ValueError: setting an array element with a sequence.

[gsierrar]

I am running Orthofinder (version 2.5.5) with the following command:

orthofinder.py -d -M msa -t 50 -f /datos/home/frodaf/Gina/Solanum_orthofinder

And everything seems nice before starting msa trees, then:

Analysing Orthogroups

2024-04-29 18:55:22 : Starting MSA/Trees
Species tree: Using 214 orthogroups with minimum of 48.8% of species having single-copy genes in any orthogroup

Inferring multiple sequence alignments for species tree

2024-04-29 18:56:10 : Done 0 of 214
2024-04-29 18:56:26 : Done 100 of 214
Error: sequence 22 has length 325, previous was 326
WARNING: Unknown caught unknown exception
Error: sequence 37 has length 928, previous was 929
WARNING: Unknown caught unknown exception
Error: sequence 25 has length 718, previous was 719
WARNING: Unknown caught unknown exception
Error: sequence 33 has length 487, previous was 488
WARNING: Unknown caught unknown exception
Error: sequence 36 has length 444, previous was 445
WARNING: Unknown caught unknown exception
Error: sequence 32 has length 1551, previous was 1552
WARNING: Unknown caught unknown exception
Error: sequence 29 has length 553, previous was 554
WARNING: Unknown caught unknown exception
Error: sequence 30 has length 313, previous was 314
WARNING: Unknown caught unknown exception
Error: sequence 28 has length 905, previous was 906
WARNING: Unknown caught unknown exception
Error: sequence 25 has length 401, previous was 402
WARNING: Unknown caught unknown exception
Error: sequence 24 has length 834, previous was 835
WARNING: Unknown caught unknown exception
Error: sequence 25 has length 541, previous was 542
WARNING: Unknown caught unknown exception
Error: sequence 26 has length 608, previous was 610
WARNING: Unknown caught unknown exception
Error: sequence 33 has length 933, previous was 934
WARNING: Unknown caught unknown exception
Error: sequence 24 has length 1087, previous was 1088
WARNING: Unknown caught unknown exception
Error: sequence 31 has length 523, previous was 524
WARNING: Unknown caught unknown exception
Error: sequence 35 has length 599, previous was 600
WARNING: Unknown caught unknown exception
Error: sequence 25 has length 889, previous was 890
WARNING: Unknown caught unknown exception
Error: sequence 30 has length 655, previous was 656
WARNING: Unknown caught unknown exception
Error: sequence 20 has length 1207, previous was 1208
WARNING: Unknown caught unknown exception
Traceback (most recent call last):
File "/datos/home/frodaf/OrthoFinder_source/orthofinder.py", line 7, in
main(args)
File "/datos/home/frodaf/OrthoFinder_source/scripts_of/main.py", line 1778, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/datos/home/frodaf/OrthoFinder_source/scripts_of/main.py", line 1540, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/datos/home/frodaf/OrthoFinder_source/scripts_of/orthologues.py", line 966, in OrthologuesWorkflow
seqs_alignments_dirs = treeGen.DoTrees(ogSet.OGs(qInclAll=True),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/datos/home/frodaf/OrthoFinder_source/scripts_of/trees_msa.py", line 377, in DoTrees
CreateConcatenatedAlignment(iOgsForSpeciesTree, ogs, self.GetAlignmentFilename, concatenated_algn_fn, fSingleCopy)
File "/datos/home/frodaf/OrthoFinder_source/scripts_of/trees_msa.py", line 249, in CreateConcatenatedAlignment
M = np.array([list(concatentaedAlignments[name]) for name in names])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (84,) + inhomogeneous part.

I do not fully understand what this error means, I have checked the files I am using but they seems good fasta files. For this run I am using cds from anotated genomes and rna-seq data.

Thanks in advanced.