Table 4.
Jobs in the GeneTree pipeline for Ensembl release 49
| Analysis | Number of jobs | Failed jobs | Granularity |
|---|---|---|---|
| GenomeDumpFasta | 39 | - | 1 per genome |
| GenomeLoadMembers | 39 | - | 1 per genome |
| GenomeSubmitPep | 39 | - | 1 per genome |
| CreateBlastRules | 39 | - | 1 per genome |
| SubmitPep_* | 682412 | - | 1 per peptide |
| blast_* | 26614068 | - | All vs all peptides |
| UpdatePAFids | 1 | - | 1 per pipeline |
| PAFCluster | 1 | - | 1 per pipeline |
| Muscle | 26484 | 7 | 1 per genetree |
| BreakPAFCluster | 95 | - | As many as required |
| TreeBeST | 26477 | 9 | 1 per genetree |
| OrthoTree | 26468 | - | 1 per genetree |
| CreateHomology_dNdSJob | 1 | - | 1 per pipeline |
| Homology_dNdS | 3646340 | 1364 | 1 per orthologous gene pair |
| Threshold_on_dS | 1 | - | 1 per pipeline |
| TOTAL | 31022503 | 1380 | |
This table shows the final number of jobs run for each analysis during the execution of the GeneTree pipeline for 39 species. All the SubmitPep_xxxxx and blast_yyyyy jobs have been grouped for simplicity. The table also shows the number of jobs that failed. Muscle and TreeBeST jobs were recovered using the BreakPAFCluster analysis. This breaks the cluster and creates new Muscle jobs.