Time (s): 604.05
Running mummer4; done!
Elapsed time: 3241.187788248062
Fetching file-type-specific parser; start
total length of alignments: 4499696
Fetching file-type-specific parser; done
Elapsed time: 49.78715515136719
Identifying core-snps; start
max sites: inf
min prevalence: 0.9
min MAF: 0.01
total number of sites: 4499696
min. prevalence: 0.9
min. alt. frequency: 0.01
masked by prev_mask: 3220879
masked by snp_mask: 1396696
masked by wildcard_mask: 4499696
Identifying core-snps; done
Elapsed time: 145.05135822296143
Writing snps to VCF; start
Writing snps to VCF; done!
Elapsed time: 281.08589911460876
Database building; start
[load] loading core-genome consensus sequence from /mnt/f/steno_last_round/parsnp/input/SM-325416.fna
the loaded core-genome has a consensus sequence of 4499696 bases
[load] loading key coordinates on core-genome from /mnt/f/maast/out/coords.tsv
a total of 9272 divisions was found
[load] loading core snps from /mnt/f/maast/out/core_snps.vcf
a total of 548290 core snps was found
[searching] start to search 31-mers
a total of 15340719 kmer records was found
Traceback (most recent call last):
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1395, in
main()
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1390, in main
end2end_main(args)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1339, in end2end_main
build_db_main(args)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1291, in build_db_main
run_kmerset_validate(args)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 684, in run_kmerset_validate
out, err = run_command(command)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 256, in run_command
p = sp.Popen(cmd, shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
File "/mnt/e/Miniconda3/lib/python3.9/subprocess.py", line 951, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/mnt/e/Miniconda3/lib/python3.9/subprocess.py", line 1770, in _execute_child
self.pid = _posixsubprocess.fork_exec(
OSError: [Errno 12] Cannot allocate memory
I face running the complete pipeline
my usage
maast$ maast end_to_end --in-dir /mnt/f/steno_last_round/parsnp/input/ --out-dir /mnt/f/maast/out/ --min-prev 0.9 --snp-freq 0.01
Time (s): 604.05 Running mummer4; done! Elapsed time: 3241.187788248062 Fetching file-type-specific parser; start total length of alignments: 4499696 Fetching file-type-specific parser; done Elapsed time: 49.78715515136719 Identifying core-snps; start max sites: inf min prevalence: 0.9 min MAF: 0.01 total number of sites: 4499696 min. prevalence: 0.9 min. alt. frequency: 0.01 masked by prev_mask: 3220879 masked by snp_mask: 1396696 masked by wildcard_mask: 4499696 Identifying core-snps; done Elapsed time: 145.05135822296143 Writing snps to VCF; start Writing snps to VCF; done! Elapsed time: 281.08589911460876 Database building; start [load] loading core-genome consensus sequence from /mnt/f/steno_last_round/parsnp/input/SM-325416.fna the loaded core-genome has a consensus sequence of 4499696 bases
[load] loading key coordinates on core-genome from /mnt/f/maast/out/coords.tsv a total of 9272 divisions was found
[load] loading core snps from /mnt/f/maast/out/core_snps.vcf a total of 548290 core snps was found
[searching] start to search 31-mers a total of 15340719 kmer records was found
Traceback (most recent call last): File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1395, in
main()
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1390, in main
end2end_main(args)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1339, in end2end_main
build_db_main(args)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 1291, in build_db_main
run_kmerset_validate(args)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 684, in run_kmerset_validate
out, err = run_command(command)
File "/mnt/e/Miniconda3/share/maast-1.0.8-0/bin/maast.py", line 256, in run_command
p = sp.Popen(cmd, shell=True, stdout=sp.PIPE, stderr=sp.PIPE)
File "/mnt/e/Miniconda3/lib/python3.9/subprocess.py", line 951, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/mnt/e/Miniconda3/lib/python3.9/subprocess.py", line 1770, in _execute_child
self.pid = _posixsubprocess.fork_exec(
OSError: [Errno 12] Cannot allocate memory