Different mapping with different -t threads ?

[tseemann]

Is MapCaller deterministic? If i run with different number of threads I get different mappings. And the more threads, the more mappings (approximately).

    -t        Result
-----------------------------------------------------
     1        812958 ( 90.05%) reads are mapped properly.
     2        813000 ( 90.06%) reads are mapped properly.
     3        813028 ( 90.06%) reads are mapped properly.
     4        813036 ( 90.06%) reads are mapped properly.
     5        813062 ( 90.07%) reads are mapped properly.
     6        813074 ( 90.07%) reads are mapped properly.
     7        813095 ( 90.07%) reads are mapped properly.
     8        813118 ( 90.07%) reads are mapped properly.
     9        813125 ( 90.07%) reads are mapped properly.
    10        813137 ( 90.07%) reads are mapped properly.
    11        813141 ( 90.07%) reads are mapped properly.
    12        813153 ( 90.08%) reads are mapped properly.
    13        813155 ( 90.08%) reads are mapped properly.
    14        813140 ( 90.07%) reads are mapped properly.
    15        813174 ( 90.08%) reads are mapped properly.
    16        813193 ( 90.08%) reads are mapped properly.
....
    67        813160 ( 90.08%) reads are mapped properly.
    68        813157 ( 90.08%) reads are mapped properly.
    69        813180 ( 90.08%) reads are mapped properly.
    70        813134 ( 90.07%) reads are mapped properly.
    71        813207 ( 90.08%) reads are mapped properly.
    72        813171 ( 90.08%) reads are mapped properly.

[hsinnan75]

MapCaller is a deterministic method if it is running with a single thread. MapCaller will rescue unpaired alignments when it collects enough data (>1000 unique paired alignments) to estimate the actual fragment size. However, when you use different number of threads to run MapCaller, some paired-ends reads could not be rescued since MapCaller did not collect enough data to estimate the fragment size. If all reads are mapped at the same time, none of unique paired-end alignments is used to estimate the fragment size, then there will be no rescued alignments.

[tseemann]

Is this parameter relevant?
-size sequencing fragment size [500]

[hsinnan75]

MapCaller can predict the fragment size during the read mapping. If you specify the fragment size, MapCaller can use the value to remove ambiguous alignments before it predicts the fragment size.