OrthoFinder version 1.1.4 Copyright (C) 2014 David Emms This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. For details please see the License.md that came with this software. 4 thread(s) for highly parallel tasks (BLAST searches etc.) 1 thread(s) for OrthoFinder algorithm Checking required programs are installed ---------------------------------------- Test can run "makeblastdb -help" - ok Test can run "blastp -help" - ok Test can run "mcl -h" - ok Dividing up work for BLAST for parallel processing -------------------------------------------------- 2017-03-03 15:34:27 : Creating Blast database 1 of 3 2017-03-03 15:34:28 : Creating Blast database 2 of 3 2017-03-03 15:34:28 : Creating Blast database 3 of 3 Running BLAST all-versus-all ---------------------------- Using 4 thread(s) 2017-03-03 15:34:28 : This may take some time.... 2017-03-03 15:34:28 : Done 0 of 9 Running OrthoFinder algorithm ----------------------------- 2017-03-03 15:36:30 : Initial processing of each species 2017-03-03 15:36:31 : Initial processing of species 0 complete 2017-03-03 15:36:33 : Initial processing of species 1 complete 2017-03-03 15:36:34 : Initial processing of species 2 complete 2017-03-03 15:36:38 : Connected putatitive homologs 2017-03-03 15:36:39 : Writen final scores for species 0 to graph file 2017-03-03 15:36:39 : Writen final scores for species 1 to graph file 2017-03-03 15:36:39 : Writen final scores for species 2 to graph file 2017-03-03 15:36:40 : Ran MCL Writing orthogroups to file --------------------------- Orthogroups have been written to tab-delimited files: /data/antwerpen/203/vsc20345/orthofinder/caseiGroup_proteins_subset/Results_Mar03/Orthogroups.csv /data/antwerpen/203/vsc20345/orthofinder/caseiGroup_proteins_subset/Results_Mar03/Orthogroups.txt (OrthoMCL format) /data/antwerpen/203/vsc20345/orthofinder/caseiGroup_proteins_subset/Results_Mar03/Orthogroups_UnassignedGenes.csv Running Orthologue Prediction ============================= Calculating gene distances -------------------------- 2017-03-03 15:36:40 : Done 0 of 9 2017-03-03 15:36:44 : Processing species 0 2017-03-03 15:36:44 : Processing species 1 2017-03-03 15:36:45 : Processing species 2 Inferring gene and species trees -------------------------------- 2017-03-03 15:36:46 : Done 0 of 226 /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found /bin/sh: fastme: command not found 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