Table 2.
Jobs in the Pairwise alignment pipeline for Human-Pika
| Analysis | Number of jobs | Granularity |
|---|---|---|
| ChunkAndGroupDna | 4 | 2 per genome |
| CreatePairAlignerJobs | 1 | 1 per pipeline |
| BlastZ-e1886dc | 97920 | As many as required |
| UpdateMaxAlignmentLengthBeforeFD | 1 | 1 per pipeline |
| CreateFilterDuplicatesJobs | 2 | 1 per genome |
| TargetFilterDuplicates-e1886dc | 113 | 1 per human segment |
| QueryFilterDuplicates-e1886dc | 193095 | 1 per pika segment |
| UpdateMaxAlignmentLengthAfterFD | 1 | 1 per pipeline |
| DumpLargeNibForChains | 2 | 1 per genome |
| CreateAlignmentChainsJobs | 1 | 1 per pipeline |
| AlignmentChains-26aa1260 | 425698 | As many as required |
| UpdateMaxAlignmentLengthAfterChain | 1 | 1 per pipeline |
| CreateAlignmentNetsJobs | 1 | 1 per pipeline |
| AlignmentNets-34de6ee1 | 5770 | As many as required |
| UpdateMaxAlignmentLengthAfterNet | 1 | 1 per pipeline |
| PairwiseHealthCheck | 2 | 2 per pipeline |
| TOTAL | 722613 | |
This table shows the final number of jobs run for each analysis. The last column gives a short explanation on the number of jobs for each analysis. 113 human segments correspond to the 25 chromosomes (1 to 24, X, Y and MT) and an extra 88 supercontigs not yet assembled into chromosomes. The pika genome is scattered in 193095 segments. Both AlignmentChain and AlignmentNets jobs are defined by the CreateAlignmentChainJobs and CreateAlignmentNetsJobs jobs respectively.