Error executing process > 'AminoType_Phylogeny'

[SergeyBaikal]

Help solve the problem, please. I suppose it's about the program modeltest-ng. Since only the portable version was installed. Other versions have the output illegal instruction Debian 10.

Something went wrong. Check error message below and/or log files.
Error executing process > 'AminoType_Phylogeny'

Caused by:
  Process `AminoType_Phylogeny` terminated with an error exit status (2)

Command executed:

  # Protein_Alignment
  pre=$(echo vAMPirusAnalysis_AminoTypes_noTaxonomy.fasta | awk -F ".fasta" '{print $1}' )
  mafft --thread 2 --maxiterate 15000 --auto vAMPirusAnalysis_AminoTypes_noTaxonomy.fasta >${pre}_ALN.fasta
  trimal -in ${pre}_ALN.fasta -out ${pre}_aln.fasta -keepheader -fasta -automated1 -htmlout ${pre}_aln.html

  # Protein_ModelTest
  modeltest-ng -i ${pre}_aln.fasta -p 2 -o ${pre}_mt -d aa -s 203 --disable-checkpoint

  # Protein_Phylogeny
  if [ "" != "" ];then
      iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq --redo -T auto 

  elif [[ "false" != "false" && "false" != "false" ]];then
      mod=$(tail -12 ${pre}_aln.fasta.log | head -1 | awk '{print $6}')
      iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m ${mod} --redo -nt auto -b 1000

  elif [[ "false" != "false" && "false" != "false" ]];then
      mod=$(tail -12 ${pre}_aln.fasta.log | head -1 | awk '{print $6}')
      iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m ${mod} --redo -nt auto -bb 1000 -bnni

  elif [ "false" != "false" ];then
      iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m MFP --redo -nt auto -b 1000

  elif [ "false" != "false" ];then
      iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m MFP --redo -nt auto -bb 1000 -bnni

  else
      iqtree -s ${pre}_aln.fasta --prefix ${pre}_iq -m MFP --redo -nt auto -bb 1000 -bnni
  fi

Command exit status:
  2

Command output:
         4  RTREV              0     -2999.4129     59788.8257        48.7916    0.0000
         5  PMB                0     -3001.4599     59792.9199        52.8857    0.0000
         6  JTT-DCMUT          0     -3002.4592     59794.9185        54.8843    0.0000
         7  JTT                0     -3003.1980     59796.3959        56.3618    0.0000
         8  BLOSUM62           0     -3009.1494     59808.2987        68.2646    0.0000
         9  CPREV              0     -3012.6505     59815.3011        75.2669    0.0000
        10  DCMUT              0     -3020.6636     59831.3273        91.2931    0.0000
  --------------------------------------------------------------------------------
  Best model according to AICc
  ---------------------------
  Model:              LG
  lnL:                -2975.0171
  Frequencies:        0.0791 0.0559 0.0420 0.0531 0.0129 0.0408 0.0716 0.0573 0.0224 0.0622 0.0991 0.0646 0.0230 0.0423 0.0440 0.0612 0.0533 0.0121 0.0342 0.0691
  Inv. sites prop:    -
  Gamma shape:        -
  Score:              59740.0342
  Weight:             0.9999
  ---------------------------
  Parameter importances
  ---------------------------
  P.Inv:              0.0000
  Gamma:              0.0000
  Gamma-Inv:          0.0000
  Frequencies:        -
  ---------------------------
  Model averaged estimates
  ---------------------------
  P.Inv:              0.0000
  Alpha:              1.3558
  Alpha-P.Inv:        1.3725
  P.Inv-Alpha:        0.0000
  Frequencies:        -

  Commands:
    > phyml  -i vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta -d aa -m LG -f m -v 0 -a 0 -c 1 -o tlr
    > raxmlHPC-SSE3 -s vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta -m PROTGAMMALG -n EXEC_NAME -p PARSIMONY_SEED
    > raxml-ng --msa vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta --model LG
    > paup -s vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta
    > iqtree -s vAMPirusAnalysis_AminoTypes_noTaxonomy_aln.fasta -m LG
  Summary:

  Partition 1/1:
                           Model         Score        Weight
  ----------------------------------------------------------
         BIC               LG+G4     6500.8375        0.8969
         AIC               LG+G4     6118.5972        0.7310
        AICc                  LG    59740.0342        0.9999

  Execution results written to vAMPirusAnalysis_AminoTypes_noTaxonomy_mt.out
  Starting tree written to vAMPirusAnalysis_AminoTypes_noTaxonomy_mt.tree

Command error:

  004-0154-0 (thread    1) identical     
  004-0154-0 (thread    1) worse      

  004-0155-0 (thread    1) identical     
  004-0155-0 (thread    1) worse      

  004-0156-1 (thread    2) identical     
  004-0156-1 (thread    1) identical     
  004-0156-1 (thread    1) worse      

  004-0157-1 (thread    2) worse      

  004-0158-1 (thread    2) identical     
  004-0158-1 (thread    2) worse      

  004-0159-0 (thread    1) identical     
  004-0159-0 (thread    1) worse      

  004-0160-0 (thread    2) identical     
  004-0160-0 (thread    2) worse      

  004-0161-1 (thread    1) identical     
  004-0161-1 (thread    1) worse      

  004-0162-1 (thread    2) identical     
  004-0162-1 (thread    2) worse      

  Converged.

  Converged2.
  done
  dvtditr (aa) Version 7.407
  alg=A, model=BLOSUM62, 1.53, -0.00, -0.00, noshift, amax=0.0
  2 thread(s)

  Strategy:
   L-INS-i (Probably most accurate, very slow)
   Iterative refinement method (<16) with LOCAL pairwise alignment information

  If unsure which option to use, try 'mafft --auto input > output'.
  For more information, see 'mafft --help', 'mafft --man' and the mafft page.

  The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
  It tends to insert more gaps into gap-rich regions than previous versions.
  To disable this change, add the --leavegappyregion option.

  [error] modeltest-ng: Warning: Substitution schemes will be ignored
  Invalid "--prefix" option.

Work dir:
  /home/sergey/vAMPirus-1.0.1/work/10/1f1ee7200415d6140fe9e55b229236

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

[Aveglia]

Hi Sergey, thank you for bringing this issue to my attention.

Could you share with me your initial "launch" command and vampirus.config file; then go into that work directory (/home/sergey/vAMPirus-1.0.1/work/10/1f1ee7200415d6140fe9e55b229236) and share with me the .command.sh and the .command.err files?

We also just released version 2.0.0 which might fix the problem if you want to try to update vAMPirus and re-run.

[SergeyBaikal]

The same problem was in the new version. I sent the files to your mail.

[Aveglia]

Ah, shoot, ok, sorry about that.

Which email did you send the files to? I see the comments in my inbox but I do not see the files attached. Can you resend the files to vampirushelp@gmail.com?

[SergeyBaikal]

Well done.