According to the veritymap.log the run completed successfully:
02:09:13 59.8Gb INFO: Finished exporting long (>= 5000 bp) regions without solid k-mers to "/public/groups/vg/jeizenga/centromere/reads/PAN010/verity_map_output_alpha/veritymap/no_solid_kmers.bed"
02:09:13 59.8Gb INFO: Computing chains and sam records...
65:45:26 59.8Gb INFO: Finished outputting chains to "/public/groups/vg/jeizenga/centromere/reads/PAN010/verity_map_output_alpha/veritymap/chains.tsv" and sam records to "/public/groups/vg/jeizenga/centromere/reads/PAN010/verity_map_output_alpha/veritymap/alignments.sam"
65:46:31 59.8Gb INFO: Thank you for using VerityMap!
Traceback (most recent call last):
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/main.py", line 61, in <module>
main()
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/venv/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/venv/lib/python3.10/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/venv/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/venv/lib/python3.10/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/main.py", line 54, in main
do(assemblies, reads_fname, datatype, out_dir, threads, no_reuse, is_careful)
File "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/../veritymap/py_src/mapper.py", line 154, in do
make_plotly_html(assemblies, all_data, out_dir)
ile "/public/groups/vg/jeizenga/GitHub/VerityMap/veritymap/../veritymap/py_src/reporting.py", line 36, in make_plotly_html
data['coverage'] = coverage[ref_name]
KeyError: 'haplotype1-0000013'
A feature of this run that might be relevant is that I tried to address the previously reported speed issues by enriching for reads containing alpha satellite sequences. It's conceivable that some contigs had no alpha satellite-containing reads map to them, in which case perhaps they weren't entered into this dictionary?
For what it's worth, this is a good example of why I suggested in my previous issue that the analysis module be accessible without re-running the mapping code, as the mapping took several days to complete.
I ran with this command:
According to the
veritymap.logthe run completed successfully:However, after the logger gave that output, Python threw an error apparently linked to this line in the plotting function: https://github.com/ablab/VerityMap/blob/d24aa797be9c977dbcb9164ecfe18b3af6e4a026/veritymap/py_src/reporting.py#L36
A feature of this run that might be relevant is that I tried to address the previously reported speed issues by enriching for reads containing alpha satellite sequences. It's conceivable that some contigs had no alpha satellite-containing reads map to them, in which case perhaps they weren't entered into this dictionary?
For what it's worth, this is a good example of why I suggested in my previous issue that the analysis module be accessible without re-running the mapping code, as the mapping took several days to complete.