marbl/harvest

parsnp failed to generate phylogeny

Opened this issue · 2 comments

haol04 commented

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

<>

-->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

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

-->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!