search

zhangrengang / SubPhaser

Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.
https://doi.org/10.1111/nph.18173
GNU General Public License v3.0
53 stars 12 forks source link

IndexError: cannot do a non-empty take from an empty axes. #15

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

Hi, I got the following error with my dataset when I was trying to pre-assign all 40 chromosomes to 2 subgenomes. Apparently, SubPhaser re-assigned all chromosomes to SG1. With a smaller number of assignments, SubPhaser successfully completed in the same genome with a smaller number of homologous chromosome assignments, as you suggested in #7.

22-12-23 03:08:56 [INFO] Version: 1.2.5
22-12-23 03:08:56 [INFO] Arguments: {'genomes': ['/gfe_data/species_genome/Nepenthes_gracilis_male_HiC.fa.gz'], 'sg_cfgs': ['/gfe_data/species_subphaser_cfg/Nepenthes_gracilis_subphaser_cfg.txt'], 'labels': None, 'no_label': True, 'target': None, 'sg_assigned': None, 'sep': '|', 'custom_features': None, 'prefix': 'Nepenthes_gracilis.', 'outdir': 'Nepenthes_gracilis.subphaser', 'tmpdir': 'Nepenthes_gracilis.tmp', 'k': 15, 'min_fold': 2, 'min_freq': 200, 'baseline': 1, 'lower_count': 3, 'min_prop': None, 'max_freq': 1000000000.0, 'max_prop': None, 'low_mem': None, 'by_count': False, 're_filter': False, 'nsg': None, 'replicates': 1000, 'jackknife': 50, 'max_pval': 0.05, 'test_method': 'ttest_ind', 'figfmt': 'pdf', 'heatmap_colors': ('green', 'black', 'red'), 'heatmap_options': "Rowv=T,Colv=T,scale='col',dendrogram='row',labCol=F,trace='none',key=T,key.title=NA,density.info='density',main=NA,xlab='Differential kmers',margins=c(2.5,12)", 'just_core': False, 'disable_ltr': False, 'ltr_detectors': ['ltr_harvest'], 'ltr_finder_options': '-w 2 -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.8', 'ltr_harvest_options': '-seqids yes -similar 80 -vic 10 -seed 20 -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6', 'tesorter_options': '-db rexdb -dp2', 'all_ltr': False, 'intact_ltr': False, 'exclude_exchanges': False, 'non_specific': False, 'mu': 1.3e-08, 'disable_ltrtree': False, 'subsample': 1000, 'ltr_domains': ['INT', 'RT', 'RH'], 'trimal_options': '-automated1', 'tree_method': 'FastTree', 'tree_options': '', 'ggtree_options': "branch.length='none', layout='circular'", 'disable_circos': False, 'window_size': 1000000, 'disable_blocks': False, 'aligner': 'minimap2', 'aligner_options': '-x asm20 -n 10', 'min_block': 100000, 'alt_cfgs': None, 'chr_ordered': None, 'ncpu': 4, 'max_memory': '32', 'cleanup': False, 'overwrite': False}
22-12-23 03:08:56 [INFO] Target chromosomes: ['scaffold2', 'scaffold1', 'scaffold8', 'scaffold11', 'scaffold12', 'scaffold3', 'scaffold17', 'scaffold23', 'scaffold24', 'scaffold40', 'scaffold4', 'scaffold22', 'scaffold30', 'scaffold33', 'scaffold39', 'scaffold5', 'scaffold13', 'scaffold16', 'scaffold18', 'scaffold26', 'scaffold6', 'scaffold15', 'scaffold20', 'scaffold32', 'scaffold38', 'scaffold7', 'scaffold14', 'scaffold27', 'scaffold28', 'scaffold29', 'scaffold9', 'scaffold19', 'scaffold21', 'scaffold34', 'scaffold36', 'scaffold10', 'scaffold25', 'scaffold31', 'scaffold35', 'scaffold37']
22-12-23 03:08:56 [INFO] Splitting genomes by chromosome into `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.`
22-12-23 03:09:08 [INFO] New check point file: `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.split.ok`
22-12-23 03:09:08 [INFO] Chromosomes: ['scaffold2', 'scaffold1', 'scaffold8', 'scaffold11', 'scaffold12', 'scaffold3', 'scaffold17', 'scaffold23', 'scaffold24', 'scaffold40', 'scaffold4', 'scaffold22', 'scaffold30', 'scaffold33', 'scaffold39', 'scaffold5', 'scaffold13', 'scaffold16', 'scaffold18', 'scaffold26', 'scaffold6', 'scaffold15', 'scaffold20', 'scaffold32', 'scaffold38', 'scaffold7', 'scaffold14', 'scaffold27', 'scaffold28', 'scaffold29', 'scaffold9', 'scaffold19', 'scaffold21', 'scaffold34', 'scaffold36', 'scaffold10', 'scaffold25', 'scaffold31', 'scaffold35', 'scaffold37']
22-12-23 03:09:08 [INFO] Chromosome Number: 40
22-12-23 03:09:08 [INFO] CONFIG: [[['scaffold2'], ['scaffold1', 'scaffold8', 'scaffold11', 'scaffold12']], [['scaffold3'], ['scaffold17', 'scaffold23', 'scaffold24', 'scaffold40']], [['scaffold4'], ['scaffold22', 'scaffold30', 'scaffold33', 'scaffold39']], [['scaffold5'], ['scaffold13', 'scaffold16', 'scaffold18', 'scaffold26']], [['scaffold6'], ['scaffold15', 'scaffold20', 'scaffold32', 'scaffold38']], [['scaffold7'], ['scaffold14', 'scaffold27', 'scaffold28', 'scaffold29']], [['scaffold9'], ['scaffold19', 'scaffold21', 'scaffold34', 'scaffold36']], [['scaffold10'], ['scaffold25', 'scaffold31', 'scaffold35', 'scaffold37']]]
22-12-23 03:09:08 [INFO] Genome size: 746,713,351 bp
22-12-23 03:09:08 [INFO] ###Step: Kmer Count
22-12-23 03:09:08 [INFO] Counting kmer by jellyfish
22-12-23 03:09:08 [INFO] Start Pool with 4 process(es)
.
.
.
22-12-23 03:13:26 [INFO] Bootstrap: mean Adjusted Rand-Index: 0.9428; mean V-measure score: 0.9295
22-12-23 03:13:26 [INFO] Subgenome assignments: OrderedDict([('scaffold2', 'SG1'), ('scaffold1', 'SG1'), ('scaffold8', 'SG1'), ('scaffold11', 'SG1'), ('scaffold12', 'SG1'), ('scaffold3', 'SG1'), ('scaffold17', 'SG1'), ('scaffold23', 'SG1'), ('scaffold24', 'SG1'), ('scaffold40', 'SG1'), ('scaffold4', 'SG1'), ('scaffold22', 'SG1'), ('scaffold30', 'SG2'), ('scaffold33', 'SG2'), ('scaffold39', 'SG1'), ('scaffold5', 'SG1'), ('scaffold13', 'SG1'), ('scaffold16', 'SG1'), ('scaffold18', 'SG1'), ('scaffold26', 'SG1'), ('scaffold6', 'SG1'), ('scaffold15', 'SG1'), ('scaffold20', 'SG1'), ('scaffold32', 'SG1'), ('scaffold38', 'SG1'), ('scaffold7', 'SG1'), ('scaffold14', 'SG1'), ('scaffold27', 'SG1'), ('scaffold28', 'SG1'), ('scaffold29', 'SG1'), ('scaffold9', 'SG1'), ('scaffold19', 'SG1'), ('scaffold21', 'SG1'), ('scaffold34', 'SG1'), ('scaffold36', 'SG1'), ('scaffold10', 'SG1'), ('scaffold25', 'SG1'), ('scaffold31', 'SG1'), ('scaffold35', 'SG1'), ('scaffold37', 'SG1')])
22-12-23 03:13:26 [INFO] Outputing `chromosome` - `subgenome` assignments to `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.chrom-subgenome.tsv`
22-12-23 03:13:26 [INFO] Outputing significant differiential `kmer` - `subgenome` maps to `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.sig.kmer-subgenome.tsv`
22-12-23 03:13:26 [INFO] Start Pool with 4 process(es)
22-12-23 03:13:26 [INFO] 9 significant subgenome-specific kmers
22-12-23 03:13:26 [INFO]    9 SG2-specific kmers
22-12-23 03:13:27 [INFO] run CMD: `Rscript /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.kmer.mat.R`
22-12-23 03:13:27 [INFO] Outputing PCA plot to `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.kmer_pca.pdf`
22-12-23 03:13:28 [INFO] Outputing `coordinate` - `subgenome` maps to `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.subgenome.bin.count`
22-12-23 03:13:28 [INFO] Start Pool with 4 process(es)
.
.
.
22-12-23 03:14:47 [INFO] Processed 94 sequences
22-12-23 03:14:47 [INFO] 92 (97.87%) sequences contain subgenome-specific kmers
22-12-23 03:14:47 [INFO] 100.00% of 9 subgenome-specific kmers are mapped
22-12-23 03:14:47 [INFO] New check point file: `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.Nepenthes_gracilis.k15_q200_f2.subgenome.bin.count.ok`
22-12-23 03:14:47 [INFO] Enriching subgenome by chromosome window (size: 1000000)
22-12-23 03:14:47 [INFO] Start Pool with 4 process(es)
.
.
.
22-12-23 03:21:31 [INFO] finished with 0 commands uncompleted
22-12-23 03:21:32 [INFO] New check point file: `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.LTR.scn.ok`
22-12-23 03:21:32 [INFO] 23051 LTRs identified
22-12-23 03:21:32 [INFO] Extracting inner sequences of LTRs to classify by `TEsorter`
22-12-23 03:21:32 [INFO] run CMD: `TEsorter /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.LTR.inner.fa -db rexdb -dp2 -p 4 -pre /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.LTR.inner.fa -tmp /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.LTR &> /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.LTR.inner.fa.tesort.log`
22-12-23 03:39:13 [INFO] New check point file: `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.LTR.tesort.ok`
22-12-23 03:39:13 [INFO] By TEsorter, 13396 (58.1%) are classified as LTRs, of which 5538 (41.3%) are intact with complete protein domains
22-12-23 03:39:13 [INFO] After filtering, 13202 / 23051 (57.3%) LTRs retained
22-12-23 03:39:13 [INFO] Outputing `coordinate` - `LTR` maps to `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.ltr.bin.count`
22-12-23 03:39:13 [INFO] Start Pool with 4 process(es)
22-12-23 03:39:23 [INFO] Processed 13202 sequences
22-12-23 03:39:23 [INFO] 204 (1.55%) sequences contain subgenome-specific kmers
22-12-23 03:39:23 [INFO] 44.44% of 9 subgenome-specific kmers are mapped
22-12-23 03:39:25 [INFO] New check point file: `/gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.tmp/Nepenthes_gracilis.Nepenthes_gracilis.k15_q200_f2.ltr.bin.count.ok`
22-12-23 03:39:25 [INFO] Enriching subgenome-specific LTR-RTs
22-12-23 03:39:25 [INFO] Start Pool with 4 process(es)
/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/Stats.py:157: RuntimeWarning: invalid value encountered in divide
  ratios = np.array(row) / np.array(total)
/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/Stats.py:157: RuntimeWarning: invalid value encountered in divide
  ratios = np.array(row) / np.array(total)
/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/Stats.py:157: RuntimeWarning: invalid value encountered in divide
  ratios = np.array(row) / np.array(total)
/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/Stats.py:157: RuntimeWarning: invalid value encountered in divide
  ratios = np.array(row) / np.array(total)
22-12-23 03:39:25 [INFO] Output: /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.ltr.enrich
22-12-23 03:39:25 [INFO] 0 significant subgenome-specific LTR-RTs
22-12-23 03:39:28 [INFO] Summary of overall LTR insertion age (million years):
/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3432: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/core/_methods.py:190: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/opt/conda/envs/biotools/bin/subphaser", line 33, in <module>
    sys.exit(load_entry_point('subphaser==1.2.5', 'console_scripts', 'subphaser')())
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/__main__.py", line 784, in main
    pipeline.run()
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/__main__.py", line 518, in run
    ltr_bedlines, enrich_ltr_bedlines = self.step_ltr(d_kmers) if not self.disable_ltr else ([],[])
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/__main__.py", line 602, in step_ltr
    enrich_ltrs = LTR.plot_insert_age(ltrs, d_enriched, prefix, 
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/LTR.py", line 515, in plot_insert_age
    d_info = summary_ltr_time(d_data, fout)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/LTR.py", line 601, in summary_ltr_time
    np.median(xages), abs(np.percentile(xages, 2.5)), np.percentile(xages, 97.5)))
  File "<__array_function__ internals>", line 180, in percentile
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4166, in percentile
    return _quantile_unchecked(
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4424, in _quantile_unchecked
    r, k = _ureduce(a,
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 3725, in _ureduce
    r = func(a, **kwargs)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4593, in _quantile_ureduce_func
    result = _quantile(arr,
  File "/opt/conda/envs/biotools/lib/python3.9/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 "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 190, in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
  File "/opt/conda/envs/biotools/lib/python3.9/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.
zhangrengang commented 1 year ago

Are your final assignments (>With a smaller number of assignments, SubPhaser successfully completed in the same genome with a smaller number of homologous chromosome assignments) correct?

kfuku52 commented 1 year ago

Sorry, my writing was a little strange because I wrote the above comment just before I went to bed last night. SubPhaser was completed, but the final assignments didn't seem to be correct (given our data on the synteny and subgenome dominance of this decaploid plant). On the other hand, we have no evidence that this species is an allopolyploid, so the fact that SubPhaser does not phase well may mean autopolyploidy or that the ancestral species were very similar to each other.

zhangrengang commented 1 year ago

For decaploid, it is hard to phase as there may be 2-5 subgenomes in fact and it maybe very complicated in nature. I have successfully phased upon to octoploid with 4 subgenomes. As there are no more priors, you may have to make more tries. However, your config file may be set like:

scaffold2 scaffold1 scaffold8 scaffold11 scaffold12  
scaffold3 scaffold17 scaffold23 scaffold24 scaffold40 
.....

And -nsg can be set to control the number of subgenomes, and -baseline can be set to compare with which chromsome to identify differential kmers. For example, for a decreasingly sorted kmer in (chr0 chr1 chr2 ... chr4) , -baseline 1 will compare between chr0 and chr1, -baseline 2 will compare between chr0 and chr2, and -baseline -1 will compare between chr0 and chr4, and so on.

kfuku52 commented 1 year ago

Thank you, I started trying it. I thought the above error occurred because SubPhaser assigned all scaffolds to SG1, but I got the same error with -nsg 2 (to phase 1 dominant subgenome versus 4 recessive subgenomes) with which some scaffolds were assigned to SG2.

22-12-23 20:20:37 [INFO] Subgenome assignments: OrderedDict([('scaffold2', 'SG1'), ('scaffold1', 'SG1'), ('scaffold8', 'SG1'), ('scaffold11', 'SG1'), ('scaffold12', 'SG1'), ('scaffold3', 'SG1'), ('scaffold17', 'SG1'), ('scaffold23', 'SG1'), ('scaffold24', 'SG1'), ('scaffold40', 'SG1'), ('scaffold4', 'SG1'), ('scaffold22', 'SG1'), ('scaffold30', 'SG2'), ('scaffold33', 'SG2'), ('scaffold39', 'SG1'), ('scaffold5', 'SG1'), ('scaffold13', 'SG1'), ('scaffold16', 'SG1'), ('scaffold18', 'SG1'), ('scaffold26', 'SG1'), ('scaffold6', 'SG1'), ('scaffold15', 'SG1'), ('scaffold20', 'SG1'), ('scaffold32', 'SG1'), ('scaffold38', 'SG1'), ('scaffold7', 'SG1'), ('scaffold14', 'SG1'), ('scaffold27', 'SG1'), ('scaffold28', 'SG1'), ('scaffold29', 'SG1'), ('scaffold9', 'SG1'), ('scaffold19', 'SG1'), ('scaffold21', 'SG1'), ('scaffold34', 'SG1'), ('scaffold36', 'SG1'), ('scaffold10', 'SG1'), ('scaffold25', 'SG1'), ('scaffold31', 'SG1'), ('scaffold35', 'SG1'), ('scaffold37', 'SG1')])
.
.
.
22-12-23 20:43:39 [INFO] Output: /gfe_data/tmp/14_Nepenthes_gracilis/Nepenthes_gracilis.subphaser/Nepenthes_gracilis.k15_q200_f2.ltr.enrich
22-12-23 20:43:39 [INFO] 0 significant subgenome-specific LTR-RTs
22-12-23 20:43:39 [INFO] Summary of overall LTR insertion age (million years):
/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3432: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/core/_methods.py:190: RuntimeWarning: invalid value encountered in double_scalars
  ret = ret.dtype.type(ret / rcount)
Traceback (most recent call last):
  File "/opt/conda/envs/biotools/bin/subphaser", line 33, in <module>
    sys.exit(load_entry_point('subphaser==1.2.5', 'console_scripts', 'subphaser')())
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/__main__.py", line 784, in main
    pipeline.run()
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/__main__.py", line 518, in run
    ltr_bedlines, enrich_ltr_bedlines = self.step_ltr(d_kmers) if not self.disable_ltr else ([],[])
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/__main__.py", line 602, in step_ltr
    enrich_ltrs = LTR.plot_insert_age(ltrs, d_enriched, prefix, 
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/LTR.py", line 515, in plot_insert_age
    d_info = summary_ltr_time(d_data, fout)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/subphaser-1.2.5-py3.9.egg/subphaser/LTR.py", line 601, in summary_ltr_time
    np.median(xages), abs(np.percentile(xages, 2.5)), np.percentile(xages, 97.5)))
  File "<__array_function__ internals>", line 180, in percentile
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4166, in percentile
    return _quantile_unchecked(
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4424, in _quantile_unchecked
    r, k = _ureduce(a,
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 3725, in _ureduce
    r = func(a, **kwargs)
  File "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/lib/function_base.py", line 4593, in _quantile_ureduce_func
    result = _quantile(arr,
  File "/opt/conda/envs/biotools/lib/python3.9/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 "/opt/conda/envs/biotools/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 190, in take
    return _wrapfunc(a, 'take', indices, axis=axis, out=out, mode=mode)
  File "/opt/conda/envs/biotools/lib/python3.9/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.
zhangrengang commented 1 year ago

The error is because there are none subgenome-specific LTR-RTs identified (the phasing step maybe failed). -disable_ltr can skip this step but is somewhat not meaningful. You may assume -nsg 5.

kfuku52 commented 1 year ago

Thank you. I tried -nsg 5, but the phasing wasn't successful.

image
zhangrengang commented 1 year ago

Yes, too few differential kmers.

kfuku52 commented 1 year ago

Should I close this issue if the IndexError is intended?

zhangrengang commented 1 year ago

OK. I will change it to "warning".

kfuku52 commented 1 year ago

I am closing this issue as the bug seems to have been fixed. Thank you!