Closed waweey closed 3 months ago
Jerrythafast
commented
11 months ago Hi @waweey,
FDSTools currently does not support Python 3.12. We have a fix for this in the next release, which should come later this month, but for now my advise is to downgrade to Python 3.11 to avoid this issue.
I'm sorry for the inconvenience!
Jerry
waweey
commented
11 months ago Thank you, Jerry, for the prompt response
waweey
commented
11 months ago Hi again jerry, I have followed all the steps provided for the ISFG exercise 1.
For the (fdstools tssv --num-threads 8 --report tssv1-report.txt ForenSeqA ForenseqARef_R1.fasta.gz tssv1-output.txt) regards of the number of threads, the following error is observed:
**fdstools : usage: fdstools tssv [-h] [-v] [-d] [-F FORMAT] [-R FILE] [-L N] [-D DIR] At line:1 char:1
+ CategoryInfo : NotSpecified: (usage: fdstools...[-L N] [-D DIR]:String) [], RemoteException
+ FullyQualifiedErrorId : NativeCommandError
[-T THREADS] [-X] [-m MISMATCHES] [-n N] [-a N] [-B]
[-M ACTION]
LIBRARY [IN] [OUT]
fdstools tssv: error: argument LIBRARY: Sequence for chr13:20327551..20327614 is unavailable and could not be downloaded automatically. Please run 'strnaming refseq-cache chr13:20327551..20327614' on a system with internet
access and manually transfer the downloaded files to 'C:\Users\q8dj\.strnaming-cache'.**I have a PC with internet connection and I have tried to cash the chr13 manually but still the error is still showing.
**strnaming : usage: strnaming [-h] [-v] [-d] ACTION ... At line:1 char:1
+ CategoryInfo : NotSpecified: (usage: strnamin...[-d] ACTION ...:String) [], RemoteException
+ FullyQualifiedErrorId : NativeCommandErrorstrnaming: error: Sequence for chr13:20327551..20327614 is unavailable and could not be downloaded automatically. Please run 'strnaming refseq-cache chr13:20327551..20327614' on a system with internet access and manually transfer the downloaded files to 'C:\Users\q8dj.strnaming-cache'. Something went wrong while trying to cache refseq range chr13:20327551..20327614**
Jerrythafast
commented
11 months ago Hi @waweey,
Looks like for some reason FDSTools/STRNaming is unable to contact the Ensembl REST API. It should download the reference sequence by contacting http://rest.ensembl.org/sequence/region/human/chr13:20324353..20336640?content-type=text/plain
Could you try if that link works (in a web browser or using a command-line utility such as cURL/wget) on that PC?
If it does, I'm curious if we can get more information by adding --debug to the command like this:
strnaming refseq-cache --debug chr13:20327551..20327614Hi Jerry,
PS C:\Users\q8dj> strnaming refseq-cache --debug chr13:20327551..20327614
**strnaming : usage: strnaming [-h] [-v] [-d] ACTION ... At line:1 char:1
+ CategoryInfo : NotSpecified: (usage: strnamin...[-d] ACTION ...:String) [], RemoteException
+ FullyQualifiedErrorId : NativeCommandErrorstrnaming: error: The following arguments are not known. Please check spelling and argument order: '--debug'.**
PS C:\Users\q8dj> strnaming --debug refseq-cache chr13:20327551..20327614 strnaming : Traceback (most recent call last): At line:1 char:1
+ CategoryInfo : NotSpecified: (Traceback (most recent call last)::String) [], RemoteException
+ FullyQualifiedErrorId : NativeCommandError
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 147, in _get_chunk
with gzip.open(chunkfilepath, "rt") as f:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\gzip.py", line 174, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\q8dj\\.strnaming-cache\\refseq-13-1654.txt.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 91, in acquire
self.lock = LOCK_FILE.open("x")
^^^^^^^^^^^^^^^^^^^
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\pathlib.py", line 1044, in open
return io.open(self, mode, buffering, encoding, errors, newline)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileExistsError: [Errno 17] File exists: 'C:\\Users\\q8dj\\.strnaming-cache\\cache.lock'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 155, in _get_chunk
with LockFile():
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 82, in __enter__
self.acquire()
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 95, in acquire
raise ValueError(
ValueError: Failed to acquire lock within 60 seconds; please remove lock file manually if this problem persists (C:\Users\q8dj\.strnaming-cache\cache.lock)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Scripts\strnaming.exe\__main__.py", line 7, in <module>
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\strnaming.py", line 162, in main
cProfile.runctx("args.func(args)", globals(), locals(), sort="tottime")
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\cProfile.py", line 20, in runctx
return _pyprofile._Utils(Profile).runctx(statement, globals, locals,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\profile.py", line 63, in runctx
prof.runctx(statement, globals, locals)
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\cProfile.py", line 101, in runctx
exec(cmd, globals, locals)
File "<string>", line 1, in <module>
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\strnaming.py", line 88, in run_refseq_cache
refseq_cache.get_refseq(rng.group(1), int(rng.group(2)), int(rng.group(3)))
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 204, in get_refseq
seq += _get_chunk(chromosome, chunk, skip, length)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\q8dj\AppData\Local\Programs\Python\Python311\Lib\site-packages\strnaming\refseq_cache.py", line 177, in _get_chunk
raise ValueError(
ValueError: Sequence for chr13:20327551..20327614 is unavailable and could not be downloaded automatically. Please run 'strnaming refseq-cache chr13:20327551..20327614' on a system with internet access and manually transfer the downloaded files to 'C:\Users\q8dj\.strnaming-cache'.
Something went wrong while trying to cache refseq range chr13:20327551..20327614
2600 function calls (2560 primitive calls) in 60.118 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
240 60.087 0.250 60.087 0.250 {built-in method time.sleep}
243 0.023 0.000 0.024 0.000 {built-in method io.open}
1 0.004 0.004 60.117 60.117 refseq_cache.py:87(acquire)
241 0.001 0.000 0.026 0.000 pathlib.py:1036(open)
243 0.001 0.000 0.001 0.000 pathlib.py:546(__fspath__)
247 0.000 0.000 0.000 0.000 pathlib.py:536(__str__)
242 0.000 0.000 0.000 0.000 {built-in method time.time}
241 0.000 0.000 0.000 0.000 {built-in method io.text_encoding}
7/1 0.000 0.000 0.000 0.000 _parser.py:509(_parse)
10/1 0.000 0.000 0.000 0.000 _compiler.py:37(_compile)
5/1 0.000 0.000 0.000 0.000 _parser.py:449(_parse_sub)
1 0.000 0.000 60.118 60.118 {built-in method builtins.exec}
1 0.000 0.000 0.000 0.000 {built-in method nt.stat}
8 0.000 0.000 0.000 0.000 _compiler.py:241(_optimize_charset)
1 0.000 0.000 0.000 0.000 {built-in method nt.mkdir}
1 0.000 0.000 0.000 0.000 _compiler.py:571(_code)
13/4 0.000 0.000 0.000 0.000 _parser.py:174(getwidth)
1 0.000 0.000 60.117 60.117 refseq_cache.py:134(_get_chunk)
57 0.000 0.000 0.000 0.000 _parser.py:164(__getitem__)
53 0.000 0.000 0.000 0.000 _parser.py:233(__next)
169 0.000 0.000 0.000 0.000 {method 'append' of 'list' objects}
135/123 0.000 0.000 0.000 0.000 {built-in method builtins.len}
42 0.000 0.000 0.000 0.000 _parser.py:254(get)
1 0.000 0.000 0.001 0.001 __init__.py:272(_compile)
1 0.000 0.000 60.118 60.118 strnaming.py:80(run_refseq_cache)
1 0.000 0.000 60.117 60.117 refseq_cache.py:185(get_refseq)
1 0.000 0.000 0.000 0.000 _compiler.py:509(_compile_info)
2 0.000 0.000 0.000 0.000 pathlib.py:56(parse_parts)
1 0.000 0.000 0.000 0.000 {built-in method builtins.print}
1 0.000 0.000 0.000 0.000 _parser.py:972(parse)
39 0.000 0.000 0.000 0.000 _parser.py:249(match)
73 0.000 0.000 0.000 0.000 {built-in method builtins.isinstance}
8 0.000 0.000 0.000 0.000 _compiler.py:214(_compile_charset)
2 0.000 0.000 0.000 0.000 pathlib.py:484(_parse_args)
2 0.000 0.000 0.000 0.000 gzip.py:25(open)
1 0.000 0.000 0.001 0.001 _compiler.py:738(compile)
2 0.000 0.000 0.000 0.000 {method 'format' of 'str' objects}
2 0.000 0.000 0.000 0.000 pathlib.py:530(_make_child)
18 0.000 0.000 0.000 0.000 _parser.py:286(tell)
3 0.000 0.000 0.000 0.000 _parser.py:94(closegroup)
28 0.000 0.000 0.000 0.000 {method 'find' of 'bytearray' objects}
2 0.000 0.000 0.000 0.000 enum.py:686(__call__)
18 0.000 0.000 0.000 0.000 _parser.py:172(append)
20 0.000 0.000 0.000 0.000 _parser.py:160(__len__)
1 0.000 0.000 0.001 0.001 __init__.py:163(match)
4 0.000 0.000 0.000 0.000 _parser.py:369(_escape)
4 0.000 0.000 0.000 0.000 pathlib.py:523(_format_parsed_parts)
25 0.000 0.000 0.000 0.000 {built-in method builtins.min}
2 0.000 0.000 0.000 0.000 enum.py:1516(__and__)
1 0.000 0.000 0.000 0.000 pathlib.py:1111(mkdir)
6 0.000 0.000 0.000 0.000 _parser.py:446(_uniq)
2 0.000 0.000 0.000 0.000 cp1252.py:18(encode)
1 0.000 0.000 0.000 0.000 _compiler.py:384(_mk_bitmap)
3 0.000 0.000 0.000 0.000 _parser.py:82(opengroup)
11 0.000 0.000 0.000 0.000 _parser.py:109(__init__)
1 0.000 0.000 0.000 0.000 _parser.py:224(__init__)
1 0.000 0.000 0.000 0.000 _compiler.py:386(<listcomp>)
1 0.000 0.000 60.118 60.118 <string>:1(<module>)
2 0.000 0.000 0.000 0.000 pathlib.py:515(_from_parsed_parts)
2 0.000 0.000 0.000 0.000 gzip.py:134(__init__)
1 0.000 0.000 0.000 0.000 pathlib.py:1008(stat)
1 0.000 0.000 0.000 0.000 pathlib.py:1245(is_dir)
8 0.000 0.000 0.000 0.000 _parser.py:79(groups)
1 0.000 0.000 60.117 60.117 refseq_cache.py:81(__enter__)
6 0.000 0.000 0.000 0.000 {built-in method fromkeys}
3 0.000 0.000 0.000 0.000 _compiler.py:396(_simple)
2 0.000 0.000 0.000 0.000 pathlib.py:147(splitroot)
2 0.000 0.000 0.000 0.000 pathlib.py:765(__truediv__)
2 0.000 0.000 0.000 0.000 {method 'match' of 're.Pattern' objects}
20 0.000 0.000 0.000 0.000 {built-in method builtins.ord}
1 0.000 0.000 0.000 0.000 _compiler.py:434(_get_literal_prefix)
1 0.000 0.000 0.000 0.000 gzip.py:323(closed)
2 0.000 0.000 0.000 0.000 {built-in method _codecs.charmap_encode}
4 0.000 0.000 0.000 0.000 {method 'join' of 'str' objects}
2 0.000 0.000 0.000 0.000 enum.py:1093(__new__)
1 0.000 0.000 0.000 0.000 {built-in method _sre.compile}
1 0.000 0.000 0.000 0.000 _compiler.py:465(_get_charset_prefix)
6 0.000 0.000 0.000 0.000 {method 'get' of 'dict' objects}
1 0.000 0.000 0.000 0.000 _parser.py:73(__init__)
1 0.000 0.000 0.000 0.000 _parser.py:956(fix_flags)
3 0.000 0.000 0.000 0.000 _compiler.py:31(_combine_flags)
4 0.000 0.000 0.000 0.000 {method 'replace' of 'str' objects}
4 0.000 0.000 0.000 0.000 {built-in method builtins.max}
2 0.000 0.000 0.000 0.000 _compiler.py:568(isstring)
2 0.000 0.000 0.000 0.000 {built-in method __new__ of type object at 0x00007FF8DC518F90}
2 0.000 0.000 0.000 0.000 pathlib.py:94(join_parsed_parts)
4 0.000 0.000 0.000 0.000 {method 'group' of 're.Match' objects}
2 0.000 0.000 0.000 0.000 {built-in method sys.intern}
3 0.000 0.000 0.000 0.000 _parser.py:168(__setitem__)
1 0.000 0.000 0.000 0.000 refseq_cache.py:79(__init__)
2 0.000 0.000 0.000 0.000 _compiler.py:426(_get_iscased)
1 0.000 0.000 0.000 0.000 {method 'translate' of 'bytearray' objects}
2 0.000 0.000 0.000 0.000 {built-in method nt.fspath}
2 0.000 0.000 0.000 0.000 {method 'extend' of 'list' objects}
1 0.000 0.000 0.000 0.000 {method 'disable' of '_lsprof.Profiler' objects}
1 0.000 0.000 0.000 0.000 {built-in method _stat.S_ISDIR}
2 0.000 0.000 0.000 0.000 {method 'reverse' of 'list' objects}
1 0.000 0.000 0.000 0.000 {method 'items' of 'dict' objects}Hi @waweey,
Strangely, it appears that STRNaming hasn't cleant up its lock file during an earlier attempt. Could you try again after manually deleting this file? C:\Users\q8dj\.strnaming-cache\cache.lock
Jerry
Jerrythafast
commented
3 months ago Fixed in v2.1.0
Hi,
I have encountered this issue:
FDSTools failed to load 'allelefinder': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bganalyse': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bgcorrect': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bgestimate': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bghomraw': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bghomstats': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bgmerge': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'bgpredict': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'findnewalleles': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'libconvert': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'library': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'pipeline': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'samplestats': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'seqconvert': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'stuttermark': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'stuttermodel': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'tssv': 'FileFinder' object has no attribute 'find_module' FDSTools failed to load 'vis': 'FileFinder' object has no attribute 'find_module'
Can you please suggest a solution? I have tried reinstalling FDStools and installing it again but the same issue exists. I am running the most updated version of python