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marbl / parsnp

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.
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tutorial fails #60

Closed tbrown99 closed 4 years ago

tbrown99 commented 5 years ago

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

<>

-->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 am running the software on a debian machine.

bkille commented 4 years ago

There was an issue with genbank parsing in version 1.2. I'm closing this as I believe it is fixed in 1.5