Not sure what this is, but I saw a clue that this might happen due to bad input. It coincided with an error in the align-families.py process that was feeding it. I think it omitted some families (actually, individual read alignments), which could cause this.
While processing duplex AAAAAACATGCACAGGCAAGTTAT:
Traceback (most recent call last):
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/make-consensi.py", line 341, in process_duplex
dcss = make_dcss(sscss)
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/make-consensi.py", line 415, in make_dcss
assert len(dcss) == 0 or len(dcss) == 2, len(dcss)
AssertionError: 1
Traceback (most recent call last):
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/make-consensi.py", line 491, in <module>
sys.exit(main(sys.argv))
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/make-consensi.py", line 236, in main
pool.compute(duplex, barcode)
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/parallel_tools.py", line 90, in compute
result = FakeResult(self.function(*all_args, **all_kwargs))
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/make-consensi.py", line 341, in process_duplex
dcss = make_dcss(sscss)
File "/nfs/thumper.galaxyproject.org/home/nick/code/duplex/make-consensi.py", line 415, in make_dcss
assert len(dcss) == 0 or len(dcss) == 2, len(dcss)
AssertionError: 1
Not sure what this is, but I saw a clue that this might happen due to bad input. It coincided with an error in the
align-families.pyprocess that was feeding it. I think it omitted some families (actually, individual read alignments), which could cause this.