Warnings and Error when running CallM genomes

[jfy133]

Hello,

I'm trying to generate a reference database for GT-Pro using CallM.

When I try running on the reference genomes included in the attachment, and run teh following command, I get the error below

Command:

software/CallM/CallM genomes --fna-dir data/genomes/arachnia_propionica_allinone --rep-fna data/genomes/arachnia_propionica/data/GCF_001592325.1/GCF_001592325.1_ASM159232v1_genomic.fna --out-dir data/callm-databases/arachnia_propionica

Error:

<...>
Reading reference genome
   count contigs: 1
   count sites: 3449360
Initializing alignments
   count genomes: 9
Reading alignment blocks
Reading SNPs
Writing fasta
   path: data/callm-databases/arachnia_propionica/temp/mummer4/arachnia_propionica_allinone/msa.fa

Done!
Time (s): 10.25
Running mummer4; done!
Elapsed time: 50.30968403816223
Fetching file-type-specific parser; start
9
[[b'-' b'-' b'-' ..., b'-' b'-' b'-']
 [b'C' b'C' b'G' ..., b'G' b'C' b'C']
 [b'C' b'C' b'G' ..., b'G' b'C' b'C']
 ..., 
 [b'C' b'C' b'G' ..., b'G' b'C' b'C']
 [b'C' b'C' b'G' ..., b'G' b'C' b'C']
 [b'-' b'-' b'-' ..., b'-' b'-' b'-']]
False
[0 0 0 ..., 0 0 0]
[[0 0 0 ..., 0 0 0]
 [0 0 0 ..., 0 0 0]
 [0 0 7 ..., 7 0 0]
 [7 7 0 ..., 0 7 7]
 [0 0 0 ..., 0 0 0]
 [2 2 2 ..., 2 2 2]]
(6, 3449360)
total length of alignments: 3449360
Fetching file-type-specific parser; done
Elapsed time: 4.082759618759155
Identifying core-snps; start
max sites: inf
min prevalence: 1.0
min MAF: 0.01
warning: cannot splice less than 2 alignments
total number of sites: 3449360
min. prevalence: 1.0
min. alt. frequency: 0.01
masked by prev_mask: 357341
masked by snp_mask: 197456
masked by wildcard_mask: 3449360
/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/snps_io/align_assembly.py:228: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  freq_row[snp_freqs[:,i] == None] = -1
Traceback (most recent call last):
  File "/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/bin/CallM.py", line 1239, in <module>
    main()
  File "/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/bin/CallM.py", line 1230, in main
    call_snps_main(args)
  File "/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/bin/CallM.py", line 1132, in call_snps_main
    align_assembs = align_assembly.call_snps(site_assembly, args['max_sites'], args['min_prev'], args['snp_freq'])
  File "/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/snps_io/align_assembly.py", line 346, in call_snps
    aa.id_core_genome(min_prev, snp_freq)
  File "/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/snps_io/align_assembly.py", line 186, in id_core_genome
    self.snps = self.id_snps(calling_mask)
  File "/home/jfellows/Documents/git/jfy133/strainfacts-experiment/software/CallM/snps_io/align_assembly.py", line 228, in id_snps
    freq_row[snp_freqs[:,i] == None] = -1
IndexError: in the future, 0-d boolean arrays will be interpreted as a valid boolean index

data.tar.gz