GA/VG Error Log

## Output from one array process

GraphAligner bioconda 1.0.17b-
Load graph from # graph location
Build minimizer seeder from the graph
Minimizer seeds, length 15, window size 20, density 10
Seed cluster size 1
Extend up to 5 seed clusters
Alignment bandwidth 10, tangle effort 1000
Clip alignment ends with identity < 66%
X-drop DP score cutoff 14705
Backtrace from 10 highest scoring local maxima per cluster
write alignments to # gam file
Align
Alignment finished
Input reads: 580260 (3658115898bp)
Seeds found: 9491908149
Seeds extended: 2887363
Reads with a seed: 577823 (3658105894bp)
Reads with an alignment: 577575 (3302469894bp)
Alignments: 9417997 (3704266867bp) (8245932 additional alignments discarded)
End-to-end alignments: 116749 (567688549bp)
Alignment broke with some reads. Look at stderr output.
surjecting back to graph

## Errors from one array process

GraphAligner bioconda 1.0.17b-
src/GraphAlignerBitvectorCommon.h:1118: Assertion 'previous.node(neighbor).endSlice.scoreEnd >= scoreHere-(eq?0:1)' failed. Read: m140612_020550_42156_c100652082550000001823118110071460_s1_p0/127893/42129_54356. Seed: 0+,0,0,0
src/GraphAlignerBitvectorCommon.h:1118: Assertion 'previous.node(neighbor).endSlice.scoreEnd >= scoreHere-(eq?0:1)' failed. Read: m140612_082500_42156_c100652082550000001823118110071461_s1_p0/17608/11349_18935. Seed: 0+,0,0,0
src/GraphAlignerBitvectorCommon.h:1118: Assertion 'previous.node(neighbor).endSlice.scoreEnd >= scoreHere-(eq?0:1)' failed. Read: m140614_092436_42156_c100652052550000001823118110071490_s1_p0/83855/20478_34565. Seed: 0+,0,0,0
src/GraphAlignerBitvectorCommon.h:1118: Assertion 'previous.node(neighbor).endSlice.scoreEnd >= scoreHere-(eq?0:1)' failed. Read: m141004_003611_42156_c100717212550000001823136902281550_s1_p0/120532/0_11601. Seed: 0+,0,0,0
warning:[vg::get_sequence_dictionary] No reference-sense paths available in the graph; falling back to generic paths.
warning[vg::Surjector]: Refusing to perform very large alignment against 102712 bp strand split subgraph for read m140612_020550_42156_c100652082550000001823118110071460_s1_p0/641/0_28728; suppressing further warnings.