calctruequality.sh - Exception in thread "main" java.lang.AssertionError with callvars

[masalgar]

Hi,

I'm trying to run the [assemble_polyg_meta_v1.sh](https://github.com/bbushnell/BBTools/blob/master/pipelines/assemble_polyg_meta_v1.sh) pipeline. However, I have run into an issue in the step with calctruequality.sh:

(bbtools-env) [masalgar@cn-1055 2.Cleaned_reads]$ ../bbmap/calctruequality.sh in=clean.sam.gz usetiles ref=quick.fa callvars
java -ea  --add-modules jdk.incubator.vector -Xmx257637m -Xms257637m -cp /home/masalgar/DeiC-KU-L59/users/masalgar/CF_metagenome/BBtools_assembly/bbmap/bbtools.jar jgi.CalcTrueQuality in=clean.sam.gz usetiles ref=quick.fa callvars
WARNING: Using incubator modules: jdk.incubator.vector
Executing jgi.CalcTrueQuality [in=clean.sam.gz, usetiles, ref=quick.fa, callvars]

Executing var2.CallVariants [in=clean.sam.gz, ref=quick.fa, realign=false, ploidy=1, prefilter=true]

Loading reference.
Time:   3.007 seconds.
Loading the prefilter.
Added 301596839 events to prefilter; approximately 125934 were unique.
The prefilter is 0.00% full.
Time:   89.835 seconds.

Processing input files.
Time:   84.786 seconds.
Memory: max=270180m, total=270180m, free=207123m, used=63057m

Processing variants.
Exception in thread "main" java.lang.AssertionError
        at var2.VarMap.processVariantsMT_inner(VarMap.java:434)
        at var2.VarMap.processVariantsMT(VarMap.jav.a:409)
        at var2.CallVariants.processVariants(CallVariants.java:997)
        at var2.CallVariants.makeVarMap(CallVariants.java:827)
        at var2.CallVariants.process(CallVariants.java:739)
        at jgi.CalcTrueQuality.process(CalcTrueQuality.java:270)
        at jgi.CalcTrueQuality.main(CalcTrueQuality.java:60)

I don't run into this error if I don't use the callvars flag. I have ruled out memory limitations, as the job never fills out all the RAM in the node I'm using. In addition, I don't think it's a multi-threading issue, because I have run this command with threads=1, and even in a node with just 1 core for good measure, but I still got the same issue.

I would kindly appreciate any insights or suggestions to fix this problem. Is it safe to use the -da flag to bypass this error?

[bsaintjo]

Can you validate what version of BBTools version you are using by running bbversion.sh?

Can you provide some details on clean.sam.gz and how it was generated and any processing may have involved base quality scores? And if you can find a subset of reads that generate the AssertionError?

Thank you!rm