Error when using sepp with vsearch clustered rep-seqs

I used vsearch and gg138 97_otus.qza to generate rep-seqs.qza.(qiime2-2019.10)

qiime vsearch cluster-features-closed-reference --i-table table.qza --i-sequences rep-seqs.qza --i-reference-sequences 97_otus-gg138.qza --p-perc-identity 0.97 --o-clustered-table table.qza --o-clustered-sequences rep-seqs.qza --o-unmatched-sequences unmatched.qza

And when I used sepp-refs-gg-13-8.qza to construct tree.qza, it failed.
qiime fragment-insertion sepp --i-representative-sequences rep-seqs.qza --i-reference-database sepp-refs-gg-13-8.qza --o-tree tree.qza --o-placements tree_placements.qza
But when I used sepp-refs-silva.qza, it succeeded.
I also clustered using silva 97_otus.qza, and sepp succeeded with rep-seqs-gg138.qza but failed with
rep-seqs-gg138.qza.
Here’s the log.
Removing /tmp/tmp.JHJh3WXKRU/sepp-tmp-I0AQYafXyG
Traceback (most recent call last):
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File β€œ</home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>”, line 2, in sepp
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 77, in sepp
debug)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command β€˜[β€˜run-sepp.sh’, β€˜/tmp/qiime2-archive-vyxvxuz0/191a4857-22be-41e0-a15b-99ed22118d59/data/dna-sequences.fasta’, β€˜q2-fragment-insertion’, β€˜-x’, β€˜48’, β€˜-A’, β€˜1000’, β€˜-P’, β€˜5000’, β€˜-a’, β€˜/tmp/qiime2-archive-rfvls27f/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/aligned-dna-sequences.fasta’, β€˜-t’, β€˜/tmp/qiime2-archive-rfvls27f/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/tree.nwk’, β€˜-r’, β€˜/tmp/qiime2-archive-rfvls27f/e44b5e78-31e5-4a0f-9041-494bc3ca2df2/data/raxml-info.txt’]’ returned non-zero exit status 1.

Welcome to the forum @Ryuk!

I am not sure what is going on with SEPP, but just want to point out that you should not really need to use SEPP here. One of the motivations for using closed-reference OTU clustering is to splice your sequences into a reference tree, so that you can use that reference tree instead of attempting to build your own from short marker-gene sequences. So after using closed-reference OTU clustering with Greengenes you should just use the associated reference tree from Greengenes, instead of attempting to build your own.

The Greengenes reference tree I think is the same that fragment-insertion uses by default so in theory it looks like you are just trying to clone this tree with a subset of the reference sequences, which is a redundant exercise.

I hope that helps!

1 Like

Thanks very much for your reply! I am a little confused with this part. I tried qiime phylogeny align-to-tree-mafft-fasttree and qiime fragment-insertion sepp to construct tree.qza, and the latter separated my samples better. I understand that using sepp-refs-gg-13-8.qza after closed-reference clustering is redundant. I don’t understand why it goes wrong with sepp-refs-gg-13-8.qza after clustering with 97_otus-gg138.qza but it’s ok after using 97_otus-silva.qza. In my understanding, if I align the sequences using 97_otus-gg138.qza, then it’s quicker when align them using sepp-refs-gg-13-8.qza. So I would be really grateful if you can tell me how I misunderstand this part.

Yes that is expected, but both are unnecessary after using closed-reference OTU clustering, since you should just use the greengenes reference tree instead of trying to build your own.

I also do not know why this would error. I am pinging @Stefan to see if he may have an idea. Since this is not a normal operation (using SEPP after closed-ref OTU clustering) this is not an error that is really worth troubleshooting, but it could be of interest to the q2-fragment-insertion developers. Thanks for reporting this @Ryuk!

@Ryuk,
Could you please re-run sepp with the --p-debug option, and share the output here? Thanks.

Yes that is expected, but both are unnecessary after using closed-reference OTU clustering, since you should just use the greengenes reference tree instead of trying to build your own.

I am a rookie so actually don’t know how to use the greengene reference after closed-reference OTU to generate tree.qza. So I would be really grateful if you could give me a clue.

Could you please re-run sepp with the --p-debug option, and share the output here? Thanks.

I run the command with --p-debug option and here’s the results:
Plugin error from fragment-insertion:

  Command '['run-sepp.sh', '/tmp/qiime2-archive-qzbe0rtu/a4999c1c-3669-432e-a06d-1447be00583f/data/dna-sequences.fasta', 'q2-fragment-insertion', '-x', '48', '-A', '1000', '-P', '5000', '-a', '/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta', '-t', '/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk', '-r', '/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt', '-b', '1']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-13eeq2gp.log

And here’s the log:
========= Execution of SEPP failed with exit code 1 =================
temporary working directories are NOT deleted for further inspection:
$tmp = /tmp/tmp.2VC8I2fH9G/sepp-tmp-uvrrg0RcRj
$tmpssd = /tmp/tmp.2VC8I2fH9G/sepp-tempssd-m2oYbz8Yfl
--------- Content of STDOUT -----------------------------------------
--------- Content of STDERR -----------------------------------------
[10:37:10] config.py (line 315): DEBUG: Main configuration file at /home/bio/Softs/miniconda3/envs/qiime2-2019.10/share/sepp/sepp/main.config
[10:37:10] config.py (line 349): INFO: Seed number: 297834
[10:37:10] algorithm.py (line 259): INFO: Reading input alignment: <_io.TextIOWrapper name=’/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta’ mode=β€˜r’ encoding=β€˜UTF-8’>
[10:37:12] algorithm.py (line 265): INFO: Reading input tree: <_io.TextIOWrapper name=’/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk’ mode=β€˜r’ encoding=β€˜UTF-8’>
[10:37:49] algorithm.py (line 240): INFO: Decomposition Sizes are set to alignment: 1000 placement: 5000
[10:38:15] tree.py (line 341): DEBUG: breaking_edge length = 0.011286416230032107, centroid
[10:38:17] tree.py (line 347): DEBUG: Tree 1 has 102088 nodes, tree 2 has 101364 nodes
[10:38:18] tree.py (line 341): DEBUG: breaking_edge length = 0.019165971284648108, centroid
[10:38:19] tree.py (line 347): DEBUG: Tree 1 has 57063 nodes, tree 2 has 45025 nodes
[10:38:20] tree.py (line 341): DEBUG: breaking_edge length = 0.007525566770650204, centroid
[10:38:20] tree.py (line 347): DEBUG: Tree 1 has 28927 nodes, tree 2 has 28136 nodes
[10:38:20] tree.py (line 341): DEBUG: breaking_edge length = 0.008253743433561687, centroid
[10:38:21] tree.py (line 347): DEBUG: Tree 1 has 11918 nodes, tree 2 has 17009 nodes
[10:38:21] tree.py (line 341): DEBUG: breaking_edge length = 0.009282369381384914, centroid
[10:38:21] tree.py (line 347): DEBUG: Tree 1 has 5762 nodes, tree 2 has 6156 nodes
[10:38:21] tree.py (line 341): DEBUG: breaking_edge length = 0.0065597563932948515, centroid
[10:38:21] tree.py (line 347): DEBUG: Tree 1 has 2880 nodes, tree 2 has 2882 nodes
[10:38:21] tree.py (line 341): DEBUG: breaking_edge length = 0.0014239269691207106, centroid
[10:38:21] tree.py (line 347): DEBUG: Tree 1 has 3030 nodes, tree 2 has 3126 nodes
[10:38:21] tree.py (line 341): DEBUG: breaking_edge length = 0.005853272863988634, centroid
[10:38:21] tree.py (line 347): DEBUG: Tree 1 has 8092 nodes, tree 2 has 8917 nodes
[10:38:22] tree.py (line 341): DEBUG: breaking_edge length = 0.003986692067426808, centroid
[10:38:22] tree.py (line 347): DEBUG: Tree 1 has 3944 nodes, tree 2 has 4148 nodes
[10:38:22] tree.py (line 341): DEBUG: breaking_edge length = 0.005298815532455535, centroid
[10:38:22] tree.py (line 347): DEBUG: Tree 1 has 3147 nodes, tree 2 has 5770 nodes
[10:38:22] tree.py (line 341): DEBUG: breaking_edge length = 0.002373523320650732, centroid
[10:38:22] tree.py (line 347): DEBUG: Tree 1 has 2931 nodes, tree 2 has 2839 nodes
[10:38:22] tree.py (line 341): DEBUG: breaking_edge length = 0.011364674205169007, centroid
[10:38:22] tree.py (line 347): DEBUG: Tree 1 has 15197 nodes, tree 2 has 12939 nodes
[10:38:23] tree.py (line 341): DEBUG: breaking_edge length = 0.0025821787215626014, centroid
[10:38:23] tree.py (line 347): DEBUG: Tree 1 has 7236 nodes, tree 2 has 7961 nodes
[10:38:23] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:23] tree.py (line 347): DEBUG: Tree 1 has 3354 nodes, tree 2 has 3882 nodes
[10:38:23] tree.py (line 341): DEBUG: breaking_edge length = 0.008525324509034187, centroid
[10:38:23] tree.py (line 347): DEBUG: Tree 1 has 4227 nodes, tree 2 has 3734 nodes
[10:38:23] tree.py (line 341): DEBUG: breaking_edge length = 0.019472514885203268, centroid
[10:38:23] tree.py (line 347): DEBUG: Tree 1 has 6629 nodes, tree 2 has 6310 nodes
[10:38:23] tree.py (line 341): DEBUG: breaking_edge length = 0.007756022049913704, centroid
[10:38:23] tree.py (line 347): DEBUG: Tree 1 has 3140 nodes, tree 2 has 3489 nodes
[10:38:23] tree.py (line 341): DEBUG: breaking_edge length = 0.010672100991138422, centroid
[10:38:23] tree.py (line 347): DEBUG: Tree 1 has 3002 nodes, tree 2 has 3308 nodes
[10:38:24] tree.py (line 341): DEBUG: breaking_edge length = 0.011081495491701414, centroid
[10:38:24] tree.py (line 347): DEBUG: Tree 1 has 21461 nodes, tree 2 has 23564 nodes
[10:38:25] tree.py (line 341): DEBUG: breaking_edge length = 0.0026184044258968104, centroid
[10:38:25] tree.py (line 347): DEBUG: Tree 1 has 9825 nodes, tree 2 has 11636 nodes
[10:38:25] tree.py (line 341): DEBUG: breaking_edge length = 0.005480817119908248, centroid
[10:38:25] tree.py (line 347): DEBUG: Tree 1 has 4004 nodes, tree 2 has 5821 nodes
[10:38:25] tree.py (line 341): DEBUG: breaking_edge length = 0.004502502988216382, centroid
[10:38:25] tree.py (line 347): DEBUG: Tree 1 has 2609 nodes, tree 2 has 3212 nodes
[10:38:25] tree.py (line 341): DEBUG: breaking_edge length = 0.00595727102721055, centroid
[10:38:25] tree.py (line 347): DEBUG: Tree 1 has 5758 nodes, tree 2 has 5878 nodes
[10:38:25] tree.py (line 341): DEBUG: breaking_edge length = 0.010124145180426442, centroid
[10:38:25] tree.py (line 347): DEBUG: Tree 1 has 2466 nodes, tree 2 has 3292 nodes
[10:38:25] tree.py (line 341): DEBUG: breaking_edge length = 0.019265073755401985, centroid
[10:38:25] tree.py (line 347): DEBUG: Tree 1 has 2530 nodes, tree 2 has 3348 nodes
[10:38:26] tree.py (line 341): DEBUG: breaking_edge length = 0.009164998230994032, centroid
[10:38:26] tree.py (line 347): DEBUG: Tree 1 has 11001 nodes, tree 2 has 12563 nodes
[10:38:26] tree.py (line 341): DEBUG: breaking_edge length = 0.016055961086158668, centroid
[10:38:26] tree.py (line 347): DEBUG: Tree 1 has 6466 nodes, tree 2 has 4535 nodes
[10:38:26] tree.py (line 341): DEBUG: breaking_edge length = 0.024069274087150695, centroid
[10:38:26] tree.py (line 347): DEBUG: Tree 1 has 2800 nodes, tree 2 has 3666 nodes
[10:38:26] tree.py (line 341): DEBUG: breaking_edge length = 0.009249765840572695, centroid
[10:38:26] tree.py (line 347): DEBUG: Tree 1 has 5003 nodes, tree 2 has 7560 nodes
[10:38:26] tree.py (line 341): DEBUG: breaking_edge length = 0.004903609384928019, centroid
[10:38:27] tree.py (line 347): DEBUG: Tree 1 has 2583 nodes, tree 2 has 2420 nodes
[10:38:27] tree.py (line 341): DEBUG: breaking_edge length = 0.010932097833641003, centroid
[10:38:27] tree.py (line 347): DEBUG: Tree 1 has 3360 nodes, tree 2 has 4200 nodes
[10:38:28] tree.py (line 341): DEBUG: breaking_edge length = 0.021686306460503176, centroid
[10:38:29] tree.py (line 347): DEBUG: Tree 1 has 49576 nodes, tree 2 has 51788 nodes
[10:38:29] tree.py (line 341): DEBUG: breaking_edge length = 0.006124603192402527, centroid
[10:38:30] tree.py (line 347): DEBUG: Tree 1 has 19676 nodes, tree 2 has 29900 nodes
[10:38:30] tree.py (line 341): DEBUG: breaking_edge length = 0.03318057456069088, centroid
[10:38:30] tree.py (line 347): DEBUG: Tree 1 has 7849 nodes, tree 2 has 11827 nodes
[10:38:30] tree.py (line 341): DEBUG: breaking_edge length = 0.008355171165723525, centroid
[10:38:30] tree.py (line 347): DEBUG: Tree 1 has 3490 nodes, tree 2 has 4359 nodes
[10:38:30] tree.py (line 341): DEBUG: breaking_edge length = 0.01908179455710282, centroid
[10:38:31] tree.py (line 347): DEBUG: Tree 1 has 6559 nodes, tree 2 has 5268 nodes
[10:38:31] tree.py (line 341): DEBUG: breaking_edge length = 0.008097858779601709, centroid
[10:38:31] tree.py (line 347): DEBUG: Tree 1 has 3361 nodes, tree 2 has 3198 nodes
[10:38:31] tree.py (line 341): DEBUG: breaking_edge length = 0.006268505722548297, centroid
[10:38:31] tree.py (line 347): DEBUG: Tree 1 has 2877 nodes, tree 2 has 2391 nodes
[10:38:31] tree.py (line 341): DEBUG: breaking_edge length = 0.020951519195480314, centroid
[10:38:31] tree.py (line 347): DEBUG: Tree 1 has 16832 nodes, tree 2 has 13068 nodes
[10:38:31] tree.py (line 341): DEBUG: breaking_edge length = 0.005678262679271758, centroid
[10:38:32] tree.py (line 347): DEBUG: Tree 1 has 8101 nodes, tree 2 has 8731 nodes
[10:38:32] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:32] tree.py (line 347): DEBUG: Tree 1 has 4093 nodes, tree 2 has 4008 nodes
[10:38:32] tree.py (line 341): DEBUG: breaking_edge length = 0.01330068265240652, centroid
[10:38:32] tree.py (line 347): DEBUG: Tree 1 has 5257 nodes, tree 2 has 3474 nodes
[10:38:32] tree.py (line 341): DEBUG: breaking_edge length = 0.013369602899790717, centroid
[10:38:32] tree.py (line 347): DEBUG: Tree 1 has 2637 nodes, tree 2 has 2620 nodes
[10:38:32] tree.py (line 341): DEBUG: breaking_edge length = 0.005509623929184219, centroid
[10:38:32] tree.py (line 347): DEBUG: Tree 1 has 6017 nodes, tree 2 has 7051 nodes
[10:38:32] tree.py (line 341): DEBUG: breaking_edge length = 0.009082985981155096, centroid
[10:38:32] tree.py (line 347): DEBUG: Tree 1 has 3163 nodes, tree 2 has 2854 nodes
[10:38:33] tree.py (line 341): DEBUG: breaking_edge length = 0.02324545624709188, centroid
[10:38:33] tree.py (line 347): DEBUG: Tree 1 has 4540 nodes, tree 2 has 2511 nodes
[10:38:33] tree.py (line 341): DEBUG: breaking_edge length = 0.03744292117262364, centroid
[10:38:34] tree.py (line 347): DEBUG: Tree 1 has 25811 nodes, tree 2 has 25977 nodes
[10:38:34] tree.py (line 341): DEBUG: breaking_edge length = 0.01848701921060616, centroid
[10:38:34] tree.py (line 347): DEBUG: Tree 1 has 12116 nodes, tree 2 has 13695 nodes
[10:38:34] tree.py (line 341): DEBUG: breaking_edge length = 0.005124727016921674, centroid
[10:38:34] tree.py (line 347): DEBUG: Tree 1 has 6079 nodes, tree 2 has 6037 nodes
[10:38:34] tree.py (line 341): DEBUG: breaking_edge length = 0.008756625605911436, centroid
[10:38:34] tree.py (line 347): DEBUG: Tree 1 has 3196 nodes, tree 2 has 2883 nodes
[10:38:35] tree.py (line 341): DEBUG: breaking_edge length = 0.026821326104941437, centroid
[10:38:35] tree.py (line 347): DEBUG: Tree 1 has 3232 nodes, tree 2 has 2805 nodes
[10:38:35] tree.py (line 341): DEBUG: breaking_edge length = 0.012302737280561705, centroid
[10:38:35] tree.py (line 347): DEBUG: Tree 1 has 7622 nodes, tree 2 has 6073 nodes
[10:38:35] tree.py (line 341): DEBUG: breaking_edge length = 0.01508695542224731, centroid
[10:38:35] tree.py (line 347): DEBUG: Tree 1 has 4083 nodes, tree 2 has 3539 nodes
[10:38:35] tree.py (line 341): DEBUG: breaking_edge length = 0.018353602680109223, centroid
[10:38:35] tree.py (line 347): DEBUG: Tree 1 has 2328 nodes, tree 2 has 3745 nodes
[10:38:35] tree.py (line 341): DEBUG: breaking_edge length = 0.02379218672494081, centroid
[10:38:36] tree.py (line 347): DEBUG: Tree 1 has 14876 nodes, tree 2 has 11101 nodes
[10:38:36] tree.py (line 341): DEBUG: breaking_edge length = 0.015041459748877366, centroid
[10:38:36] tree.py (line 347): DEBUG: Tree 1 has 6947 nodes, tree 2 has 7929 nodes
[10:38:36] tree.py (line 341): DEBUG: breaking_edge length = 0.0037434274706524633, centroid
[10:38:36] tree.py (line 347): DEBUG: Tree 1 has 3110 nodes, tree 2 has 3837 nodes
[10:38:36] tree.py (line 341): DEBUG: breaking_edge length = 0.008890822484579883, centroid
[10:38:36] tree.py (line 347): DEBUG: Tree 1 has 3520 nodes, tree 2 has 4409 nodes
[10:38:36] tree.py (line 341): DEBUG: breaking_edge length = 0.009114024962735718, centroid
[10:38:36] tree.py (line 347): DEBUG: Tree 1 has 5317 nodes, tree 2 has 5784 nodes
[10:38:36] tree.py (line 341): DEBUG: breaking_edge length = 0.009112119966961336, centroid
[10:38:36] tree.py (line 347): DEBUG: Tree 1 has 2039 nodes, tree 2 has 3278 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 0.016139167780924484, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 2954 nodes, tree 2 has 2830 nodes
[10:38:37] exhaustive.py (line 351): INFO: Breaking into 62 placement subsets.
[10:38:37] exhaustive.py (line 363): DEBUG: Placement subset P_0 has 2880 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 0.00935442039870685, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 1528 nodes, tree 2 has 1352 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 0.0076468354818962124, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 616 nodes, tree 2 has 912 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 506 nodes, tree 2 has 846 nodes
[10:38:37] exhaustive.py (line 384): DEBUG: Placement subset P_0 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:37] exhaustive.py (line 388): DEBUG: Placement subset P_0 has 2880 taxa:
[10:38:37] exhaustive.py (line 363): DEBUG: Placement subset P_1 has 2882 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 0.01832626683131673, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 1345 nodes, tree 2 has 1537 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 0.0048994738498321635, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 502 nodes, tree 2 has 843 nodes
[10:38:37] tree.py (line 341): DEBUG: breaking_edge length = 0.011733488040192514, centroid
[10:38:37] tree.py (line 347): DEBUG: Tree 1 has 765 nodes, tree 2 has 772 nodes
[10:38:37] exhaustive.py (line 384): DEBUG: Placement subset P_1 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:37] exhaustive.py (line 388): DEBUG: Placement subset P_1 has 2882 taxa:
[10:38:37] exhaustive.py (line 363): DEBUG: Placement subset P_2 has 3030 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.011464547972173448, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 1461 nodes, tree 2 has 1569 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.012871733516959472, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 639 nodes, tree 2 has 822 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.024852045817883812, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 676 nodes, tree 2 has 893 nodes
[10:38:38] exhaustive.py (line 384): DEBUG: Placement subset P_2 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:38] exhaustive.py (line 388): DEBUG: Placement subset P_2 has 3030 taxa:
[10:38:38] exhaustive.py (line 363): DEBUG: Placement subset P_3 has 3126 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.005430839521740418, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 1684 nodes, tree 2 has 1442 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.032301310653248164, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 941 nodes, tree 2 has 743 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.0006446879400051927, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 823 nodes, tree 2 has 619 nodes
[10:38:38] exhaustive.py (line 384): DEBUG: Placement subset P_3 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:38] exhaustive.py (line 388): DEBUG: Placement subset P_3 has 3126 taxa:
[10:38:38] exhaustive.py (line 363): DEBUG: Placement subset P_4 has 3944 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.005833813057961295, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 1951 nodes, tree 2 has 1993 nodes
[10:38:38] tree.py (line 341): DEBUG: breaking_edge length = 0.0027379015429108765, centroid
[10:38:38] tree.py (line 347): DEBUG: Tree 1 has 1057 nodes, tree 2 has 894 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.007128566041691296, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 505 nodes, tree 2 has 552 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.004532254554751639, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 807 nodes, tree 2 has 1186 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.011389118710383915, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 699 nodes, tree 2 has 487 nodes
[10:38:39] exhaustive.py (line 384): DEBUG: Placement subset P_4 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:38:39] exhaustive.py (line 388): DEBUG: Placement subset P_4 has 3944 taxa:
[10:38:39] exhaustive.py (line 363): DEBUG: Placement subset P_5 has 4148 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.00538051043869418, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 1928 nodes, tree 2 has 2220 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 1001 nodes, tree 2 has 927 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.007030295139389666, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 559 nodes, tree 2 has 442 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.002416131389361286, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 1131 nodes, tree 2 has 1089 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.0024012191470116056, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 569 nodes, tree 2 has 562 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.004261142938405837, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 533 nodes, tree 2 has 556 nodes
[10:38:39] exhaustive.py (line 384): DEBUG: Placement subset P_5 has 7 alignment subsets: [0, 1, 2, 3, 4, 5, 6]
[10:38:39] exhaustive.py (line 388): DEBUG: Placement subset P_5 has 4148 taxa:
[10:38:39] exhaustive.py (line 363): DEBUG: Placement subset P_6 has 3147 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.003334551692780699, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 1502 nodes, tree 2 has 1645 nodes
[10:38:39] tree.py (line 341): DEBUG: breaking_edge length = 0.009884851705649178, centroid
[10:38:39] tree.py (line 347): DEBUG: Tree 1 has 692 nodes, tree 2 has 810 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.007716645541986607, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 776 nodes, tree 2 has 869 nodes
[10:38:40] exhaustive.py (line 384): DEBUG: Placement subset P_6 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:40] exhaustive.py (line 388): DEBUG: Placement subset P_6 has 3147 taxa:
[10:38:40] exhaustive.py (line 363): DEBUG: Placement subset P_7 has 2931 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.0049059230365094955, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 1463 nodes, tree 2 has 1468 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.008266358302178683, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 559 nodes, tree 2 has 904 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.007322155913788179, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 655 nodes, tree 2 has 813 nodes
[10:38:40] exhaustive.py (line 384): DEBUG: Placement subset P_7 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:40] exhaustive.py (line 388): DEBUG: Placement subset P_7 has 2931 taxa:
[10:38:40] exhaustive.py (line 363): DEBUG: Placement subset P_8 has 2839 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.006924347484982536, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 1490 nodes, tree 2 has 1349 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.001598892417978356, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 751 nodes, tree 2 has 739 nodes
[10:38:40] tree.py (line 341): DEBUG: breaking_edge length = 0.0038759861281452705, centroid
[10:38:40] tree.py (line 347): DEBUG: Tree 1 has 751 nodes, tree 2 has 598 nodes
[10:38:40] exhaustive.py (line 384): DEBUG: Placement subset P_8 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:40] exhaustive.py (line 388): DEBUG: Placement subset P_8 has 2839 taxa:
[10:38:40] exhaustive.py (line 363): DEBUG: Placement subset P_9 has 3354 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 1502 nodes, tree 2 has 1852 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 624 nodes, tree 2 has 878 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 0.00538682284408089, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 928 nodes, tree 2 has 924 nodes
[10:38:41] exhaustive.py (line 384): DEBUG: Placement subset P_9 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:41] exhaustive.py (line 388): DEBUG: Placement subset P_9 has 3354 taxa:
[10:38:41] exhaustive.py (line 363): DEBUG: Placement subset P_10 has 3882 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 0.0009274694863467721, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 1567 nodes, tree 2 has 2315 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 0.0023744807782685126, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 639 nodes, tree 2 has 928 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 0.005979661808469399, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 1338 nodes, tree 2 has 977 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 0.005182447687179944, centroid
[10:38:41] tree.py (line 347): DEBUG: Tree 1 has 614 nodes, tree 2 has 724 nodes
[10:38:41] exhaustive.py (line 384): DEBUG: Placement subset P_10 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:41] exhaustive.py (line 388): DEBUG: Placement subset P_10 has 3882 taxa:
[10:38:41] exhaustive.py (line 363): DEBUG: Placement subset P_11 has 4227 nodes
[10:38:41] tree.py (line 341): DEBUG: breaking_edge length = 0.00226427984361924, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 2066 nodes, tree 2 has 2161 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 1058 nodes, tree 2 has 1008 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 469 nodes, tree 2 has 589 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 507 nodes, tree 2 has 501 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.0048709864777869375, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 1232 nodes, tree 2 has 929 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.029397755528747092, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 650 nodes, tree 2 has 582 nodes
[10:38:42] exhaustive.py (line 384): DEBUG: Placement subset P_11 has 7 alignment subsets: [0, 1, 2, 3, 4, 5, 6]
[10:38:42] exhaustive.py (line 388): DEBUG: Placement subset P_11 has 4227 taxa:
[10:38:42] exhaustive.py (line 363): DEBUG: Placement subset P_12 has 3734 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.019328795873724706, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 2030 nodes, tree 2 has 1704 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.006993954625156256, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 1081 nodes, tree 2 has 949 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.02375108030188694, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 629 nodes, tree 2 has 452 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.002431634709901127, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 930 nodes, tree 2 has 774 nodes
[10:38:42] exhaustive.py (line 384): DEBUG: Placement subset P_12 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:42] exhaustive.py (line 388): DEBUG: Placement subset P_12 has 3734 taxa:
[10:38:42] exhaustive.py (line 363): DEBUG: Placement subset P_13 has 3140 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.008372007732527222, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 1988 nodes, tree 2 has 1152 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.017386979187756644, centroid
[10:38:42] tree.py (line 347): DEBUG: Tree 1 has 1084 nodes, tree 2 has 904 nodes
[10:38:42] tree.py (line 341): DEBUG: breaking_edge length = 0.008071687030202071, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 372 nodes, tree 2 has 712 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.009630603491061557, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 520 nodes, tree 2 has 632 nodes
[10:38:43] exhaustive.py (line 384): DEBUG: Placement subset P_13 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:43] exhaustive.py (line 388): DEBUG: Placement subset P_13 has 3140 taxa:
[10:38:43] exhaustive.py (line 363): DEBUG: Placement subset P_14 has 3489 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.007454667437222568, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 1546 nodes, tree 2 has 1943 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.003892402805227049, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 677 nodes, tree 2 has 869 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.004436570609331216, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 1068 nodes, tree 2 has 875 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.004768537449755016, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 533 nodes, tree 2 has 535 nodes
[10:38:43] exhaustive.py (line 384): DEBUG: Placement subset P_14 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:43] exhaustive.py (line 388): DEBUG: Placement subset P_14 has 3489 taxa:
[10:38:43] exhaustive.py (line 363): DEBUG: Placement subset P_15 has 3002 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.0076614065297279845, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 1413 nodes, tree 2 has 1589 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.013399745609852343, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 749 nodes, tree 2 has 664 nodes
[10:38:43] tree.py (line 341): DEBUG: breaking_edge length = 0.0120780900651376, centroid
[10:38:43] tree.py (line 347): DEBUG: Tree 1 has 845 nodes, tree 2 has 744 nodes
[10:38:43] exhaustive.py (line 384): DEBUG: Placement subset P_15 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:43] exhaustive.py (line 388): DEBUG: Placement subset P_15 has 3002 taxa:
[10:38:43] exhaustive.py (line 363): DEBUG: Placement subset P_16 has 3308 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.01003707972709339, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 1424 nodes, tree 2 has 1884 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.01069659325385671, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 705 nodes, tree 2 has 719 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.01192242157692702, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 968 nodes, tree 2 has 916 nodes
[10:38:44] exhaustive.py (line 384): DEBUG: Placement subset P_16 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:44] exhaustive.py (line 388): DEBUG: Placement subset P_16 has 3308 taxa:
[10:38:44] exhaustive.py (line 363): DEBUG: Placement subset P_17 has 4004 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.0024047484462297423, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 1995 nodes, tree 2 has 2009 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.007740242944830139, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 971 nodes, tree 2 has 1024 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.013907402757600239, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 544 nodes, tree 2 has 480 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.00319339140448722, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 1168 nodes, tree 2 has 841 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.0022577028062313012, centroid
[10:38:44] tree.py (line 347): DEBUG: Tree 1 has 588 nodes, tree 2 has 580 nodes
[10:38:44] exhaustive.py (line 384): DEBUG: Placement subset P_17 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:38:44] exhaustive.py (line 388): DEBUG: Placement subset P_17 has 4004 taxa:
[10:38:44] exhaustive.py (line 363): DEBUG: Placement subset P_18 has 2609 nodes
[10:38:44] tree.py (line 341): DEBUG: breaking_edge length = 0.006422874793509993, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 1202 nodes, tree 2 has 1407 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.004049710434532913, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 589 nodes, tree 2 has 613 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.0033699456631077064, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 670 nodes, tree 2 has 737 nodes
[10:38:45] exhaustive.py (line 384): DEBUG: Placement subset P_18 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:45] exhaustive.py (line 388): DEBUG: Placement subset P_18 has 2609 taxa:
[10:38:45] exhaustive.py (line 363): DEBUG: Placement subset P_19 has 3212 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.006170362560038824, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 1643 nodes, tree 2 has 1569 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.0063900639115986565, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 598 nodes, tree 2 has 1045 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.010652842168268777, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 520 nodes, tree 2 has 525 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.005533667510828335, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 743 nodes, tree 2 has 826 nodes
[10:38:45] exhaustive.py (line 384): DEBUG: Placement subset P_19 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:45] exhaustive.py (line 388): DEBUG: Placement subset P_19 has 3212 taxa:
[10:38:45] exhaustive.py (line 363): DEBUG: Placement subset P_20 has 2466 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.0016087326873544545, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 1248 nodes, tree 2 has 1218 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.001614954775377712, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 682 nodes, tree 2 has 566 nodes
[10:38:45] tree.py (line 341): DEBUG: breaking_edge length = 0.00328555762552318, centroid
[10:38:45] tree.py (line 347): DEBUG: Tree 1 has 642 nodes, tree 2 has 576 nodes
[10:38:45] exhaustive.py (line 384): DEBUG: Placement subset P_20 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:45] exhaustive.py (line 388): DEBUG: Placement subset P_20 has 2466 taxa:
[10:38:45] exhaustive.py (line 363): DEBUG: Placement subset P_21 has 3292 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.013187058826826126, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 1698 nodes, tree 2 has 1594 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.0037295652503947815, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 844 nodes, tree 2 has 854 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.040402986259688564, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 1020 nodes, tree 2 has 574 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.017255785714992672, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 525 nodes, tree 2 has 495 nodes
[10:38:46] exhaustive.py (line 384): DEBUG: Placement subset P_21 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:46] exhaustive.py (line 388): DEBUG: Placement subset P_21 has 3292 taxa:
[10:38:46] exhaustive.py (line 363): DEBUG: Placement subset P_22 has 2530 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.007684204417191333, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 1278 nodes, tree 2 has 1252 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.0037868837244449437, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 648 nodes, tree 2 has 630 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.024682311804702685, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 751 nodes, tree 2 has 501 nodes
[10:38:46] exhaustive.py (line 384): DEBUG: Placement subset P_22 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:46] exhaustive.py (line 388): DEBUG: Placement subset P_22 has 2530 taxa:
[10:38:46] exhaustive.py (line 363): DEBUG: Placement subset P_23 has 3348 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.006147227312350953, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 1669 nodes, tree 2 has 1679 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.009626012906821508, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 845 nodes, tree 2 has 824 nodes
[10:38:46] tree.py (line 341): DEBUG: breaking_edge length = 0.02735763448015751, centroid
[10:38:46] tree.py (line 347): DEBUG: Tree 1 has 696 nodes, tree 2 has 983 nodes
[10:38:46] exhaustive.py (line 384): DEBUG: Placement subset P_23 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:46] exhaustive.py (line 388): DEBUG: Placement subset P_23 has 3348 taxa:
[10:38:46] exhaustive.py (line 363): DEBUG: Placement subset P_24 has 2800 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 0.01668687961088385, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 1340 nodes, tree 2 has 1460 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 0.0033699962347591575, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 839 nodes, tree 2 has 501 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 0.009575913578913516, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 711 nodes, tree 2 has 749 nodes
[10:38:47] exhaustive.py (line 384): DEBUG: Placement subset P_24 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:47] exhaustive.py (line 388): DEBUG: Placement subset P_24 has 2800 taxa:
[10:38:47] exhaustive.py (line 363): DEBUG: Placement subset P_25 has 3666 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 0.012484577139763683, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 1824 nodes, tree 2 has 1842 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 1093 nodes, tree 2 has 731 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 0.0036296227751344444, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 616 nodes, tree 2 has 477 nodes
[10:38:47] tree.py (line 341): DEBUG: breaking_edge length = 0.03101453781466249, centroid
[10:38:47] tree.py (line 347): DEBUG: Tree 1 has 872 nodes, tree 2 has 970 nodes
[10:38:47] exhaustive.py (line 384): DEBUG: Placement subset P_25 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:47] exhaustive.py (line 388): DEBUG: Placement subset P_25 has 3666 taxa:
[10:38:47] exhaustive.py (line 363): DEBUG: Placement subset P_26 has 4535 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.006026876442421737, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 1812 nodes, tree 2 has 2723 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.01949962572577154, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 917 nodes, tree 2 has 895 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.012076784021962269, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 1369 nodes, tree 2 has 1354 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.003037012040590945, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 679 nodes, tree 2 has 690 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.015661231306387767, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 664 nodes, tree 2 has 690 nodes
[10:38:48] exhaustive.py (line 384): DEBUG: Placement subset P_26 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:38:48] exhaustive.py (line 388): DEBUG: Placement subset P_26 has 4535 taxa:
[10:38:48] exhaustive.py (line 363): DEBUG: Placement subset P_27 has 2583 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.012582899494831436, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 1537 nodes, tree 2 has 1046 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.010521289712348253, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 804 nodes, tree 2 has 733 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.012287276455992197, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 502 nodes, tree 2 has 544 nodes
[10:38:48] exhaustive.py (line 384): DEBUG: Placement subset P_27 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:48] exhaustive.py (line 388): DEBUG: Placement subset P_27 has 2583 taxa:
[10:38:48] exhaustive.py (line 363): DEBUG: Placement subset P_28 has 2420 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.011106007962038127, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 1147 nodes, tree 2 has 1273 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.017569695061335516, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 570 nodes, tree 2 has 577 nodes
[10:38:48] tree.py (line 341): DEBUG: breaking_edge length = 0.013784455816882169, centroid
[10:38:48] tree.py (line 347): DEBUG: Tree 1 has 545 nodes, tree 2 has 728 nodes
[10:38:48] exhaustive.py (line 384): DEBUG: Placement subset P_28 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:48] exhaustive.py (line 388): DEBUG: Placement subset P_28 has 2420 taxa:
[10:38:48] exhaustive.py (line 363): DEBUG: Placement subset P_29 has 3360 nodes
[10:38:53] tree.py (line 341): DEBUG: breaking_edge length = 0.014592312968043515, centroid
[10:38:53] tree.py (line 347): DEBUG: Tree 1 has 1333 nodes, tree 2 has 2027 nodes
[10:38:53] tree.py (line 341): DEBUG: breaking_edge length = 0.028053363220467913, centroid
[10:38:53] tree.py (line 347): DEBUG: Tree 1 has 679 nodes, tree 2 has 654 nodes
[10:38:53] tree.py (line 341): DEBUG: breaking_edge length = 0.01137323181557509, centroid
[10:38:53] tree.py (line 347): DEBUG: Tree 1 has 1039 nodes, tree 2 has 988 nodes
[10:38:53] tree.py (line 341): DEBUG: breaking_edge length = 0.010931251860729943, centroid
[10:38:53] tree.py (line 347): DEBUG: Tree 1 has 525 nodes, tree 2 has 514 nodes
[10:38:53] exhaustive.py (line 384): DEBUG: Placement subset P_29 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:53] exhaustive.py (line 388): DEBUG: Placement subset P_29 has 3360 taxa:
[10:38:53] exhaustive.py (line 363): DEBUG: Placement subset P_30 has 4200 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.01709828972661003, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 2181 nodes, tree 2 has 2019 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.04872756789902086, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 1064 nodes, tree 2 has 1117 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.009453267560602352, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 531 nodes, tree 2 has 533 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.010696109888666254, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 633 nodes, tree 2 has 484 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.013967121110542307, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 913 nodes, tree 2 has 1106 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.016646555011472164, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 523 nodes, tree 2 has 583 nodes
[10:38:54] exhaustive.py (line 384): DEBUG: Placement subset P_30 has 7 alignment subsets: [0, 1, 2, 3, 4, 5, 6]
[10:38:54] exhaustive.py (line 388): DEBUG: Placement subset P_30 has 4200 taxa:
[10:38:54] exhaustive.py (line 363): DEBUG: Placement subset P_31 has 3490 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.0031700197666921577, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 1595 nodes, tree 2 has 1895 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 0.0007908852455579469, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 759 nodes, tree 2 has 836 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 1049 nodes, tree 2 has 846 nodes
[10:38:54] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:54] tree.py (line 347): DEBUG: Tree 1 has 479 nodes, tree 2 has 570 nodes
[10:38:54] exhaustive.py (line 384): DEBUG: Placement subset P_31 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:54] exhaustive.py (line 388): DEBUG: Placement subset P_31 has 3490 taxa:
[10:38:54] exhaustive.py (line 363): DEBUG: Placement subset P_32 has 4359 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.011941697571823538, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 1684 nodes, tree 2 has 2675 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.00482016881507614, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 879 nodes, tree 2 has 805 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.013586753633704615, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 1386 nodes, tree 2 has 1289 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.005793577871124276, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 856 nodes, tree 2 has 530 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.006884255670209848, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 645 nodes, tree 2 has 644 nodes
[10:38:55] exhaustive.py (line 384): DEBUG: Placement subset P_32 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:38:55] exhaustive.py (line 388): DEBUG: Placement subset P_32 has 4359 taxa:
[10:38:55] exhaustive.py (line 363): DEBUG: Placement subset P_33 has 3361 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.0016463991980431552, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 1645 nodes, tree 2 has 1716 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.0007831151129813372, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 635 nodes, tree 2 has 1010 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.0017091138426460323, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 490 nodes, tree 2 has 520 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.009754466557039947, centroid
[10:38:55] tree.py (line 347): DEBUG: Tree 1 has 855 nodes, tree 2 has 861 nodes
[10:38:55] exhaustive.py (line 384): DEBUG: Placement subset P_33 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:55] exhaustive.py (line 388): DEBUG: Placement subset P_33 has 3361 taxa:
[10:38:55] exhaustive.py (line 363): DEBUG: Placement subset P_34 has 3198 nodes
[10:38:55] tree.py (line 341): DEBUG: breaking_edge length = 0.014652258629655423, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 1703 nodes, tree 2 has 1495 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.006253965861260327, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 836 nodes, tree 2 has 867 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 743 nodes, tree 2 has 752 nodes
[10:38:56] exhaustive.py (line 384): DEBUG: Placement subset P_34 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:56] exhaustive.py (line 388): DEBUG: Placement subset P_34 has 3198 taxa:
[10:38:56] exhaustive.py (line 363): DEBUG: Placement subset P_35 has 2877 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.002205730886966342, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 1469 nodes, tree 2 has 1408 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.013641925172654135, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 681 nodes, tree 2 has 788 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.004137210617775521, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 521 nodes, tree 2 has 887 nodes
[10:38:56] exhaustive.py (line 384): DEBUG: Placement subset P_35 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:56] exhaustive.py (line 388): DEBUG: Placement subset P_35 has 2877 taxa:
[10:38:56] exhaustive.py (line 363): DEBUG: Placement subset P_36 has 2391 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.005295024768675224, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 1127 nodes, tree 2 has 1264 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.00835995163410181, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 492 nodes, tree 2 has 635 nodes
[10:38:56] tree.py (line 341): DEBUG: breaking_edge length = 0.006653935754997235, centroid
[10:38:56] tree.py (line 347): DEBUG: Tree 1 has 616 nodes, tree 2 has 648 nodes
[10:38:56] exhaustive.py (line 384): DEBUG: Placement subset P_36 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:56] exhaustive.py (line 388): DEBUG: Placement subset P_36 has 2391 taxa:
[10:38:56] exhaustive.py (line 363): DEBUG: Placement subset P_37 has 4093 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.0034496887256853476, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 2050 nodes, tree 2 has 2043 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.010445378255608925, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 900 nodes, tree 2 has 1150 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.012218126161603275, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 580 nodes, tree 2 has 570 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.002406289997825065, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 895 nodes, tree 2 has 1148 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.006203605725158104, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 444 nodes, tree 2 has 704 nodes
[10:38:57] exhaustive.py (line 384): DEBUG: Placement subset P_37 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:38:57] exhaustive.py (line 388): DEBUG: Placement subset P_37 has 4093 taxa:
[10:38:57] exhaustive.py (line 363): DEBUG: Placement subset P_38 has 4008 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.013565428426353525, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 1880 nodes, tree 2 has 2128 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.0006757471832032268, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 909 nodes, tree 2 has 971 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.008878901744903007, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 1195 nodes, tree 2 has 933 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.003730770706577289, centroid
[10:38:57] tree.py (line 347): DEBUG: Tree 1 has 582 nodes, tree 2 has 613 nodes
[10:38:57] exhaustive.py (line 384): DEBUG: Placement subset P_38 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:57] exhaustive.py (line 388): DEBUG: Placement subset P_38 has 4008 taxa:
[10:38:57] exhaustive.py (line 363): DEBUG: Placement subset P_39 has 2637 nodes
[10:38:57] tree.py (line 341): DEBUG: breaking_edge length = 0.010760621752530005, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 1324 nodes, tree 2 has 1313 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.007017359256469025, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 686 nodes, tree 2 has 638 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.016280082884444155, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 675 nodes, tree 2 has 638 nodes
[10:38:58] exhaustive.py (line 384): DEBUG: Placement subset P_39 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:58] exhaustive.py (line 388): DEBUG: Placement subset P_39 has 2637 taxa:
[10:38:58] exhaustive.py (line 363): DEBUG: Placement subset P_40 has 2620 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.010494209513210243, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 1082 nodes, tree 2 has 1538 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.0029370011387167246, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 534 nodes, tree 2 has 548 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.014596890001872594, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 720 nodes, tree 2 has 818 nodes
[10:38:58] exhaustive.py (line 384): DEBUG: Placement subset P_40 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:58] exhaustive.py (line 388): DEBUG: Placement subset P_40 has 2620 taxa:
[10:38:58] exhaustive.py (line 363): DEBUG: Placement subset P_41 has 3474 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.010149513743709062, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 1701 nodes, tree 2 has 1773 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.002293041963446743, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 641 nodes, tree 2 has 1060 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.007182489264630988, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 527 nodes, tree 2 has 533 nodes
[10:38:58] tree.py (line 341): DEBUG: breaking_edge length = 0.0163097487649608, centroid
[10:38:58] tree.py (line 347): DEBUG: Tree 1 has 873 nodes, tree 2 has 900 nodes
[10:38:58] exhaustive.py (line 384): DEBUG: Placement subset P_41 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:38:58] exhaustive.py (line 388): DEBUG: Placement subset P_41 has 3474 taxa:
[10:38:58] exhaustive.py (line 363): DEBUG: Placement subset P_42 has 3163 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 0.008646500349530083, centroid
[10:38:59] tree.py (line 347): DEBUG: Tree 1 has 1474 nodes, tree 2 has 1689 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 0.0036617539819440445, centroid
[10:38:59] tree.py (line 347): DEBUG: Tree 1 has 735 nodes, tree 2 has 739 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 0.006522841177789927, centroid
[10:38:59] tree.py (line 347): DEBUG: Tree 1 has 941 nodes, tree 2 has 748 nodes
[10:38:59] exhaustive.py (line 384): DEBUG: Placement subset P_42 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:59] exhaustive.py (line 388): DEBUG: Placement subset P_42 has 3163 taxa:
[10:38:59] exhaustive.py (line 363): DEBUG: Placement subset P_43 has 2854 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 0.001896472464619754, centroid
[10:38:59] tree.py (line 347): DEBUG: Tree 1 has 1151 nodes, tree 2 has 1703 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:38:59] tree.py (line 347): DEBUG: Tree 1 has 520 nodes, tree 2 has 631 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 0.0075965102984319015, centroid
[10:38:59] tree.py (line 347): DEBUG: Tree 1 has 891 nodes, tree 2 has 812 nodes
[10:38:59] exhaustive.py (line 384): DEBUG: Placement subset P_43 has 4 alignment subsets: [0, 1, 2, 3]
[10:38:59] exhaustive.py (line 388): DEBUG: Placement subset P_43 has 2854 taxa:
[10:38:59] exhaustive.py (line 363): DEBUG: Placement subset P_44 has 4540 nodes
[10:38:59] tree.py (line 341): DEBUG: breaking_edge length = 0.005974498079791249, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 2166 nodes, tree 2 has 2374 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.0022267801721080885, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 1323 nodes, tree 2 has 843 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.01210262704201125, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 563 nodes, tree 2 has 760 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.0008440677677741164, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 1082 nodes, tree 2 has 1292 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.001598523583775668, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 370 nodes, tree 2 has 712 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.0026177296649215753, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 744 nodes, tree 2 has 548 nodes
[10:39:00] exhaustive.py (line 384): DEBUG: Placement subset P_44 has 7 alignment subsets: [0, 1, 2, 3, 4, 5, 6]
[10:39:00] exhaustive.py (line 388): DEBUG: Placement subset P_44 has 4540 taxa:
[10:39:00] exhaustive.py (line 363): DEBUG: Placement subset P_45 has 2511 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.008834908795051504, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 1123 nodes, tree 2 has 1388 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.007095636556766039, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 534 nodes, tree 2 has 589 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.008035263821549654, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 532 nodes, tree 2 has 856 nodes
[10:39:00] exhaustive.py (line 384): DEBUG: Placement subset P_45 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:00] exhaustive.py (line 388): DEBUG: Placement subset P_45 has 2511 taxa:
[10:39:00] exhaustive.py (line 363): DEBUG: Placement subset P_46 has 3196 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.007762717762582742, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 1595 nodes, tree 2 has 1601 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.006034733750266037, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 863 nodes, tree 2 has 732 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.004358431398251882, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 1034 nodes, tree 2 has 567 nodes
[10:39:00] tree.py (line 341): DEBUG: breaking_edge length = 0.017587343214136766, centroid
[10:39:00] tree.py (line 347): DEBUG: Tree 1 has 520 nodes, tree 2 has 514 nodes
[10:39:00] exhaustive.py (line 384): DEBUG: Placement subset P_46 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:39:00] exhaustive.py (line 388): DEBUG: Placement subset P_46 has 3196 taxa:
[10:39:00] exhaustive.py (line 363): DEBUG: Placement subset P_47 has 2883 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.0009437496128607473, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 1193 nodes, tree 2 has 1690 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 1.00000050002909e-06, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 531 nodes, tree 2 has 662 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.002861042009043352, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 856 nodes, tree 2 has 834 nodes
[10:39:01] exhaustive.py (line 384): DEBUG: Placement subset P_47 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:01] exhaustive.py (line 388): DEBUG: Placement subset P_47 has 2883 taxa:
[10:39:01] exhaustive.py (line 363): DEBUG: Placement subset P_48 has 3232 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.0216356170267648, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 1837 nodes, tree 2 has 1395 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.004497009914583751, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 733 nodes, tree 2 has 1104 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.011790107452464895, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 406 nodes, tree 2 has 698 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.0037338353836556693, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 678 nodes, tree 2 has 717 nodes
[10:39:01] exhaustive.py (line 384): DEBUG: Placement subset P_48 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:39:01] exhaustive.py (line 388): DEBUG: Placement subset P_48 has 3232 taxa:
[10:39:01] exhaustive.py (line 363): DEBUG: Placement subset P_49 has 2805 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.006169621116181137, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 1501 nodes, tree 2 has 1304 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.007145073356457818, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 757 nodes, tree 2 has 744 nodes
[10:39:01] tree.py (line 341): DEBUG: breaking_edge length = 0.013742268864964659, centroid
[10:39:01] tree.py (line 347): DEBUG: Tree 1 has 702 nodes, tree 2 has 602 nodes
[10:39:01] exhaustive.py (line 384): DEBUG: Placement subset P_49 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:01] exhaustive.py (line 388): DEBUG: Placement subset P_49 has 2805 taxa:
[10:39:02] exhaustive.py (line 363): DEBUG: Placement subset P_50 has 4083 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.00326678186523618, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 2517 nodes, tree 2 has 1566 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.013049094305145247, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 1260 nodes, tree 2 has 1257 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.0008785700432288079, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 611 nodes, tree 2 has 649 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.0015246577193644226, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 752 nodes, tree 2 has 505 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.01160507180744362, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 808 nodes, tree 2 has 758 nodes
[10:39:02] exhaustive.py (line 384): DEBUG: Placement subset P_50 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:39:02] exhaustive.py (line 388): DEBUG: Placement subset P_50 has 4083 taxa:
[10:39:02] exhaustive.py (line 363): DEBUG: Placement subset P_51 has 3539 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.029869257281909117, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 1670 nodes, tree 2 has 1869 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.006084690315368525, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 816 nodes, tree 2 has 854 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.006334466420572088, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 838 nodes, tree 2 has 1031 nodes
[10:39:02] tree.py (line 341): DEBUG: breaking_edge length = 0.010596795716468542, centroid
[10:39:02] tree.py (line 347): DEBUG: Tree 1 has 468 nodes, tree 2 has 563 nodes
[10:39:02] exhaustive.py (line 384): DEBUG: Placement subset P_51 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:39:02] exhaustive.py (line 388): DEBUG: Placement subset P_51 has 3539 taxa:
[10:39:02] exhaustive.py (line 363): DEBUG: Placement subset P_52 has 2328 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.0045789191306680275, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 996 nodes, tree 2 has 1332 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.01758354076518616, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 650 nodes, tree 2 has 682 nodes
[10:39:03] exhaustive.py (line 384): DEBUG: Placement subset P_52 has 3 alignment subsets: [0, 1, 2]
[10:39:03] exhaustive.py (line 388): DEBUG: Placement subset P_52 has 2328 taxa:
[10:39:03] exhaustive.py (line 363): DEBUG: Placement subset P_53 has 3745 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.007193466974011251, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 2006 nodes, tree 2 has 1739 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.020436275463506542, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 910 nodes, tree 2 has 1096 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.01683891843683715, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 587 nodes, tree 2 has 509 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.01823930090806943, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 766 nodes, tree 2 has 973 nodes
[10:39:03] exhaustive.py (line 384): DEBUG: Placement subset P_53 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:39:03] exhaustive.py (line 388): DEBUG: Placement subset P_53 has 3745 taxa:
[10:39:03] exhaustive.py (line 363): DEBUG: Placement subset P_54 has 3110 nodes
[10:39:03] tree.py (line 341): DEBUG: breaking_edge length = 0.008715336645059609, centroid
[10:39:03] tree.py (line 347): DEBUG: Tree 1 has 1483 nodes, tree 2 has 1627 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.002178112356471838, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 758 nodes, tree 2 has 725 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.009026032409360531, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 829 nodes, tree 2 has 798 nodes
[10:39:04] exhaustive.py (line 384): DEBUG: Placement subset P_54 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:04] exhaustive.py (line 388): DEBUG: Placement subset P_54 has 3110 taxa:
[10:39:04] exhaustive.py (line 363): DEBUG: Placement subset P_55 has 3837 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.0022659513936872247, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 2067 nodes, tree 2 has 1770 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.00915834501304725, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 1015 nodes, tree 2 has 1052 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.010390641368592466, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 489 nodes, tree 2 has 526 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.022288070405784177, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 512 nodes, tree 2 has 540 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.02453309347162251, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 903 nodes, tree 2 has 867 nodes
[10:39:04] exhaustive.py (line 384): DEBUG: Placement subset P_55 has 6 alignment subsets: [0, 1, 2, 3, 4, 5]
[10:39:04] exhaustive.py (line 388): DEBUG: Placement subset P_55 has 3837 taxa:
[10:39:04] exhaustive.py (line 363): DEBUG: Placement subset P_56 has 3520 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.0038682512366218537, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 1698 nodes, tree 2 has 1822 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.011308005582572504, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 952 nodes, tree 2 has 746 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.03678215359018498, centroid
[10:39:04] tree.py (line 347): DEBUG: Tree 1 has 681 nodes, tree 2 has 1141 nodes
[10:39:04] tree.py (line 341): DEBUG: breaking_edge length = 0.04450806180571564, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 604 nodes, tree 2 has 537 nodes
[10:39:05] exhaustive.py (line 384): DEBUG: Placement subset P_56 has 5 alignment subsets: [0, 1, 2, 3, 4]
[10:39:05] exhaustive.py (line 388): DEBUG: Placement subset P_56 has 3520 taxa:
[10:39:05] exhaustive.py (line 363): DEBUG: Placement subset P_57 has 4409 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.02038200180718162, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 2168 nodes, tree 2 has 2241 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.010836008589637436, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 1168 nodes, tree 2 has 1000 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.0060801559491084085, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 615 nodes, tree 2 has 553 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.0239932465098908, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 1132 nodes, tree 2 has 1109 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.04243542115641398, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 583 nodes, tree 2 has 549 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.014039195487442604, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 564 nodes, tree 2 has 545 nodes
[10:39:05] exhaustive.py (line 384): DEBUG: Placement subset P_57 has 7 alignment subsets: [0, 1, 2, 3, 4, 5, 6]
[10:39:05] exhaustive.py (line 388): DEBUG: Placement subset P_57 has 4409 taxa:
[10:39:05] exhaustive.py (line 363): DEBUG: Placement subset P_58 has 2039 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.019328882488943412, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 828 nodes, tree 2 has 1211 nodes
[10:39:05] tree.py (line 341): DEBUG: breaking_edge length = 0.005981170527112243, centroid
[10:39:05] tree.py (line 347): DEBUG: Tree 1 has 706 nodes, tree 2 has 505 nodes
[10:39:05] exhaustive.py (line 384): DEBUG: Placement subset P_58 has 3 alignment subsets: [0, 1, 2]
[10:39:05] exhaustive.py (line 388): DEBUG: Placement subset P_58 has 2039 taxa:
[10:39:05] exhaustive.py (line 363): DEBUG: Placement subset P_59 has 3278 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.008429992463088874, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 1674 nodes, tree 2 has 1604 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.00852326336983957, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 765 nodes, tree 2 has 909 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.05082291101695925, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 616 nodes, tree 2 has 988 nodes
[10:39:06] exhaustive.py (line 384): DEBUG: Placement subset P_59 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:06] exhaustive.py (line 388): DEBUG: Placement subset P_59 has 3278 taxa:
[10:39:06] exhaustive.py (line 363): DEBUG: Placement subset P_60 has 2954 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.029860579816062112, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 1626 nodes, tree 2 has 1328 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.007322069595397516, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 834 nodes, tree 2 has 792 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.009659256246375555, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 663 nodes, tree 2 has 665 nodes
[10:39:06] exhaustive.py (line 384): DEBUG: Placement subset P_60 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:06] exhaustive.py (line 388): DEBUG: Placement subset P_60 has 2954 taxa:
[10:39:06] exhaustive.py (line 363): DEBUG: Placement subset P_61 has 2830 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.019887240393236, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 1551 nodes, tree 2 has 1279 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.012334030934947353, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 764 nodes, tree 2 has 787 nodes
[10:39:06] tree.py (line 341): DEBUG: breaking_edge length = 0.0965499465590565, centroid
[10:39:06] tree.py (line 347): DEBUG: Tree 1 has 785 nodes, tree 2 has 494 nodes
[10:39:06] exhaustive.py (line 384): DEBUG: Placement subset P_61 has 4 alignment subsets: [0, 1, 2, 3]
[10:39:06] exhaustive.py (line 388): DEBUG: Placement subset P_61 has 2830 taxa:
[10:39:06] exhaustive.py (line 398): INFO: Breaking into 292 alignment subsets.
[10:39:06] algorithm.py (line 278): DEBUG: start reading fragment files and breaking to at least 12 chunks but at most 20000 sequences
Traceback (most recent call last):
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/bin/run_sepp.py”, line 4, in
import(β€˜pkg_resources’).run_script(β€˜sepp==4.3.10’, β€˜run_sepp.py’)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/pkg_resources/init.py”, line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/pkg_resources/init.py”, line 1462, in run_script
exec(code, namespace, namespace)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp-4.3.10-py3.6.egg-info/scripts/run_sepp.py”, line 26, in
ExhaustiveAlgorithm().run()
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/algorithm.py”, line 156, in run
self.root_problem = self.build_subproblems()
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/exhaustive.py”, line 401, in build_subproblems
fragment_chunk_files = self.create_fragment_files()
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/exhaustive.py”, line 421, in create_fragment_files
return self.read_and_divide_fragments(frag_chunk_count)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/sepp/algorithm.py”, line 293, in read_and_divide_fragments
(len(ids_overlap), β€œβ€™\n '”.join(ids_overlap)))
ValueError: Your input fragment file contains 212 sequences, whose names overlap with names in your reference. Please rename your input fragments and re-start. Duplicate names are:
β€˜370098’
β€˜750071’
β€˜191797’
β€˜352902’
β€˜25947’
β€˜216550’
β€˜197105’
β€˜196909’
β€˜367977’
β€˜186841’
β€˜295094’
β€˜668514’
β€˜188881’
β€˜537894’
β€˜329313’
β€˜175751’
β€˜4309760’
β€˜2189140’
β€˜173565’
β€˜350121’
β€˜336614’
β€˜190490’
β€˜4468384’
β€˜4307094’
β€˜147105’
β€˜4391009’
β€˜536831’
β€˜1076587’
β€˜4476780’
β€˜174755’
β€˜194097’
β€˜307238’
β€˜16054’
β€˜4329090’
β€˜188646’
β€˜345111’
β€˜1888677’
β€˜292041’
β€˜4339144’
β€˜585227’
β€˜185420’
β€˜186020’
β€˜309433’
β€˜192720’
β€˜583117’
β€˜4323393’
β€˜185787’
β€˜348007’
β€˜176828’
β€˜3562626’
β€˜246930’
β€˜580008’
β€˜294606’
β€˜4436552’
β€˜264967’
β€˜168289’
β€˜183864’
β€˜190529’
β€˜4095596’
β€˜72820’
β€˜180082’
β€˜358749’
β€˜314996’
β€˜369822’
β€˜360861’
β€˜314095’
β€˜2365946’
β€˜208927’
β€˜365496’
β€˜3449122’
β€˜91557’
β€˜362078’
β€˜194360’
β€˜182186’
β€˜187324’
β€˜175642’
β€˜540862’
β€˜342427’
β€˜3138798’
β€˜310886’
β€˜213885’
β€˜368490’
β€˜221784’
β€˜186974’
β€˜235262’
β€˜149131’
β€˜186592’
β€˜526682’
β€˜4448492’
β€˜158404’
β€˜322505’
β€˜179861’
β€˜194896’
β€˜181432’
β€˜4352760’
β€˜183748’
β€˜179319’
β€˜367215’
β€˜564140’
β€˜4454586’
β€˜215269’
β€˜332317’
β€˜215097’
β€˜276149’
β€˜4323124’
β€˜4379034’
β€˜169182’
β€˜196713’
β€˜193191’
β€˜185961’
β€˜359538’
β€˜362767’
β€˜568118’
β€˜695612’
β€˜327598’
β€˜176645’
β€˜216710’
β€˜182483’
β€˜851865’
β€˜199524’
β€˜178885’
β€˜185034’
β€˜305946’
β€˜509416’
β€˜357046’
β€˜352733’
β€˜325437’
β€˜2198356’
β€˜289867’
β€˜910353’
β€˜197111’
β€˜366797’
β€˜199422’
β€˜323135’
β€˜196769’
β€˜181791’
β€˜187099’
β€˜579608’
β€˜222842’
β€˜180045’
β€˜355450’
β€˜911496’
β€˜4349261’
β€˜125624’
β€˜325808’
β€˜523036’
β€˜4435396’
β€˜3390534’
β€˜361727’
β€˜2201955’
β€˜4302904’
β€˜313672’
β€˜355291’
β€˜3166216’
β€˜301253’
β€˜3090117’
β€˜553611’
β€˜359581’
β€˜4301511’
β€˜1017181’
β€˜866280’
β€˜296394’
β€˜183030’
β€˜310979’
β€˜350277’
β€˜287508’
β€˜555945’
β€˜116529’
β€˜216290’
β€˜2979308’
β€˜215963’
β€˜181834’
β€˜2201995’
β€˜341460’
β€˜187517’
β€˜544859’
β€˜192055’
β€˜214682’
β€˜198945’
β€˜840376’
β€˜181234’
β€˜313968’
β€˜338992’
β€˜340476’
β€˜359872’
β€˜842291’
β€˜310574’
β€˜193591’
β€˜312973’
β€˜362327’
β€˜369109’
β€˜190975’
β€˜186851’
β€˜148121’
β€˜190260’
β€˜540055’
β€˜528357’
β€˜348009’
β€˜4439603’
β€˜294270’
β€˜189896’
β€˜357312’
β€˜177061’
β€˜825808’
β€˜208479’
β€˜197539’
β€˜367304’
β€˜189384’
β€˜360508’
β€˜332803’
β€˜4453773’
β€˜4336940’
=====================================================================
Traceback (most recent call last):
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File β€œ</home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-299>”, line 2, in sepp
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 77, in sepp
debug)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_fragment_insertion/_insertion.py”, line 53, in _run
subprocess.run(cmd, check=True, cwd=cwd)
File β€œ/home/bio/Softs/miniconda3/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command β€˜[β€˜run-sepp.sh’, β€˜/tmp/qiime2-archive-qzbe0rtu/a4999c1c-3669-432e-a06d-1447be00583f/data/dna-sequences.fasta’, β€˜q2-fragment-insertion’, β€˜-x’, β€˜48’, β€˜-A’, β€˜1000’, β€˜-P’, β€˜5000’, β€˜-a’, β€˜/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/aligned-dna-sequences.fasta’, β€˜-t’, β€˜/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/tree.nwk’, β€˜-r’, β€˜/tmp/qiime2-archive-u_qfkwbg/a14c6180-506b-4ecb-bacb-9cb30bc3044b/data/raxml-info.txt’, β€˜-b’, β€˜1’]’ returned non-zero exit status 1.

Thanks!

The greengenes releases come with a bunch of reference trees. Choose the correct tree (matches the reference sequences that you used for closed-reference OTU clustering) and import to QIIME 2 as described here (but as a Rooted tree):
https://docs.qiime2.org/2019.10/tutorials/importing/#phylogenetic-trees

Thanks for sharing that info! Looks like the problem is actually pretty straightforward:

So doing closed-reference OTU clustering and then attempting to graft those fragments into a tree does not work because those sequences are already in the tree and tip names must be unique… so this is not a bug, this is just a sensible error to prevent improper use of SEPP.

Import that tree instead of using SEPP. Good luck!

2 Likes

Thank you very much! I read the tutorial about importing tree files but I didn’t know when I should import my own tree. And it didn’t occur to me that I could use --p-debug option to check the error information. I’m so lucky to learn from the great guys like you in this forum. Thanks again for your instruction!

1 Like