根据课程学习中，执行代码orthofinder.py -f pep -S diamond -M msa -A muscle -T fasttree -t 1 -a 1 后，后台nohup文件报错如下，但是查看了文件权限和文件的实际路径都有该文件，且文件大小不为0。这几天运行了好几次，都是卡在这个步骤上。在2024年年初利用你们提供的共享服务器解析另外一个物种的时候，用的是同样的代码，并没有报错。请问是代码的问题，还是什么？如果是代码的问题该如何调整，让解析顺利进行呢？？
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list index out of range
2025-06-06 08:34:28 : Done 5000 of 32458
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004708.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004709.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004710.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004711.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004712.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004713.fa
WARNING: Unknown caught unknown exception
ERROR, input file does not exist: /home/us070/GC/02.gene_family/pep/OrthoFinder/Results_Jun06/WorkingDirectory/Alignments_ids/OG0004714.fa
2025-06-07 14:57:00 : Done orthogroups
Analysing Orthogroups
=====================
2025-06-07 14:57:01 : Starting MSA/Trees
Species tree: Using 969 orthogroups with minimum of 81.2% of species having single-copy genes in any orthogroup
Inferring multiple sequence alignments for species tree
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2025-06-07 14:57:14 : Done 0 of 969
2025-06-07 15:01:56 : Done 100 of 969
2025-06-07 15:06:15 : Done 200 of 969
Traceback (most recent call last):
File "/share/work/biosoft/OrthoFinder/latest//orthofinder.py", line 7, in <module>
main(args)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/__main__.py", line 1778, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/__main__.py", line 1540, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/orthologues.py", line 966, in OrthologuesWorkflow
seqs_alignments_dirs = treeGen.DoTrees(ogSet.OGs(qInclAll=True),
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 377, in DoTrees
CreateConcatenatedAlignment(iOgsForSpeciesTree, ogs, self.GetAlignmentFilename, concatenated_algn_fn, fSingleCopy)
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 224, in CreateConcatenatedAlignment
alignment = ReadAlignment(alignment_filename_function(iOg))
File "/share/work/biosoft/OrthoFinder/OrthoFinder_v2.5.4/scripts_of/trees_msa.py", line 197, in ReadAlignment
with open(fn, 'r') as infile:
FileNotFoundError: [Errno 2] No such file or directory: '/work/02.gene_family/pep/OrthoFinder/Results_Jun06_2/WorkingDirectory/Alignments_ids/OG0012262.fa'