>>> cd.dissolve()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/geopandas/geodataframe.py", line 1538, in dissolve
g = self.groupby(group_keys=False, **groupby_kwargs)[self.geometry.name].agg(
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pandas/core/groupby/generic.py", line 259, in aggregate
return self._python_agg_general(func, *args, **kwargs)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1173, in _python_agg_general
result, counts = self.grouper.agg_series(obj, f)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pandas/core/groupby/ops.py", line 691, in agg_series
return self._aggregate_series_pure_python(obj, func)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pandas/core/groupby/ops.py", line 741, in _aggregate_series_pure_python
res = func(group)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1160, in <lambda>
f = lambda x: func(x, *args, **kwargs)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/geopandas/geodataframe.py", line 1535, in merge_geometries
merged_geom = block.unary_union
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/geopandas/base.py", line 728, in unary_union
return self.geometry.values.unary_union()
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/geopandas/array.py", line 652, in unary_union
return vectorized.unary_union(self.data)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/geopandas/_vectorized.py", line 892, in unary_union
return _pygeos_to_shapely(pygeos.union_all(data))
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pygeos/decorators.py", line 80, in wrapped
return func(*args, **kwargs)
File "/Users/joefedorowicz/Development/virtualenvs/briefcase/lib/python3.9/site-packages/pygeos/set_operations.py", line 388, in union_all
result = lib.unary_union(collections, **kwargs)
pygeos.GEOSException: IllegalArgumentException: Argument must be Polygonal or LinearRing
import yfinance as yf
ticker = "AAPL"
stockdata = yf.download(ticker, start="2021-1-1", end="2021-1-10")
-----------------------------------------
Exception in thread Thread-1
Traceback (most recent call last):
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\threading.py", line 973, in _bootstrap_inner
self.run()
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\threading.py", line 910, in run
self._target(*self._args, **self._kwargs)
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\site-packages\multitasking\__init__.py", line 102, in _run_via_pool
return callee(*args, **kwargs)
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\site-packages\yfinance\multi.py", line 169, in _download_one_threaded
data = _download_one(ticker, start, end, auto_adjust, back_adjust,
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\site-packages\yfinance\multi.py", line 181, in _download_one
return Ticker(ticker).history(period=period, interval=interval,
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\site-packages\yfinance\base.py", line 157, in history
data = data.json()
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\site-packages\requests\models.py", line 900, in json
return complexjson.loads(self.text, **kwargs)
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\json\__init__.py", line 346, in loads
return _default_decoder.decode(s)
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\json\decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "C:\Users\Admin\AppData\Local\Programs\Python\Python39\lib\json\decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
try reinstalling/upgrading yfinance and make sure you are connected to internet
then execute
import yfinance as yf
stockdata = yf.download("AAPL", start="2021-01-01", end="2021-01-10")
print(stockdata)
after executing I got
[*********************100%***********************] 1 of 1 completed
Open High Low Close Adj Close Volume
Date
2020-12-31 134.080002 134.740005 131.720001 132.690002 132.267349 99116600
2021-01-04 133.520004 133.610001 126.760002 129.410004 128.997803 143301900
2021-01-05 128.889999 131.740005 128.429993 131.009995 130.592697 97664900
2021-01-06 127.720001 131.050003 126.379997 126.599998 126.196747 155088000
2021-01-07 128.360001 131.630005 127.860001 130.919998 130.502991 109578200
2021-01-08 132.429993 132.630005 130.229996 132.050003 131.629379 105158200
If your problem exists, please let me know which IDE you are using to execute the code
When I try to get values for a list of keys using asyncio_redis or aioredis, I am getting the following error. I know it is about something python socket, but unable to resolve the error. I attached both the code and error log with this issue. Here keys are a list of large byte arrays. get_params_redis is called by multiple processes. Any help would be appreciated, thanks!
async def multi_get_key_redis(keys):
redis = await aioredis.create_redis_pool(
'redis://localhost')
result =[]
for key in keys:
result.append(await redis.get(key))
# assert result == await asyncio.gather(*keys)
# return result
redis.close()
await redis.wait_closed()
print(result)
return result
def get_params_redis(shapes):
i = -1
params=[]
keys = []
for s in range(len(shapes)):
keys.append(s)
values = asyncio.get_event_loop().run_until_complete(multi_get_key_redis(keys))
for shape in shapes:
i = i + 1
param_np = pc._loads(values[i]).reshape(shape)
param_tensor = torch.nn.Parameter(torch.from_numpy(param_np))
params.append(param_tensor)
return params
Error Log:
Process Process-1:
Traceback (most recent call last):
File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/Users/srujithpoondla/largescaleml_project/train_redis.py", line 33, in train_redis
train_redis_epoch(epoch, args, model, train_loader, optimizer,shapes_len, loop)
File "/Users/srujithpoondla/largescaleml_project/train_redis.py", line 43, in train_redis_epoch
params = get_params_redis(shapes_len,loop)
File "/Users/srujithpoondla/largescaleml_project/common_functions.py", line 76, in get_params_redis
params = loop.run_until_complete(multi_get_key_redis(keys))
File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/base_events.py", line 454, in run_until_complete
self.run_forever()
File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/base_events.py", line 421, in run_forever
self._run_once()
File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/asyncio/base_events.py", line 1395, in _run_once
event_list = self._selector.select(timeout)
File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/selectors.py", line 577, in select
kev_list = self._kqueue.control(None, max_ev, timeout)
OSError: [Errno 9] Bad file descriptor
I created a BIOM file, yyy.biom, using the functions make_biom and write_biom of the R package biomformat, version 1.2.0.
yyy.biom looks like:
"id":{},
"format":["Biological Observation Matrix 1.0.0-dev"],
"format_url":["http://biom-format.org/documentation/format_versions/biom-1.0.html"],
"type":["OTU table"],
"generated_by":["biomformat 1.2.0"],
"date":["2017-09-21 14:36:28"],
"matrix_type":["dense"],
"matrix_element_type":["int"],
"shape":[5,6],
"rows":[
{"id":["GG_OTU_1"],"metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]},
{"id":["GG_OTU_2"],"metadata":["k__Bacteria","p__Cyanobacteria","c__Nostocophycideae","o__Nostocales","f__Nostocaceae","g__Dolichospermum","s__"]},
{"id":["GG_OTU_3"],"metadata":["k__Archaea","p__Euryarchaeota","c__Methanomicrobia","o__Methanosarcinales","f__Methanosarcinaceae","g__Methanosarcina","s__"]},
{"id":["GG_OTU_4"],"metadata":["k__Bacteria","p__Firmicutes","c__Clostridia","o__Halanaerobiales","f__Halanaerobiaceae","g__Halanaerobium","s__Halanaerobiumsaccharolyticum"]},
{"id":["GG_OTU_5"],"metadata":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]}
],
"columns":[
{"id":["Sample1"],"metadata":["CGCTTATCGAGA","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample2"],"metadata":["CATACCAGTAGC","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample3"],"metadata":["CTCTCTACCTGT","CATGCTGCCTCCCGTAGGAGT","gut","human gut"]},
{"id":["Sample4"],"metadata":["CTCTCGGCCTGT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]},
{"id":["Sample5"],"metadata":["CTCTCTACCAAT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]},
{"id":["Sample6"],"metadata":["CTAACTACCAAT","CATGCTGCCTCCCGTAGGAGT","skin","human skin"]}
],
"data": [[0,0,1,0,0,0],
[5,1,0,2,3,1],
[0,0,1,4,2,0],
[2,1,1,0,0,1],
[0,1,1,0,0,0]]
BIOM validation returns an error:
$ biom validate-table -i yyy.biom
Traceback (most recent call last):
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/bin/biom", line 6, in <module>
sys.exit(biom.cli.cli())
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 49, in validate_table
valid, report = _validate_table(input_fp, format_version, detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 62, in _validate_table
detailed_report=detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 113, in __call__
detailed_report=detailed_report)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 97, in run
return self._validate_json(**kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 305, in _validate_json
status_msg = method(table_json)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/cli/table_validator.py", line 496, in _valid_type
if value.lower() not in self.TableTypes:
AttributeError: 'list' object has no attribute 'lower'
I tried importing to QIIME 2 and got this error:
Traceback (most recent call last):
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
view_type=source_format)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/sdk/result.py", line 192, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
result = transformation(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in transformation
new_view = transformer(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/qiime2/core/transform.py", line 207, in wrapped
file_view = transformer(view)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2_types/feature_table/_transformer.py", line 128, in _8
data = _parse_biom_table_v100(ff)
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/q2_types/feature_table/_transformer.py", line 46, in _parse_biom_table_v100
table = biom.Table.from_json(json.load(fh))
File "/home/akense/programs/miniconda3/envs/qiime2.env.analysis/lib/python3.5/site-packages/biom_format-2.1.5-py3.5-linux-x86_64.egg/biom/table.py", line 3672, in from_json
dtype = MATRIX_ELEMENT_TYPE[json_table['matrix_element_type']]
TypeError: unhashable type: 'list'
QIIME 2 support suggested that the format 1.0.0-dev might be causing the issue. Could that be it? If so is there a way to change format?
Thanks!