Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
-->Reading Genome (asm, fasta) files from ./mers49..
|->[OK]
-->Reading Genbank file(s) for reference (.gbk) ./ref/EMC_2012.gbk..
|->[OK]
-->Running Parsnp multi-MUM search and libMUSCLE aligner..
ERROR
The following command failed:
/tmp/_MEIaVjATQ/parsnp /home/tbrown/Kate/Harvest-Linux64-v1.1.2/P_2019_05_15_181215575876/parsnpAligner.ini
Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.
ERROR
I tried to run the tutorial from this web site: https://harvest.readthedocs.io/en/latest/content/parsnp/tutorial.html,
using the command given on the same website: ./parsnp -g ./ref/EMC_2012.gbk -d ./mers49 -c
I got this output:
tbrown@debian1:~/Kate/Harvest-Linux64-v1.1.2$ ./parsnp -g ./ref/EMC_2012.gbk -d ./mers49 -c |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
SETTINGS: |-refgenome: ./ref/EMC_2012.gbk.fna |-aligner: libMUSCLE |-seqdir: ./mers49 |-outdir: /home/tbrown/Kate/Harvest-Linux64-v1.1.2/P_2019_05_15_181215575876 |-OS: Linux |-threads: 32
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-->Reading Genome (asm, fasta) files from ./mers49.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) ./ref/EMC_2012.gbk.. |->[OK] -->Running Parsnp multi-MUM search and libMUSCLE aligner.. ERROR The following command failed:
I am running the software on a debian machine.