Orthofinder, MSA has failed

Open stephen-14 opened this issue 3 years ago • 1 comments

Hello everyone, I'm running orthofinder and I faced with a problem at step making gene tree (MSA). It's warning that list index out of range. and the number of ortholog is low percentage (40%). Does anyone know Whats wrong with my annalysis?? Many thanks! orthofinder -t 48 -M msa -S diamond -d -A mafft -T fasttree -I 1.5 -f samples/

2022-09-17 11:54:26 : Starting OrthoFinder 2.5.4 48 thread(s) for highly parallel tasks (BLAST searches etc.) 6 thread(s) for OrthoFinder algorithm

Checking required programs are installed

Test can run "mcl -h" - ok Test can run "mafft /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory//_dependencies_check/SimpleTest.fa" - ok Test can run "FastTree /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory//_dependencies_check/SimpleTest.fa" - ok

Dividing up work for BLAST for parallel processing

2022-09-17 11:54:44 : Creating blast_nucl database 1 of 14 2022-09-17 11:54:45 : Creating blast_nucl database 2 of 14 2022-09-17 11:54:49 : Creating blast_nucl database 3 of 14 2022-09-17 11:54:50 : Creating blast_nucl database 4 of 14 2022-09-17 11:54:51 : Creating blast_nucl database 5 of 14 2022-09-17 11:54:59 : Creating blast_nucl database 6 of 14 2022-09-17 11:54:59 : Creating blast_nucl database 7 of 14 2022-09-17 11:55:00 : Creating blast_nucl database 8 of 14 2022-09-17 11:55:04 : Creating blast_nucl database 9 of 14 2022-09-17 11:55:05 : Creating blast_nucl database 10 of 14 2022-09-17 11:55:13 : Creating blast_nucl database 11 of 14 2022-09-17 11:55:14 : Creating blast_nucl database 12 of 14 2022-09-17 11:55:17 : Creating blast_nucl database 13 of 14 2022-09-17 11:55:17 : Creating blast_nucl database 14 of 14

Running blast_nucl all-versus-all

Using 48 thread(s) 2022-09-17 11:55:17 : This may take some time.... 2022-09-17 11:55:17 : Done 0 of 196 2022-09-17 11:56:45 : Done 10 of 196 2022-09-17 11:57:44 : Done 20 of 196 2022-09-17 11:58:17 : Done 30 of 196 2022-09-17 11:58:43 : Done 40 of 196 2022-09-17 11:59:09 : Done 50 of 196 2022-09-17 12:00:02 : Done 60 of 196 2022-09-17 12:00:36 : Done 70 of 196 2022-09-17 12:01:03 : Done 80 of 196 2022-09-17 12:01:22 : Done 90 of 196 2022-09-17 12:01:51 : Done 100 of 196 2022-09-17 12:02:00 : Done 110 of 196 2022-09-17 12:02:08 : Done 120 of 196 2022-09-17 12:02:18 : Done 130 of 196 2022-09-17 12:02:31 : Done 140 of 196 2022-09-17 12:26:40 : Done all-versus-all sequence search

Running OrthoFinder algorithm

2022-09-17 12:26:49 : Initial processing of each species 2022-09-17 12:26:50 : Initial processing of species 5 complete 2022-09-17 12:27:00 : Initial processing of species 6 complete 2022-09-17 12:27:01 : Initial processing of species 2 complete 2022-09-17 12:27:02 : Initial processing of species 8 complete 2022-09-17 12:27:14 : Initial processing of species 0 complete 2022-09-17 12:27:22 : Initial processing of species 3 complete 2022-09-17 12:27:40 : Initial processing of species 10 complete 2022-09-17 12:27:45 : Initial processing of species 12 complete 2022-09-17 12:27:46 : Initial processing of species 13 complete 2022-09-17 12:28:09 : Initial processing of species 1 complete 2022-09-17 12:28:16 : Initial processing of species 11 complete 2022-09-17 12:28:16 : Initial processing of species 7 complete 2022-09-17 12:29:11 : Initial processing of species 4 complete 2022-09-17 12:29:13 : Initial processing of species 9 complete 2022-09-17 12:29:38 : Connected putative homologues 2022-09-17 12:29:38 : Written final scores for species 5 to graph file 2022-09-17 12:29:41 : Written final scores for species 3 to graph file 2022-09-17 12:29:45 : Written final scores for species 2 to graph file 2022-09-17 12:29:45 : Written final scores for species 8 to graph file 2022-09-17 12:29:45 : Written final scores for species 6 to graph file 2022-09-17 12:29:49 : Written final scores for species 0 to graph file 2022-09-17 12:29:55 : Written final scores for species 10 to graph file 2022-09-17 12:29:55 : Written final scores for species 12 to graph file 2022-09-17 12:29:55 : Written final scores for species 13 to graph file 2022-09-17 12:30:25 : Written final scores for species 11 to graph file 2022-09-17 12:30:38 : Written final scores for species 1 to graph file 2022-09-17 12:30:40 : Written final scores for species 7 to graph file 2022-09-17 12:31:24 : Written final scores for species 9 to graph file 2022-09-17 12:31:24 : Written final scores for species 4 to graph file

WARNING: program called by OrthoFinder produced output to stderr

Command: mcl /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/OrthoFinder_graph.txt -I 1.5 -o /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/clusters_OrthoFinder_I1.5.txt -te 6 -V all

stdout

b'' stderr

b'[mcl] cut <33> instances of overlap\n' 2022-09-17 14:56:36 : Ran MCL

Writing orthogroups to file

OrthoFinder assigned 1035235 genes (39.7% of total) to 303730 orthogroups. Fifty percent of all genes were in orthogroups with 1 or more genes (G50 was 1) and were contained in the largest 570696 orthogroups (O50 was 570696). There were 2 orthogroups with all species present and 0 of these consisted entirely of single-copy genes.

2022-09-17 14:58:21 : Done orthogroups

Analysing Orthogroups

2022-09-17 14:58:26 : Starting MSA/Trees Species tree: Using 2194 orthogroups with minimum of 21.4% of species having single-copy genes in any orthogroup

Inferring multiple sequence alignments for species tree

2022-09-17 14:59:43 : Done 0 of 2194 WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range File "/home/biodiversity/miniconda3/bin/scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move fn(fns) File "/home/biodiversity/miniconda3/bin/scripts_of/trees_msa.py", line 262, in trim_fn trim.main(fn, fn, 0.1, 500, 0.75) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 94, in main msa = MSA(infn) File "/home/biodiversity/miniconda3/bin/scripts_of/trim.py", line 35, in init self.non_gap_pos[-1].extend([current_length + i for i,c in enumerate(line) if (c != "*" and c != "-")]) WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range 2022-09-17 15:31:41 : Done 1000 of 2194 WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range 2022-09-17 15:35:14 : Done 2000 of 2194 WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: list index out of range WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000023.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000031.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000036.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000037.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000038.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000040.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000043.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000058.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000067.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000070.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000075.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000322.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000336.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000372.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000374.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000464.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000544.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000550.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000613.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000705.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000718.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000764.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000794.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000882.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000894.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0000970.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0001252.fa No tree or orthologs will be inferred for this orthogroup. To correct the issue, identify & correct the problematic gene sequence and rerun. WARNING: An MSA failed for an unknown reason: /home/biodiversity/samples/OrthoFinder/Results_Sep17_2/WorkingDirectory/Alignments_ids/OG0001318.fa

Sep 18 '22 00:09 stephen-14

Hello

I have the same problem as you with MCL, do you know why? Have you found a solution for the MSA problem?

Aug 06 '24 08:08 pguenzi-tiberi