IndexError: pop from empty list in read_fastq_random

[scharch]

$ 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

[cgirardot]

I have the same error, could @axtambe comment on what is wrong please ?

[fitzgeraldZoeky]

same problem... How to handle?

[hallettmiket]

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]

Got the same problem... Any clues?

[francops1722]

I still get the error "RuntimeError: generator raised StopIteration", even after replacing while statements for itertools takewhile. Does anyone solved it?