PhylogenomicsAnalysis (legacy pipeline) failed at RAxML

[maggiesudo]

Hi PlantTribes!
I have been using the PlanTribes to perform gene clustering and have successfully run the AssemblyPostProcess and GeneFamilyClassifier. However, I fail to get the RAxML tree from the PhylogenomicsAnalysis (legacy pipeline).

This is the code I used >> /home/mpsud1/cn78_scratch/mpsud1/Ortho_Cluster_Gene/PlantTribes-master/legacy/PhylogenomicsAnalysis --orthogroup_faa geneFamilyClassification_dir/orthogroups_fasta --scaffold 12Gv1.0 --method orthomcl --pasta_alignments --tree_inference raxml --max_memory 65536 --num_threads 20

I think the alignment was performed successfully? I kept getting the following warnings and the error for RAxML:
Refused to clean '/home/mpsud1/.pasta/pastajob/tempbrvrc6cr/init_aln': not created by PASTA
'/home/mpsud1/.pasta/pastajob/tempbrvrc6cr/init_aln' is not registered as a temporary directory that was created by this process!
Refused to clean '/home/mpsud1/.pasta/pastajob/temp1a0ifb4g/init_aln': not created by PASTA
'/home/mpsud1/.pasta/pastajob/temp1a0ifb4g/init_aln' is not registered as a temporary directory that was created by this process!
Refused to clean '/home/mpsud1/.pasta/pastajob/tempa9hn4uoa/init_aln': not created by PASTA
'/home/mpsud1/.pasta/pastajob/tempa9hn4uoa/init_aln' is not registered as a temporary directory that was created by this process!

mv: cannot stat 'RAxML_bipartitions.': No such file or directory
rm: cannot remove 'RAxML_bestTree.': No such file or directory
rm: cannot remove 'RAxML_bipartitionsBranchLabels.': No such file or directory
rm: cannot remove 'RAxML_bootstrap.': No such file or directory
rm: cannot remove 'RAxML_info.*': No such file or directory

What I did was I ran the GeneFamilyPhylogeny pipeline using the alignment files I got from PhylogenomicsAnalysis (legacy pipeline). It seems to be working for now. Would that be okay? Also, how do I confirm that I have got all the alignments?
This is the command I used >> /home/mpsud1/cn78_scratch/mpsud1/Ortho_Cluster_Gene/PlantTribes-master/pipelines/GeneFamilyPhylogenyBuilder --orthogroup_aln phylogenomicsAnalysis_dir/orthogroups_aln --scaffold 12Gv1.0 --method orthomcl --tree_inference raxml --num_threads 20

Thank you in advance! I hope to hear from you soon.