IndexError: list index out of range

[yi1873]

Error in ".../anaconda3/envs/SuperPang/lib/python3.8/site-packages/SuperPang/lib/Assembler.py", line 829, in reconstruct_sequence
if k[:-1] == kmers[-1][1:]:
IndexError: list index out of range

[fpusan]

Hi!
Can you share the input genomes and the command you used so I can try to reproduce the error?

[yi1873]

Species: Mycobacterium tuberculosis
Taxid: 1773
Genome：316 complete genomes in GenBank (https://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt)
Command: SuperPang.py --fasta genome/*.fa --output-dir 1773/pangenome --force-overwrite -t 20 --assume-complete -b 0.95 -i 0.95 -k 301

[yi1873]

You can also test E.coli with all complete genomes in GenBank, get the same error.

[fpusan]

Can reproduce with the Mycobacterium tuberculosis dataset

[yi1873]

Full errors:

multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File ".../anaconda3/envs/SuperPang/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File ".../anaconda3/envs/SuperPang/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File ".../anaconda3/envs/SuperPang/lib/python3.8/site-packages/SuperPang/lib/Assembler.py", line 846, in reconstruct_sequence
if k[:-1] == kmers[-1][1:]:
IndexError: list index out of range
"""

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

Traceback (most recent call last):
File ".../anaconda3/envs/SuperPang/bin/SuperPang.py", line 291, in
main(parse_args())
File ".../anaconda3/envs/SuperPang/bin/SuperPang.py", line 144, in main
contigs = Assembler(input_minimap2, args.ksize, args.threads).run(args.minlen, args.mincov, args.bubble_identity_threshold, args.genome_assignment_threshold, args.threads)
File ".../anaconda3/envs/SuperPang/lib/python3.8/site-packages/SuperPang/lib/Assembler.py", line 259, in run
NBP2seq = dict(zip(NBPs, self.multimap(self.reconstruct_sequence, threads, NBPs, self.vertex2hash, self.compressor)))
File ".../anaconda3/envs/SuperPang/lib/python3.8/site-packages/SuperPang/lib/Assembler.py", line 55, in multimap
res = pool.map(fun, range(len(iterable)))
File ".../anaconda3/envs/SuperPang/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File ".../anaconda3/envs/SuperPang/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
IndexError: list index out of range

[fpusan]

Thanks! I'm running it right now in my computers, adding some traces to see what could be happening.
Also, wild guess here, but does this also happen if you call it like
SuperPang.py --fasta genome/*.fa --output-dir 1773/pangenome --force-overwrite -t 20 --assume-complete -b 0.95 -i 0.95 -k 301 -n 20 ?

[fpusan]

Nevermind, I now think that the problem is due to the presence of ambiguous bases in the input fasta files
(e.g. "M" to represent either "A" or "C"). This happens for these genomes and would definitely break my code in a few places. Will think of a fix

[fpusan]

Hi again! This issue is hopefully fixed in the new version 0.9.3