IndexError: pop from empty list in read_fastq_random
Opened this issue · 5 comments
scharch commented
$ sircel --barcodes C4ML7-merged.fastq.gz --reads C4ML7-merged.fastq.gz --output_dir sircel --threads 16 --barcode_start 0 --barcode_end 16 --umi_start 16 --umi_end 26
Inspecting and pre-processing inputs
Unzipping (temporary)
Splitting reads by barcodes
Building kmer index
10000 reads indexed. Running pearsonr is 0.000000
20000 reads indexed. Running pearsonr is 0.999505
30000 reads indexed. Running pearsonr is 0.999596
40000 reads indexed. Running pearsonr is 0.999879
50000 reads indexed. Running pearsonr is 0.999887
60000 reads indexed. Running pearsonr is 0.999946
70000 reads indexed. Running pearsonr is 0.999947
80000 reads indexed. Running pearsonr is 0.999971
90000 reads indexed. Running pearsonr is 0.999973
100000 reads indexed. Running pearsonr is 0.999982
67862 unique kmers indexed
Finding cyclic paths in the barcode de Briujn graph
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/utils/IO_utils.py", line 114, in read_fastq_random
pos = offsets.pop()
IndexError: pop from empty list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/utils/IO_utils.py", line 116, in read_fastq_random
raise StopIteration
StopIteration
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/pythonenv/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/pythonenv/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/Split_reads.py", line 297, in find_path_from_kmer
subgraph = build_subgraph(offsets, barcodes_unzipped)
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/Split_reads.py", line 329, in build_subgraph
barcode_data, _ = next(barcodes_iter)
RuntimeError: generator raised StopIteration
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/nethome/schrammca/bin/sircel", line 11, in <module>
load_entry_point('sircel==0.1.2', 'console_scripts', 'sircel')()
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/__main__.py", line 5, in main
output_files = run_all(args)
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/Sircel_master.py", line 85, in run_all
output_files, elapsed_time = Split_reads.run_all(args)
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/Split_reads.py", line 70, in run_all
output_dir))
File "/nethome/schrammca/.local/lib/python3.7/site-packages/sircel-0.1.2-py3.7.egg/sircel/Split_reads.py", line 286, in find_paths
repeat(barcode_length)))
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/pythonenv/lib/python3.7/multiprocessing/pool.py", line 290, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/sysapps/cluster/software/Anaconda3/5.3.0/envs/pythonenv/lib/python3.7/multiprocessing/pool.py", line 683, in get
raise self._value
RuntimeError: generator raised StopIteration
fitzgeraldZoeky commented
same problem... How to handle?
hallettmiket commented
Is anyone still working on this? After struggling through the problems with redis, I'm stuck at the same place here running the example.
chelauk commented
Got the same problem... Any clues?
francops1722 commented
I still get the error "RuntimeError: generator raised StopIteration", even after replacing while statements for itertools takewhile. Does anyone solved it?