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Parsnp: Error creating Gingr input file #10

Open verheytb opened 9 years ago

verheytb commented 9 years ago

I'm getting an error with Parsnp at the last step creating the Gingr input file:

chaconas@chaconas-X10DRi:~/Programs/Parsnp-Linux64-v1.2$ ./parsnp -d /home/chaconas/Desktop/Projects/RDVParsnpTrial/References/GenomesAndContigs/ -g /home/chaconas/Desktop/Projects/RDVParsnpTrial/Queries/11-282_06052015.gbk -P 30000000 |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest

SETTINGS: |-refgenome: /home/chaconas/Desktop/Projects/RDVParsnpTrial/Queries/11-282_06052015.gbk.fna |-aligner: libMUSCLE |-seqdir: /home/chaconas/Desktop/Projects/RDVParsnpTrial/References/GenomesAndContigs/ |-outdir: /home/chaconas/Programs/Parsnp-Linux64-v1.2/P_2015_07_03_152715335014 |-OS: Linux |-threads: 32

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-->Reading Genome (asm, fasta) files from /home/chaconas/Desktop/Projects/RDVParsnpTrial/References/GenomesAndContigs/.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) /home/chaconas/Desktop/Projects/RDVParsnpTrial/Queries/11-282_06052015.gbk.. |->[OK] -->Calculating MUMi.. |->[OK] -->Running Parsnp multi-MUM search and libMUSCLE aligner.. |->[OK] -->Running PhiPack on LCBs to detect recombination.. |->[SKIP] -->Reconstructing core genome phylogeny.. |->[OK] -->Creating Gingr input file.. ERROR The following command failed:

/tmp/_MEIXUzQtH/harvest --midpoint-reroot -u -q -i /home/chaconas/Programs/Parsnp-Linux64-v1.2/P_2015_07_03_152715335014/parsnp.ggr -o /home/chaconas/Programs/Parsnp-Linux64-v1.2/P_2015_07_03_152715335014/parsnp.ggr -n /home/chaconas/Programs/Parsnp-Linux64-v1.2/P_2015_07_03_152715335014/parsnp.tree Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team. ERROR

haol04 commented 7 years ago

Hi, verheytb I ran into the same problem as yours. I am wondering if you have figured out the solution. Li

verheytb commented 7 years ago

I'm not exactly sure why, but we thought it might have to do with trying to use a collection of 600 genomes and contigs. So, we narrowed down the list to 230 full genomes only and it worked.

haol04 commented 7 years ago

Thanks for getting back to me. I reinstalled the program and it worked this time with the same number of genomes. Li

From: Ted Verhey [mailto:notifications@github.com] Sent: Friday, March 17, 2017 1:32 PM To: marbl/harvest Cc: Hao, Li; Comment Subject: Re: [marbl/harvest] Parsnp: Error creating Gingr input file (#10)

I'm not exactly sure why, but we thought it might have to do with trying to use a collection of 600 genomes and contigs. So, we narrowed down the list to 230 full genomes only and it worked.

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