ownHMM_library.R script fails with empty input files

rule R_script from the Combine_Toxin_SignalP.smk throws an error (below) if the input file is empty:

RuleException:
CalledProcessError in line 29 of /mnt/irisgpfs/users/sbusi/apps/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk:
Command 'source /scratch/users/sbusi/tools/miniconda3/bin/activate '/mnt/irisgpfs/users/sbusi/apps/PathoFact/.snakemake/conda/c6514c6c'; set -euo pipefail;  Rscript --vanilla /mnt/irisgpfs/users/sbusi/apps/PathoFact/.snakemake/scripts/tmpxk7hk0_a.ownHMM_library.R' returned non-zero exit status 1.
  File "/mnt/irisgpfs/users/sbusi/apps/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk", line 29, in __rule_R_script
  File "/scratch/users/sbusi/tools/miniconda3/envs/PathoFact/lib/python3.6/concurrent/futures/thread.py", line 56, in run

Failed file example:

==> /work/projects/amrwd/results/PathoFact/PathoFact_space_output/PathoFact_intermediate/TOXIN/HMM_toxin/IG4SW-M_F1_L4_NORM_GC.Input_HMM_R.csv <==
 Query_sequence HMM_Name        Significance_Evalue     Score
#Toxin

Working file example:

==> /work/projects/amrwd/results/PathoFact/PathoFact_space_output/PathoFact_intermediate/TOXIN/HMM_toxin/IIF1SW-M_F2_L1_NORM_FLT.Input_HMM_R.csv <==
 Query_sequence HMM_Name        Significance_Evalue     Score
#Toxin
0000010215      K01114_780_95_420       3.8e-78 262.5
0000013630      K01186_172      5.1e-103        344.2
0000012319      K01186_172      1.7e-08 33.1
0000019322      K01197_243      0.29    8.8
0000018125      K03699_483      2.8e-112        374.6
0000018124      K03699_483      2.3e-71 239.7
0000010016      K03699_483      1.8e-63 213.7
0000011228      K03699_483      1.5e-62 210.6