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.

Severin et al. BMC Bioinformatics 2010 11:240   doi:10.1186/1471-2105-11-240

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