Issue with DiscoverySNPCallerPluginV2

[Ira Herniter]

Hi All,

I'm having some trouble with DiscoverySNPCallerPluginV2. I'm running the GBSv2 pipeline, and everything seems to be working fine up until this point, at which point it stops working and I can't figure out from the documentation what might be going on.

Running the SAMtoGBSdb plugin:

$ /programs/tassel-5-standalone_20180419/run_pipeline.pl -Xmx100g -fork1 -SAMToGBSdbPlugin -i tagsForAlignFullvs.sam -db output/125AAxScout_gbs.db -aProp 0.0 -aLen 0 -endPlugin -runfork1 > log/SAMToGBSdbPlugin.log 2> log/SAMToGBSdbPlugin.err

Gets me the following results:

Total number of cut sites: 65095
Number of cut sites with 1 tag: 38208
Number of cut sites with 2 tags: 16431
Number of cut sites with 3 tags: 7081
Number of cut sites with more than 3 tags: 3375
[pool-1-thread-1] INFO net.maizegenetics.analysis.gbs.v2.SAMToGBSdbPlugin - Finished reading SAM file and adding tags to DB.
Total number of tags mapped: 114658 (total mappings 114658)
Tags not mapped: 26931
Tags dropped due to minimum mapq value: 0

I then run DiscoverySNPCaller:

$ /programs/tassel-5-standalone_20180419/run_pipeline.pl -Xmx100g -fork1 -DiscoverySNPCallerPluginV2 -db output/125AAxScout_gbs.db -sC “chr01” -eC “chr19” -mnLCov 0.1 -deleteOldData true -endPlugin -runfork1 > log/DiscoverySNPCallerPluginV2.log 2> log/DiscoverySNPCallerPluginV2.err

And get this result:

size of all tags in tag table=141589
size of all tissues in tissue table=0
size of all tags in mappingApproach table=2
size of all taxa in taxa table=199

Then, when I try to run SNPQualityProfiler:

$ /programs/tassel-5-standalone_20180419/run_pipeline.pl -Xmx100g -fork1 -SNPQualityProfilerPlugin -db output/125AAxScout_gbs.db -statFile output/outputStats.txt -deleteOldData true -endPlugin -runfork1 > log/SNPQualityProfilerPlugin.log 2> log/SNPQualityProfilerPlugin.err

I get this error:

ERROR: No SNP entries found in the SNP Position table.  
Please run DiscoverySNPCallerPluginV2 to call SNPs before running this plugin.

I've already run SNPCaller, so I don't know why this is happening. Any help would be greatly appreciated. 

Thanks!

Ira

[Ira Herniter]

I noticed that the SNPQualityProfiler command calls for something called a "statFile," but as far as I can tell from the documentation, DiscoverySNPCaller does not output such a file and doesn't seem to have an option to do so.