[johns.chris.a@gator4 ~]$ cd /ufrc/kawahara/johns.chris.a/AHE/TESTS/DIV_TIME_DATA/LOCI/IQ_TREE_70perc_b100/Robinson_Fould/Tree_Check [johns.chris.a@gator4 Tree_Check]$ cd .. [johns.chris.a@gator4 Robinson_Fould]$ ls allgenetrees alltrees.suptree [johns.chris.a@gator4 Robinson_Fould]$ module load raxml [johns.chris.a@gator4 Robinson_Fould]$ raxmlHPC-PTHREADS-SSE3 -f R -m GTRCAT -t alltrees.suptree -z allgenetrees -n RF WARNING: The number of threads is currently set to 0 You can specify the number of threads to run via -T numberOfThreads NumberOfThreads must be set to an integer value greater than 1 RAxML, will now set the number of threads automatically to 2 ! Found a total of 62 taxa in first tree of tree collection allgenetrees Expecting all remaining trees in collection to have the same taxon set add [CJ176] add [CJAHE10_Gracillariidae_Philodoria_sp10] add [CJAHE20_Carposinidae_Carposina_sp] add [AHE45_Gracillariidae_Philodoria_sp] add [CJAHE52_Carposinidae_Carposina_sp_10x] add [AHE35_Gracillariidae_Philodoria_sp] add [AHE33_Gracillariidae_Philodoria_sp] add [CJ265] add [I3466_Gracilliariidae_Philodoria_auromagnifica] add [AHE66_Gracillariidae_Philodoria_sp] add [CJAHE23_Carposinidae_Carposina_auromagnifica_10x] add [AHE55_Gracillariidae_Philodoria_sp] add [I3464_Gracilliariidae_Philodoria_basalis] add [AHE65_Gracillariidae_Philodoria_sp] add [CJAHE57_Carposinidae_Carposina_sp] add [CJ260] add [I3467_Gracilliariidae_Philodoria_basalis] add [AHE41_Gracillariidae_Philodoria_sp] add [CJAHE58rg_Carposinidae_Carposina_sp_10x] add [CJAHE3_Gracillariidae_Philodoria_sp3] add [AHE44_Gracillariidae_Philodoria_sp] add [I3473_Gracilliariidae_Conopomorpha_cramerella] add [calo2] add [PXYLO] add [pcit] add [DP14051_Gracillariidae_Cameraria_ohridella] add [ASK141993_Gracillariidae_Epicephala_sp] add [ASK141990_Gracillariidae_Cuphodes_wisteriae] add [Phil] add [CJ257] add [CJAHE14_Gracillariidae_Philodoria_sp14] add [AHE43_Gracillariidae_Philodoria_sp] add [AHE26_Gracillariidae_Philodoria_sp] add [CJ223] add [CJAHE5_Gracillariidae_Philodoria_sp5] add [CJAHE18_Carposinidae_Carposina_sp] add [CJAHE11_Gracillariidae_Philodoria_sp11] add [CJAHE22_Carposinidae_Carposina_sp] add [CJAHE13_Gracillariidae_Philodoria_sp13] add [CJAHE7_Gracillariidae_Philodoria_sp7] add [CJAHE17_Carposinidae_Carposina_urerana] add [CJAHE21_Carposinidae_Carposina_sp] add [AHE37_Gracillariidae_Philodoria_sp] add [CJAHE48_Carposinidae_Carposina_sp] add [CJAHE49rg_Carposinidae_Carposina_sp_10x] add [CJAHE16_Gracillariidae_Philodoria_sp16] add [CJAHE6_Gracillariidae_Philodoria_sp6] add [CJAHE12_Gracillariidae_Philodoria_sp12] add [CJAHE31_Carposinidae_Carposina_sp] add [CJAHE8_Gracillariidae_Philodoria_sp8] add [I3465_Gracilliariidae_Philodoria_wilkesiella] add [CJAHE1_Gracillariidae_Philodoria_sp1] add [AHE62_Gracillariidae_Philodoria_sp] add [AHE54_Gracillariidae_Philodoria_sp] add [AHE56_Gracillariidae_Philodoria_sp] add [CJAHE4_Gracillariidae_Philodoria_sp4] add [AHE51_Gracillariidae_Philodoria_sp] add [AHE46_Gracillariidae_Philodoria_sp] add [CJAHE19_Carposinidae_Carposina_marginestrigata] add [CJAHE27rg_Carposinidae_Carposina_marginestrigata_10x] add [AHE60_Gracillariidae_Philodoria_sp] add [AHE61_Gracillariidae_Philodoria_sp] WARNING: RAxML is not checking sequences for duplicate seqs and sites with missing data! This is the RAxML Master Pthread This is RAxML Worker Pthread Number: 1 This is RAxML version 8.2.3 released by Alexandros Stamatakis on August 12 2015. With greatly appreciated code contributions by: Andre Aberer (HITS) Simon Berger (HITS) Alexey Kozlov (HITS) Kassian Kobert (HITS) David Dao (KIT and HITS) Nick Pattengale (Sandia) Wayne Pfeiffer (SDSC) Akifumi S. Tanabe (NRIFS) RAxML large-tree plausibility-checker RAxML was called as follows: raxmlHPC-PTHREADS-SSE3 -f R -m GTRCAT -t alltrees.suptree -z allgenetrees -n RF Parsing reference tree alltrees.suptree allocated 11570 bytes The reference tree has 62 tips Found 503 trees in File allgenetrees Small tree 0 has 51 tips and 48 bipartitions Relative RF tree 0: 0.750000 Small tree 100 has 57 tips and 54 bipartitions Relative RF tree 100: 0.629630 Small tree 200 has 53 tips and 50 bipartitions Relative RF tree 200: 0.800000 Small tree 300 has 53 tips and 50 bipartitions Relative RF tree 300: 0.800000 Small tree 400 has 44 tips and 41 bipartitions Relative RF tree 400: 0.585366 Small tree 500 has 57 tips and 54 bipartitions Relative RF tree 500: 0.722222 Number of small trees skipped: 0 Average RF distance 0.674975 Large Tree: 62, Number of SmallTrees analyzed: 503 Total execution time: 0.570150 secs File containing all 503 pair-wise RF distances written to file /ufrc/kawahara/johns.chris.a/AHE/TESTS/DIV_TIME_DATA/LOCI/IQ_TREE_70perc_b100/Robinson_Fould/RAxML_RF-Distances.RF execution stats: Accumulated time Effective algorithm: 0.01838 sec Average time for effective: 0.0000365411 sec Preprocessingtime: 0.00015 sec [johns.chris.a@gator4 Robinson_Fould]$