DistanceEst error

[macmanes]

Using sga Version 0.10.13

 DistanceEst -s 200 --mind -99 -n 5 -k 99 -j 1 -o libPE.de libPE.hist -l 100 libPE.diffcontigs.sorted.bam

The error message:

 DistanceEst: MLE.cpp:126: int maximumLikelihoodEstimate(unsigned int, int, int, const std::vector<int>&, const PMF&, unsigned int, unsigned int, bool, unsigned int&): Assertion `len1 >= l' failed.`

The inputs looks fine: samtools flagstat libPE.diffcontigs.sorted.bam

 279539954 + 0 in total (QC-passed reads + QC-failed reads)
 0 + 0 duplicates 
 279539954 + 0 mapped (100.00%:-nan%)
 279539954 + 0 paired in sequencing
 139769977 + 0 read1
 139769977 + 0 read2
 0 + 0 properly paired (0.00%:-nan%)
 279539954 + 0 with itself and mate mapped
 0 + 0 singletons (0.00%:-nan%)
 279539954 + 0 with mate mapped to a different chr
 239576854 + 0 with mate mapped to a different chr (mapQ>=5)

head -3 libPE.hist -39675 3 -39664 5 -36421 3

tail -3 libPE.hist 1542 3 1585 3 1676 3

The mode size is 219 5838876

[sjackman]

What's the read length? @traymond

[jts]

I'll be out of touch for about a week, feel free to ping me if this isn't resolved. There probably isn't much I can do though, unless sga is incorrectly preparing the input into DistanceEst.