Here's a simple bug. If parsnp is run with both -c and -M, it crashes. The output is below.
Once I realized that -c could be incompatible with -M, I removed it and it behaved as expected (it also behaved as expected if -c was retained and -M was dropped).
Thanks for providing such a useful tool.
Sincerely,
Adam
p.s. are you familiar with any simple tool that will quickly calculate MUMi for pairs of genomes (so that I can do an all v. all calculation)? Thanks again!
======= run with M flag ============
parsnp -c -r ! -o ParSNP_250 -d assemblies_250/ -M
|--Parsnp v1.2--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
Dear Dr. Treangen,
Here's a simple bug. If parsnp is run with both -c and -M, it crashes. The output is below. Once I realized that -c could be incompatible with -M, I removed it and it behaved as expected (it also behaved as expected if -c was retained and -M was dropped).
Thanks for providing such a useful tool.
Sincerely, Adam
p.s. are you familiar with any simple tool that will quickly calculate MUMi for pairs of genomes (so that I can do an all v. all calculation)? Thanks again!
======= run with M flag ============ parsnp -c -r ! -o ParSNP_250 -d assemblies_250/ -M |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
SETTINGS: |-refgenome: autopick |-aligner: libMUSCLE |-seqdir: assemblies_250/ |-outdir: ParSNP_250 |-OS: Linux |-threads: 32
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-->Reading Genome (asm, fasta) files from assemblies_250/.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) .. |->[WARNING]: no genbank file provided for reference annotations, skipping.. Traceback (most recent call last): File "", line 876, in
AttributeError: 'str' object has no attribute 'close'