I’ve been experimenting with the concordance
function, and am stuck. The set up here is comparing a set of NA12878 genotypes, isolating chr22 before the comparisons.
I have been able to use concordance to successfully compare:
- a single sample against itself
- two single samples against another 10 (2 total comparisons)
- ten single samples against another 10 (10 total comparisons)
But, I tried then to compare 100 to another 100, and this fails with a stack overflow.
my command:
hundred_sum, hundred_samples, hundred_variants = hl.concordance(hundred, na12878_mt_biallelic_vars_chr22)
It begins by identifying the 100 matched samples:
2018-11-28 18:32:55 Hail: INFO: Found 100 overlapping samples
Left: 100 total samples
Right: 2437 total samples
But then fails:
at java.io.ObjectInputStream$PeekInputStream.readFully(ObjectInputStream.java:2678)
at java.io.ObjectInputStream$BlockDataInputStream.readInt(ObjectInputStream.java:3179)
at java.io.ObjectInputStream.readHandle(ObjectInputStream.java:1683)
...
at java.io.ObjectStreamClass.invokeReadObject(ObjectStreamClass.java:1170)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2177)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2068)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1572)
Hail version: 0.2-961f76d14f1e
Error summary: StackOverflowError: null
Any suggestions for what might be causing the error?