gtonkinhill
IndexError: cannot do a non-empty take from an empty axes.
Hi! I had this issue creating a core alignment using GFFs from prokka and I have no clue what could be happening. I didn't find any related issue here.
command:
panaroo \
-a core --clean-mode strict \
-t 15 \
-o results \
-i GCF_003710915.gff GCF_002951935.gff GCF_002007765.gff GCF_002951915.gff GCF_003963515.gff GCF_004000985.gff GCF_001465255.gff GCF_001187725.gff GCF_003710935.gff GCF_004117055.gff GCF_013185195.gff GCF_001420695.gff GCF_002043025.gff GCF_016406105.gff GCF_003710965.gff GCF_022701015.gff GCF_016937515.gff GCF_020923435.gff GCF_002082155.gff GCF_023523925.gff GCF_961514395.gff GCF_036700025.gff GCF_046622605.gff GCF_020923495.gff GCF_041640235.gff Idee_0013.gff GCF_042431195.gff GCF_023746555.gff GCF_003710985.gff GCF_042432825.gff GCF_017873765.gff
Iteration: 30
Iteration: 31
Iteration: 32
Iteration: 33
Iteration: 34
Iteration: 35
Iteration: 36
Iteration: 37
trimming contig ends...
refinding genes...
Number of searches to perform: 39949
Searching...
translating hits...
removing by consensus...
Updating output...
Number of refound genes: 146
collapse gene families with refound genes...
Processing depth: 1
Iteration: 1
Iteration: 2
Processing depth: 2
Iteration: 1
Processing depth: 3
Iteration: 1
Iteration: 2
Iteration: 3
Iteration: 4
Iteration: 5
Iteration: 6
Iteration: 7
Iteration: 8
Iteration: 9
Iteration: 10
Iteration: 11
Iteration: 12
Iteration: 13
Iteration: 14
Iteration: 15
Iteration: 16
Iteration: 17
Iteration: 18
Iteration: 19
Iteration: 20
Iteration: 21
Iteration: 22
Iteration: 23
Iteration: 24
Iteration: 25
writing output...
generating core genome MSAs...
Command error:
Iteration: 22
0%| | 0/1 [00:00<?, ?it/s]
100%|██████████| 1/1 [00:00<00:00, 935.60it/s]
Iteration: 23
0%| | 0/3 [00:00<?, ?it/s]
100%|██████████| 3/3 [00:00<00:00, 2890.63it/s]
Iteration: 24
0%| | 0/3 [00:00<?, ?it/s]
100%|██████████| 3/3 [00:00<00:00, 1719.21it/s]
Iteration: 25
0%| | 0/2 [00:00<?, ?it/s]
100%|██████████| 2/2 [00:00<00:00, 1275.64it/s]
writing output...
generating core genome MSAs...
0it [00:00, ?it/s]
0it [00:00, ?it/s]
0it [00:00, ?it/s]
0it [00:00, ?it/s]
Traceback (most recent call last):
File "/usr/local/bin/panaroo", line 10, in <module>
sys.exit(main())
File "/usr/local/lib/python3.10/site-packages/panaroo/__main__.py", line 510, in main
generate_core_genome_alignment(G, temp_dir, args.output_dir,
File "/usr/local/lib/python3.10/site-packages/panaroo/generate_output.py", line 526, in generate_core_genome_alignment
concatenate_core_genome_alignments(core_gene_names, output_dir, hc_threshold)
File "/usr/local/lib/python3.10/site-packages/panaroo/generate_output.py", line 399, in concatenate_core_genome_alignments
q = np.quantile(allh, [0.25,0.75])
File "<__array_function__ internals>", line 180, in quantile
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4412, in quantile
return _quantile_unchecked(
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4424, in _quantile_unchecked
r, k = _ureduce(a,
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 3725, in _ureduce
r = func(a, **kwargs)
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4593, in _quantile_ureduce_func
result = _quantile(arr,
File "/usr/local/lib/python3.10/site-packages/numpy/lib/function_base.py", line 4699, in _quantile
take(arr, indices=-1, axis=DATA_AXIS)
File "<__array_function__ internals>", line 180, in take
File "/usr/local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 190, in take
return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
File "/usr/local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 57, in _wrapfunc
return bound(*args, **kwds)
IndexError: cannot do a non-empty take from an empty axes.
Hi,
I am afraid I have not run into this issue before. It would help us a lot to diagnose the problem if you are able to confirm the Panaroo version number and attach a small reproducible example.
I didn't realize I was using an old version (1.3.2). I'll try with the current one. However, I think this issue was likely related to the high divergence between the genomes and the absence of core genes. I was analyzing species instead of strains and I couldn't get any core alignment using Roary either. Unfortunately, I can't make my example available, but if you use public genomes of different bacterial species (30 was the number I used in my experiment) you will probably get the same error. I used Prokka for the annotation.
Hi,
Thanks for getting back to us. Panaroo was not really designed to cluster different species so you would need to adjust the default clustering thresholds quite a bit.