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parsnp failed to generate phylogeny #26

Open haol04 opened 7 years ago

haol04 commented 7 years ago

I am trying to run parsnp for 330 bacteria genome (genome size ~2mb). The alignment seems to work properly. but it failed in the last step, the error message is pasted below. Your help would be greatly appreciated! Li

-bash-4.1$ ./parsnp -g ./ref/2603V-R_NC004116.gb -d GBS_WGS_2017/ -c -C -p 32

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-->Reading Genome (asm, fasta) files from GBS_WGS_2017/.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) ./ref/2603V-R_NC004116.gb.. |->[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/_MEI2r348L/harvest --midpoint-reroot -u -q -i /afs/grid.pfizer.com/vaccine/ngs/Tools/Parsnp-Linux64-v1.2/P_2017_03_16_161557720869/parsnp.ggr -o /afs/grid.pfizer.com/vaccine/ngs/Tools/Parsnp-Linux64-v1.2/P_2017_03_16_161557720869/parsnp.ggr -n /afs/grid.pfizer.com/vaccine/ngs/Tools/Parsnp-Linux64-v1.2/P_2017_03_16_161557720869/parsnp.tree Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team.

tongzhouxu commented 4 years ago

Hi, I have had the same issue and I solved it by removing the complete genomes in the directory and doing the assemblies only.

hao467 commented 3 years ago

-->Running Parsnp multi-MUM search and libMUSCLE aligner.. ERROR The following command failed:

/tmp/_MEI8TX9MJ/parsnp tree3/parsnpAligner.ini Please veryify input data and restart Parsnp. If the problem persists please contact the Parsnp development team. ERROR I am trying to run parsnp, the error message is pasted below. Your help would be greatly appreciated!