I have an error with EPA and some doubts regarding how to handle it. The error:

Command error:
  INFO Selected: Output dir: ./
  INFO Selected: Query file: 022_180-2000_DCM.query.hmmalign.masked.afa.gz
  INFO Selected: Tree file: tree.nw
  INFO Selected: Reference MSA: 022_180-2000_DCM.ref.hmmalign.masked.afa.gz
  INFO Selected: Automatic switching of use of per rate scalers
  INFO Selected: Preserving the root of the input tree
  INFO Selected: Specified model: LG+R8
  INFO Selected: Using threads: 12
  INFO     ______ ____   ___           _   __ ______
          / ____// __ \ /   |         / | / // ____/
         / __/  / /_/ // /| | ______ /  |/ // / __  
        / /___ / ____// ___ |/_____// /|  // /_/ /  
       /_____//_/    /_/  |_|      /_/ |_/ \____/ (v0.3.8)
  INFO Using model parameters:
  INFO    Rate heterogeneity: FREE (8 cats, mean),  weights&rates: (0.125,0.0652803) (0.125,0.208627) (0.125,0.376074) (0.125,0.577429) (0.125,0.830101) (0.125,1.1699) (0.125,1.69315) (0.125,3.07944) 
          Base frequencies (model): 0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 0.099081 0.0646 0.022951 0.042302 0.04404 0.061197 0.053287 0.012066 0.034155 0.069147 
          Substitution rates (model): 0.425093 0.276818 0.395144 2.48908 0.969894 1.03855 2.06604 0.358858 0.14983 0.395337 0.536518 1.12403 0.253701 1.17765 4.72718 2.1395 0.180717 0.218959 2.54787 0.751878 0.123954 0.534551 2.80791 0.36397 0.390192 2.4266 0.126991 0.301848 6.32607 0.484133 0.052722 0.332533 0.858151 0.578987 0.593607 0.31444 0.170887 5.07615 0.528768 1.69575 0.541712 1.43765 4.50924 0.191503 0.068427 2.14508 0.371004 0.089525 0.161787 4.00836 2.00068 0.045376 0.612025 0.083688 0.062556 0.523386 5.24387 0.844926 0.927114 0.01069 0.015076 0.282959 0.025548 0.017416 0.394456 1.24028 0.42586 0.02989 0.135107 0.037967 0.084808 0.003499 0.569265 0.640543 0.320627 0.594007 0.013266 0.89368 1.10525 0.075382 2.78448 1.14348 0.670128 1.16553 1.95929 4.12859 0.267959 4.81351 0.072854 0.582457 3.23429 1.67257 0.035855 0.624294 1.22383 1.08014 0.236199 0.257336 0.210332 0.348847 0.423881 0.044265 0.069673 1.80718 0.173735 0.018811 0.419409 0.611973 0.604545 0.077852 0.120037 0.245034 0.311484 0.008705 0.044261 0.296636 0.139538 0.089586 0.196961 1.73999 0.129836 0.268491 0.054679 0.076701 0.108882 0.366317 0.697264 0.442472 0.682139 0.508851 0.990012 0.584262 0.597054 5.30683 0.119013 4.14507 0.159069 4.27361 1.11273 0.078281 0.064105 1.03374 0.11166 0.232523 10.6491 0.1375 6.31236 2.59269 0.24906 0.182287 0.302936 0.619632 0.299648 1.70274 0.656604 0.023918 0.390322 0.748683 1.13686 0.049906 0.131932 0.185202 1.79885 0.099849 0.34696 2.02037 0.696175 0.481306 1.89872 0.094464 0.361819 0.165001 2.45712 7.8039 0.654683 1.33813 0.571468 0.095131 0.089613 0.296501 6.47228 0.248862 0.400547 0.098369 0.140825 0.245841 2.18816 3.15182 0.18951 0.249313
  INFO Output file: ./epa_result.jplace
  terminate called after throwing an instance of 'std::runtime_error'
    what():  Sequence with header '022_180-2000_DCM_ERR1712074.25146093_1;weight=1;' does not appear to have any non-gap sites!
  /scratch/data3/aauladell/project_big/phylotranscriptomics/work/aa/ba4d9e9061f842ee0c944df9a618b1/.command.sh: line 9:    41 Aborted                 (core dumped) epa-ng --model LG+R8 --threads 12 --query 022_180-2000_DCM.query.hmmalign.masked.afa.gz --ref-msa 022_180-2000_DCM.ref.hmmalign.masked.afa.gz --tree tree.nw

Work dir:
  /scratch/data3/aauladell/project_big/phylotranscriptomics/work/53/85520b58953e69bd4e91f9d0e0f79a