tyjo
commented
3 years ago Hi Barb,
Thanks for reaching out! It looks like CoPTR is using the complete reference genome estimator instead of the contig estimator on your MAGs.
You can check if CoPTR is correctly identifying MAGs on the "extract" step with the --check-regex flag. On the example data:
python coptr.py extract example-data/bam example-data/coverage-maps --check-regexThis should output an id for each reference genome. If you see an id for each contig, something has gone wrong. Would you run the above, and let me know the result?
If CoPTR is outputting an id for each contig, then something has gone wrong in the indexing or mapping step. A few possibilities:
- Did you index your MAGs and perform read mapping with CoPTR's wrapper around bowtie2? CoPTR adds information to keep track of complete references vs assemblies.
- Is each MAG in its own fasta file?
Tyler
BJCampbelllab
Hi- I am running about 8 high quality MAGs through CoPTR with about 20 metagenomes. I've gotten everything to work until the middle of the last step. The error is below. The command did generate a coverage-maps-genome folder within my maps folder, and there are PKL files there that look to encompass all possible contigs within each MAGs. I tried lowering the minimum reads and coverage. Any help would be greatly appreciated! Thanks, Barb
[INFO] (Mar 04, 2021 08:53:25) CoPTR: done grouping by reference genome [INFO] (Mar 04, 2021 08:53:25) CoPTR: the --restart flag can be used to start from here [INFO] (Mar 04, 2021 08:53:25) CoPTRRef: checking reference genomes multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/bcampbell/anaconda3/envs/coptr/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/bcampbell/anaconda3/envs/coptr/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/bcampbell/coptr/src/coptr_ref.py", line 813, in _parallel_helper return (ref_genome, self.estimate_ptrs(coverage_maps)) File "/home/bcampbell/coptr/src/coptr_ref.py", line 763, in estimate_ptrs read_positions, ref_genome_len, qc_result = rf.filter_reads(cm.read_positions, cm.length) File "/home/bcampbell/coptr/src/coptr_ref.py", line 108, in filter_reads filtered_read_positions, filtered_genome_length = self.filter_reads_phase1(read_positions, genome_length, bin_size) File "/home/bcampbell/coptr/src/coptr_ref.py", line 326, in filter_reads_phase1 binned_reads = self.bin_reads(read_positions, genome_length, bin_size) File "/home/bcampbell/coptr/src/coptr_ref.py", line 445, in bin_reads nbins = int(math.ceil(genome_length / bin_size)) ZeroDivisionError: float division by zero """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/bcampbell/coptr/coptr.py", line 449, in
ProgramOptions()
File "/home/bcampbell/coptr/coptr.py", line 65, in init
getattr(self, args.command)()
File "/home/bcampbell/coptr/coptr.py", line 287, in estimate
threads=args.threads, plot_folder=args.plot
File "/home/bcampbell/coptr/src/coptr_ref.py", line 935, in estimate_ptrs_coptr_ref
flat_results = pool.map(coptr_ref._parallel_helper, flat_coverage_maps)
File "/home/bcampbell/anaconda3/envs/coptr/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/bcampbell/anaconda3/envs/coptr/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
ZeroDivisionError: float division by zero