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Error handling when template > genome #59

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HadrienG opened this issue May 22, 2018 · 0 comments
Closed

Error handling when template > genome #59

HadrienG opened this issue May 22, 2018 · 0 comments
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@HadrienG
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@HadrienG
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INFO:iss.app:Starting iss generate INFO:iss.app:Using kde ErrorModel INFO:iss.app:Using lognormal abundance distribution INFO:iss.app:Using 2 cpus for read generation INFO:iss.app:Generating 5000 reads INFO:iss.app:Generating reads for record: NC_001740.1:5890-6729 INFO:iss.app:Generating reads for record: NC_018081.1:c2783521-2782661 INFO:iss.app:Generating reads for record: NC_005364.2:c967483-966185 INFO:iss.app:Generating reads for record: NC_003997.3:1351647-1352231 multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py", line 130, in simulate_read assert reverse_end < len(record.seq) AssertionError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 350, in call
return self.func(*args, **kwargs)
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py", line 131, in call
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py", line 131, in
return [func(*args, **kwargs) for func, args, kwargs in self.items]
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py", line 53, in reads
forward, reverse = simulate_read(record, ErrorModel, i)
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py", line 135, in simulate_read
read_length, len(record.seq) - read_length
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/random.py", line 199, in randrange
raise ValueError("empty range for randrange() (%d,%d, %d)" % (istart, istop, width))
ValueError: empty range for randrange() (301,284, -17)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 359, in call
raise TransportableException(text, e_type)
joblib.my_exceptions.TransportableException: TransportableException

ValueError Tue May 22 21:04:40 2018
PID: 95094Python 3.6.5: /Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/bin/python3.6
...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in call(self=<joblib.parallel.BatchedCalls object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
self.items = [(, (SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 204, 0, 'test_reads', False), {})]
132
133 def len(self):
134 return self._size
135

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in (.0=<list_iterator object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
func =
args = (SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 204, 0, 'test_reads', False)
kwargs = {}
132
133 def len(self):
134 return self._size
135

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py in reads(record=SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, n_pairs=204, cpu_number=0, output='test_reads', gc_bias=False)
48 # try:
49 # forward, reverse = simulate_read(record, ErrorModel, i)
50 # except ValueError as e:
51 # logger.error('Skipping this record: %s' % record.id)
52 # return
---> 53 forward, reverse = simulate_read(record, ErrorModel, i)
forward = undefined
reverse = undefined
record = SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[])
ErrorModel = <iss.error_models.kde.KDErrorModel object>
i = 0
54 if gc_bias:
55 stiched_seq = forward.seq + reverse.seq
56 gc_content = GC(stiched_seq)
57 if 40 < gc_content < 60:

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py in simulate_read(record=SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, i=0)
130 assert reverse_end < len(record.seq)
131 except AssertionError as e:
132 # we use random insert when the modelled template length distribution
133 # is too large
134 reverse_end = len(record.seq) - random.randrange(
--> 135 read_length, len(record.seq) - read_length
read_length = array(301)
record.seq = Seq('ATGCGGGAGTCTAGTCAAATACGTGAGACGACAGAAACAAAAATAAAATTAAGT...TAA', SingleLetterAlphabet())
136 )
137 reverse_start = reverse_end - read_length
138 bounds = (reverse_start, reverse_end)
139 # create a perfect read

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/random.py in randrange(self=<random.Random object>, start=array(301), stop=284, step=1, _int=<class 'int'>)
194 raise ValueError("non-integer stop for randrange()")
195 width = istop - istart
196 if step == 1 and width > 0:
197 return istart + self._randbelow(width)
198 if step == 1:
--> 199 raise ValueError("empty range for randrange() (%d,%d, %d)" % (istart, istop, width))
istart = 301
istop = 284
width = -17
200
201 # Non-unit step argument supplied.
202 istep = _int(step)
203 if istep != step:

ValueError: empty range for randrange() (301,284, -17)

"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py", line 699, in retrieve
self._output.extend(job.get(timeout=self.timeout))
File "/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
joblib.my_exceptions.TransportableException: TransportableException

ValueError Tue May 22 21:04:40 2018
PID: 95094Python 3.6.5: /Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/bin/python3.6
...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in call(self=<joblib.parallel.BatchedCalls object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
self.items = [(, (SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 204, 0, 'test_reads', False), {})]
132
133 def len(self):
134 return self._size
135

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in (.0=<list_iterator object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
func =
args = (SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 204, 0, 'test_reads', False)
kwargs = {}
132
133 def len(self):
134 return self._size
135

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py in reads(record=SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, n_pairs=204, cpu_number=0, output='test_reads', gc_bias=False)
48 # try:
49 # forward, reverse = simulate_read(record, ErrorModel, i)
50 # except ValueError as e:
51 # logger.error('Skipping this record: %s' % record.id)
52 # return
---> 53 forward, reverse = simulate_read(record, ErrorModel, i)
forward = undefined
reverse = undefined
record = SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[])
ErrorModel = <iss.error_models.kde.KDErrorModel object>
i = 0
54 if gc_bias:
55 stiched_seq = forward.seq + reverse.seq
56 gc_content = GC(stiched_seq)
57 if 40 < gc_content < 60:

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py in simulate_read(record=SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, i=0)
130 assert reverse_end < len(record.seq)
131 except AssertionError as e:
132 # we use random insert when the modelled template length distribution
133 # is too large
134 reverse_end = len(record.seq) - random.randrange(
--> 135 read_length, len(record.seq) - read_length
read_length = array(301)
record.seq = Seq('ATGCGGGAGTCTAGTCAAATACGTGAGACGACAGAAACAAAAATAAAATTAAGT...TAA', SingleLetterAlphabet())
136 )
137 reverse_start = reverse_end - read_length
138 bounds = (reverse_start, reverse_end)
139 # create a perfect read

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/random.py in randrange(self=<random.Random object>, start=array(301), stop=284, step=1, _int=<class 'int'>)
194 raise ValueError("non-integer stop for randrange()")
195 width = istop - istart
196 if step == 1 and width > 0:
197 return istart + self._randbelow(width)
198 if step == 1:
--> 199 raise ValueError("empty range for randrange() (%d,%d, %d)" % (istart, istop, width))
istart = 301
istop = 284
width = -17
200
201 # Non-unit step argument supplied.
202 istep = _int(step)
203 if istep != step:

ValueError: empty range for randrange() (301,284, -17)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/bin/iss", line 11, in
sys.exit(main())
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/app.py", line 403, in main
args.func(args)
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/app.py", line 169, in generate_reads
args.gc_bias) for i in range(cpus))
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py", line 789, in call
self.retrieve()
File "/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py", line 740, in retrieve
raise exception
joblib.my_exceptions.JoblibValueError: JoblibValueError

Multiprocessing exception:
...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/bin/iss in ()
6
7 from iss.app import main
8
9 if name == 'main':
10 sys.argv[0] = re.sub(r'(-script.pyw?|.exe)?$', '', sys.argv[0])
---> 11 sys.exit(main())

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/app.py in main()
398 elif args.debug:
399 logging.basicConfig(level=logging.DEBUG)
400 else:
401 logging.basicConfig(level=logging.INFO)
402
--> 403 args.func(args)
args.func =
args = Namespace(abundance='lognormal', abundance_file=... output='test_reads', quiet=False, version=False)
404 logging.shutdown()
405 except AttributeError as e:
406 logger = logging.getLogger(name)
407 logger.debug(e)

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/app.py in generate_reads(args=Namespace(abundance='lognormal', abundance_file=... output='test_reads', quiet=False, version=False))
164
165 record_file_name_list = Parallel(n_jobs=cpus)(
166 delayed(generator.reads)(
167 record, err_mod,
168 n_pairs_per_cpu, i, args.output,
--> 169 args.gc_bias) for i in range(cpus))
args.gc_bias = False
cpus = 2
170 temp_file_list.extend(record_file_name_list)
171 except KeyboardInterrupt as e:
172 logger.error('iss generate interrupted: %s' % e)
173 generator.cleanup(temp_file_list)

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in call(self=Parallel(n_jobs=2), iterable=<generator object generate_reads..>)
784 if pre_dispatch == "all" or n_jobs == 1:
785 # The iterable was consumed all at once by the above for loop.
786 # No need to wait for async callbacks to trigger to
787 # consumption.
788 self._iterating = False
--> 789 self.retrieve()
self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=2)>
790 # Make sure that we get a last message telling us we are done
791 elapsed_time = time.time() - self._start_time
792 self._print('Done %3i out of %3i | elapsed: %s finished',
793 (len(self._output), len(self._output),

Sub-process traceback:

ValueError Tue May 22 21:04:40 2018
PID: 95094Python 3.6.5: /Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/bin/python3.6
...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in call(self=<joblib.parallel.BatchedCalls object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
self.items = [(, (SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 204, 0, 'test_reads', False), {})]
132
133 def len(self):
134 return self._size
135

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/joblib/parallel.py in (.0=<list_iterator object>)
126 def init(self, iterator_slice):
127 self.items = list(iterator_slice)
128 self._size = len(self.items)
129
130 def call(self):
--> 131 return [func(*args, **kwargs) for func, args, kwargs in self.items]
func =
args = (SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), <iss.error_models.kde.KDErrorModel object>, 204, 0, 'test_reads', False)
kwargs = {}
132
133 def len(self):
134 return self._size
135

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py in reads(record=SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, n_pairs=204, cpu_number=0, output='test_reads', gc_bias=False)
48 # try:
49 # forward, reverse = simulate_read(record, ErrorModel, i)
50 # except ValueError as e:
51 # logger.error('Skipping this record: %s' % record.id)
52 # return
---> 53 forward, reverse = simulate_read(record, ErrorModel, i)
forward = undefined
reverse = undefined
record = SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[])
ErrorModel = <iss.error_models.kde.KDErrorModel object>
i = 0
54 if gc_bias:
55 stiched_seq = forward.seq + reverse.seq
56 gc_content = GC(stiched_seq)
57 if 40 < gc_content < 60:

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/site-packages/iss/generator.py in simulate_read(record=SeqRecord(seq=Seq('ATGCGGGAGTCTAGTCAAATACGTGAGAC...r. Ames chromosome, complete genome', dbxrefs=[]), ErrorModel=<iss.error_models.kde.KDErrorModel object>, i=0)
130 assert reverse_end < len(record.seq)
131 except AssertionError as e:
132 # we use random insert when the modelled template length distribution
133 # is too large
134 reverse_end = len(record.seq) - random.randrange(
--> 135 read_length, len(record.seq) - read_length
read_length = array(301)
record.seq = Seq('ATGCGGGAGTCTAGTCAAATACGTGAGACGACAGAAACAAAAATAAAATTAAGT...TAA', SingleLetterAlphabet())
136 )
137 reverse_start = reverse_end - read_length
138 bounds = (reverse_start, reverse_end)
139 # create a perfect read

...........................................................................
/Users/hadrien/.local/share/virtualenvs/workspace-w0RVuX47/lib/python3.6/random.py in randrange(self=<random.Random object>, start=array(301), stop=284, step=1, _int=<class 'int'>)
194 raise ValueError("non-integer stop for randrange()")
195 width = istop - istart
196 if step == 1 and width > 0:
197 return istart + self._randbelow(width)
198 if step == 1:
--> 199 raise ValueError("empty range for randrange() (%d,%d, %d)" % (istart, istop, width))
istart = 301
istop = 284
width = -17
200
201 # Non-unit step argument supplied.
202 istep = _int(step)
203 if istep != step:

ValueError: empty range for randrange() (301,284, -17)
@HadrienG HadrienG added the bug label May 22, 2018
@HadrienG HadrienG self-assigned this May 22, 2018
HadrienG added a commit that referenced this issue Jun 2, 2018
@HadrienG
fix for #59
b3416c0
@HadrienG HadrienG mentioned this issue Jun 2, 2018
Merged
@HadrienG HadrienG closed this as completed Jun 2, 2018
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