Trouble with MEGAHIT while running test_config.py

[marcosbarbeitos]

Hello, I have just pulled Mitoflex into an older Dell R900 server running Scientific Linux (= RHEL 7) and I am currently trying to test it using test_config.py. I keep getting the following message:

Using genetic code 5 : Invertebrate Mitochondrial code
[17:55:17 INFO ] MitoFlex : MitoFlex 0.2.9, run test_generated
[17:55:17 INFO ] MitoFlex : Arguments after parsed : 
[17:55:17 INFO ] MitoFlex : ["path=<module 'posixpath' from '/mnt/Data/anaconda3/lib/python3.9/posixpath.py'>", 'self_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test', 'workname=test_generated', 'threads=8', 'keep_temp=False', 'basedir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test', 'level=1', 'disable_local=False', 'kmer_list=[31, 39, 59, 79, 99, 119, 141]', 'depth_list=[10, 20, 20, 50, 50, 100, 100]', 'prune_level=2', 'prune_depth=2', 'cleanq1=None', 'cleanq2=None', 'deduplication=False', 'insert_size=150', 'Ns_valve=10', 'quality_valve=55', 'percentage_valve=0.2', 'keep_region=0,0', 'trimming=5000000000', 'fastq1=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test.1.fq', 'fastq2=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test.2.fq', 'fastq_alter_format=False', 'fastq_read_length=150', 'disable_taxa=False', 'min_abundance=10', 'required_taxa=Arthropoda', 'taxa_tolerance=0', 'genetic_code=5', 'clade=Arthropoda', 'max_contig_length=20000', 'wider_taxa=False', 'disable_annotation=False', 'species_name=Test sp.', 'use_hmmer=False', 'hmmer_score=5.0', 'hmmer_e=0.005', 'disable_visualization=False', 'disable_filter=False', 'disable_scaffolding=False', 'merge_method=0', 'merge_overlap=50', 'merge_start=50', 'work_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated', 'result_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.result', 'temp_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp', 'assemble_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/assemble', 'start=0', 'end=0', 'clean_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/cleandata', 'findmitoscaf_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/findmitoscaf', 'taxa_ids=[6656]', 'annotation_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/annotation', '__calling=all']
[17:55:17 DEBUG] helper : Entering <function all at 0x7fea1d637940>.
[17:55:17 DEBUG] filter : Start filtering pair-end rawdata.
[17:55:17 DEBUG] filter : Using argument : Ns=10, quality=55, start=0, end=0,limit=0.2, trimming=5000000000
[17:55:18 DEBUG] filter : Filtered 0 bytes, ratio 100.00%.
[17:55:18 DEBUG] helper : Entering <function assemble at 0x7fea1d6374c0>.
[17:55:18 INFO ] assemble : Start assembling mitochondrial sequences.
[17:55:18 DEBUG] assemble : Using kmer list : [31, 39, 59, 79, 99, 119, 141]
[17:55:18 INFO ] assemble : Initializing megahit wrapper.
/bin/sh: megahit_core: command not found
Command 'megahit_core checkpopcnt' returned non-zero exit status 127.
[17:55:18 ERROR] MitoFlex : Error when running command 'megahit_core checkpopcnt'. Exiting.
[17:55:18 ERROR] MitoFlex : A RuntimeError was occured. This is already considered in the code, but since it's thought to be errors in parts outside the MitoFlex can handle, it's NOT a bug caused by MitoFlex itself. Please check the error message and try to fix the possible cause of the crash, only as a last resort, send github a issue with a rerun with logger level set to 0.
[leom@IP116 MitoFlex]$ echo $PATH
/usr/lib64/openmpi/bin:/mnt/Data/anaconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/var/lib/snapd/snap/bin:/home/leom/.local/bin:/home/leom/bin:/mnt/Data/anaconda3/bin
[leom@IP116 MitoFlex]$ echo $PATH
/usr/lib64/openmpi/bin:/mnt/Data/anaconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/var/lib/snapd/snap/bin:/home/leom/.local/bin:/home/leom/bin:/mnt/Data/anaconda3/bin
[leom@IP116 MitoFlex]$ python3.9 MitoFlex.py --config /mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_config.py 
Using genetic code 5 : Invertebrate Mitochondrial code
[18:07:04 INFO ] MitoFlex : MitoFlex 0.2.9, run test_generated
[18:07:04 INFO ] MitoFlex : Arguments after parsed : 
[18:07:04 INFO ] MitoFlex : ["path=<module 'posixpath' from '/mnt/Data/anaconda3/lib/python3.9/posixpath.py'>", 'self_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test', 'workname=test_generated', 'threads=8', 'keep_temp=False', 'basedir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test', 'level=1', 'disable_local=False', 'kmer_list=[31, 39, 59, 79, 99, 119, 141]', 'depth_list=[10, 20, 20, 50, 50, 100, 100]', 'prune_level=2', 'prune_depth=2', 'cleanq1=None', 'cleanq2=None', 'deduplication=False', 'insert_size=150', 'Ns_valve=10', 'quality_valve=55', 'percentage_valve=0.2', 'keep_region=0,0', 'trimming=5000000000', 'fastq1=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test.1.fq', 'fastq2=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test.2.fq', 'fastq_alter_format=False', 'fastq_read_length=150', 'disable_taxa=False', 'min_abundance=10', 'required_taxa=Arthropoda', 'taxa_tolerance=0', 'genetic_code=5', 'clade=Arthropoda', 'max_contig_length=20000', 'wider_taxa=False', 'disable_annotation=False', 'species_name=Test sp.', 'use_hmmer=False', 'hmmer_score=5.0', 'hmmer_e=0.005', 'disable_visualization=False', 'disable_filter=False', 'disable_scaffolding=False', 'merge_method=0', 'merge_overlap=50', 'merge_start=50', 'work_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated', 'result_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.result', 'temp_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp', 'assemble_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/assemble', 'start=0', 'end=0', 'clean_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/cleandata', 'findmitoscaf_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/findmitoscaf', 'taxa_ids=[6656]', 'annotation_dir=/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.temp/annotation', '__calling=all']
[18:07:04 DEBUG] helper : Entering <function all at 0x7f846a4e2940>.
[18:07:04 DEBUG] filter : Start filtering pair-end rawdata.
[18:07:04 DEBUG] filter : Using argument : Ns=10, quality=55, start=0, end=0,limit=0.2, trimming=5000000000
[18:07:05 DEBUG] filter : Filtered 0 bytes, ratio 100.00%.
[18:07:05 DEBUG] helper : Entering <function assemble at 0x7f846a4e24c0>.
[18:07:05 INFO ] assemble : Start assembling mitochondrial sequences.
[18:07:05 DEBUG] assemble : Using kmer list : [31, 39, 59, 79, 99, 119, 141]
[18:07:05 INFO ] assemble : Initializing megahit wrapper.
[18:07:05 WARN ] assemble_wrapper : POPCNT is disabled since no features detected.
[18:07:05 DEBUG] assemble_wrapper : System memory status : total=64420.47MB, available=59042.20MB, used=4803.18MB, free=56416.53MB, active=5166.40MB, inactive=1642.73MB, buffers=161.61MB, cached=3039.15MB, shared=54.88MB, slab=346.76MB
[18:07:05 INFO ] assemble_wrapper : Scheduled 53137.98MB to use.
[18:07:05 DEBUG] assemble_wrapper : Converting reads to binary library.
[18:07:05 ERROR] MitoFlex : An unexpected error was happened in the MitoFlex, this could be a bug in the program, so please report it if you see this message in log.
[18:07:05 ERROR] MitoFlex : Error type : AttributeError, value : 'MEGAHIT' object has no attribute 'hwaccel'
[18:07:05 ERROR] MitoFlex : Traceback :
  File "/mnt/Data/local/MitoFlex/MitoFlex.py", line 485, in <module>
    parse_then_call(parser, pre=pre, post=post)

  File "/mnt/Data/local/MitoFlex/utility/parser.py", line 409, in parse_then_call
    func(final)

  File "/mnt/Data/local/MitoFlex/utility/helper.py", line 117, in timed_wrapper
    result = func(*args, **kwargs)

  File "/mnt/Data/local/MitoFlex/MitoFlex.py", line 287, in all
    args.fastafile = assemble(args)

  File "/mnt/Data/local/MitoFlex/utility/helper.py", line 117, in timed_wrapper
    result = func(*args, **kwargs)

  File "/mnt/Data/local/MitoFlex/MitoFlex.py", line 123, in assemble
    assembled_contigs = _assemble(fastq1=args.fastq1, fastq2=args.fastq2, base_dir=args.assemble_dir,

  File "/mnt/Data/local/MitoFlex/assemble/assemble.py", line 66, in assemble
    libread = megahit.build_lib()

  File "/mnt/Data/local/MitoFlex/assemble/assemble_wrapper.py", line 196, in build_lib
    shell_call(self.MEGAHIT_CORE, 'buildlib', self.read_lib, self.read_lib)

  File "/mnt/Data/local/MitoFlex/assemble/assemble_wrapper.py", line 103, in MEGAHIT_CORE
    return MEGAHIT_CORES[self.use_popcnt + self.hwaccel]

[18:07:05 ERROR] MitoFlex : Logging additional information
[18:07:05 ERROR] MitoFlex : [popenfile(path='/mnt/Data/local/MitoFlex/Samples/MitoFlex/test/test_generated/test_generated.log', fd=4, position=4658, mode='w', flags=557057)]
[18:07:05 ERROR] MitoFlex : {'LC_PAPER': 'pt_BR.UTF-8', 'MPI_INCLUDE': '/usr/include/openmpi-x86_64', 'MANPATH': '/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man', 'XDG_SESSION_ID': '190', 'LC_ADDRESS': 'pt_BR.UTF-8', 'HOSTNAME': 'IP116.zoologia.bio.ufpr.br', 'LC_MONETARY': 'pt_BR.UTF-8', 'SELINUX_ROLE_REQUESTED': '', 'TERM': 'xterm-256color', 'SHELL': '/bin/bash', 'HISTSIZE': '1000', 'SSH_CLIENT': '200.17.214.19 45038 22', 'CONDA_SHLVL': '0', 'PERL5LIB': '/mnt/Data/local/my_perl/trunk', 'SELINUX_USE_CURRENT_RANGE': '', 'LC_NUMERIC': 'pt_BR.UTF-8', 'SSH_TTY': '/dev/pts/0', 'QT_GRAPHICSSYSTEM_CHECKED': '1', 'MPI_PYTHON_SITEARCH': '/usr/lib64/python2.7/site-packages/openmpi', 'USER': 'leom', 'LD_LIBRARY_PATH': '/usr/lib64/openmpi/lib:/usr/local/lib64', 'LS_COLORS': 'rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:', 'LC_TELEPHONE': 'pt_BR.UTF-8', 'CONDA_EXE': '/mnt/Data/anaconda3/bin/conda', 'MPI_LIB': '/usr/lib64/openmpi/lib', '_CE_CONDA': '', 'MAIL': '/var/spool/mail/leom', 'PATH': '/usr/lib64/openmpi/bin:/mnt/Data/anaconda3/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/var/lib/snapd/snap/bin:/home/leom/.local/bin:/home/leom/bin:/mnt/Data/anaconda3/bin', 'MPI_BIN': '/usr/lib64/openmpi/bin', 'MPI_COMPILER': 'openmpi-x86_64', 'LC_IDENTIFICATION': 'pt_BR.UTF-8', 'R_LIBS': '/mnt/Data/local/R', 'PWD': '/mnt/Data/local/MitoFlex', '_LMFILES_': '/etc/modulefiles/mpi/openmpi-x86_64', 'LANG': 'en_US.UTF-8', 'MODULEPATH': '/usr/share/Modules/modulefiles:/etc/modulefiles', 'LOADEDMODULES': 'mpi/openmpi-x86_64', 'LC_MEASUREMENT': 'pt_BR.UTF-8', 'SELINUX_LEVEL_REQUESTED': '', '_CE_M': '', 'HISTCONTROL': 'ignoredups', 'MPI_SYSCONFIG': '/etc/openmpi-x86_64', 'SHLVL': '1', 'HOME': '/home/leom', 'MPI_SUFFIX': '_openmpi', 'MPI_MAN': '/usr/share/man/openmpi-x86_64', 'PYTHONPATH': '/usr/lib64/python2.7/site-packages/openmpi', 'CONDA_PYTHON_EXE': '/mnt/Data/anaconda3/bin/python', 'LOGNAME': 'leom', 'XDG_DATA_DIRS': '/home/leom/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'SSH_CONNECTION': '200.17.214.19 45038 200.17.214.111 22', 'MPI_HOME': '/usr/lib64/openmpi', 'MPI_FORTRAN_MOD_DIR': '/usr/lib64/gfortran/modules/openmpi-x86_64', 'MODULESHOME': '/usr/share/Modules', 'LESSOPEN': '||/usr/bin/lesspipe.sh %s', 'XDG_RUNTIME_DIR': '/run/user/1001', 'LC_NAME': 'pt_BR.UTF-8', 'BASH_FUNC_module()': '() {  eval `/usr/bin/modulecmd bash $*`\n}', 'OLDPWD': '/mnt/Data/local/MitoFlex/Samples', '_': '/mnt/Data/anaconda3/bin/python3.9'}
[18:07:05 ERROR] MitoFlex : pfullmem(rss=101888000, vms=530100224, shared=36438016, text=2170880, lib=0, data=53985280, dirty=0, uss=96145408, pss=98209792, swap=0)
[18:07:05 ERROR] MitoFlex : Logging ignored logs.
[18:07:05 ERROR] MitoFlex : Input file 1 has 50710098 bytes, 2 has 50710098 bytes.
[18:07:05 ERROR] MitoFlex : Output file has 50710098 bytes.
Traceback (most recent call last):
  File "/mnt/Data/local/MitoFlex/MitoFlex.py", line 485, in <module>
    parse_then_call(parser, pre=pre, post=post)
  File "/mnt/Data/local/MitoFlex/utility/parser.py", line 409, in parse_then_call
    func(final)
  File "/mnt/Data/local/MitoFlex/utility/helper.py", line 117, in timed_wrapper
    result = func(*args, **kwargs)
  File "/mnt/Data/local/MitoFlex/MitoFlex.py", line 287, in all
    args.fastafile = assemble(args)
  File "/mnt/Data/local/MitoFlex/utility/helper.py", line 117, in timed_wrapper
    result = func(*args, **kwargs)
  File "/mnt/Data/local/MitoFlex/MitoFlex.py", line 123, in assemble
    assembled_contigs = _assemble(fastq1=args.fastq1, fastq2=args.fastq2, base_dir=args.assemble_dir,
  File "/mnt/Data/local/MitoFlex/assemble/assemble.py", line 66, in assemble
    libread = megahit.build_lib()
  File "/mnt/Data/local/MitoFlex/assemble/assemble_wrapper.py", line 196, in build_lib
    shell_call(self.MEGAHIT_CORE, 'buildlib', self.read_lib, self.read_lib)
  File "/mnt/Data/local/MitoFlex/assemble/assemble_wrapper.py", line 103, in MEGAHIT_CORE
    return MEGAHIT_CORES[self.use_popcnt + self.hwaccel]
AttributeError: 'MEGAHIT' object has no attribute 'hwaccel'

I am using Megahit v1.2.9.

Any help will be greatly appreciated!

Best wishes,

Marcos

[Prunoideae]

Should be fixed in the new commit.

[marcosbarbeitos]

Hello, the fix worked, however, there is a typo in assemble_wrapper.py, line 101. It should be "megahit_core_no_hw_accel" and not "megahit_core_no_hwaccel". I corrected the typo in my local copy and it worked.

There is an additional typo in the Github page, it should be "./MitoFlex.py load-modules" and not "./MitoFlex.py load_modules".

Cheers!

Em qua., 10 de mai. de 2023 às 01:11, Li Junyu @.***> escreveu:

Should be fixed in the new commit.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

-- Marcos S. Barbeitos

Departamento de Zoologia - Sala 360 Setor de Ciências Biológicas Universidade Federal do Paraná Caixa Postal 19020 Curitiba, PR 81531-980 Brazil

Phone: (55 41) 3361-1634

[marcosbarbeitos]

I also ran into trouble trying to generate the Circos plot. I was able to get it to work using an older version cloned from https://github.com/node/circos/

[Prunoideae]

MitoFlex was developed 3 or 4 years ago. It's been a long time since I last worked on mitogenomes. I'll fix it soon.

[Prunoideae]

By the way, may I ask what Circos version you're using? I thought the Circos version in environment.yml should work fine (v0.69.8), or maybe older machines will need an older version to work properly?

[marcosbarbeitos]

Yep, my bad. I got version 0.52-4 from https://github.com/vigsterkr/circos, where Google took me when I was looking for the program.

I thought I had found the fix in an older version (0.69-3) because of the ancient commit dates in the node I pulled it from, but did not realize that the version I had was even older.

I always go for the Conda installation, but the line in MitoFlex GitHub's page is:

conda create -n {environment name here} --file requirements.txt

when I believe it should be:

conda create -n {environment name here} --file environment.yaml

I tried this latter option but it complained about not being able to parse the file. So I decided to go old school.

If you'd allow me one last question, I am trying to assemble mitochondrial genomes from ezRAD data collected from scleractinian corals.

I should therefore use Cnidarian as "required_taxa" and "clade" in the *config.py, but there is no "Cnidarian.hmm" file.

I set "disable_taxa" to True, but it will still look for Cnidarian.hmm.

Commenting out "required_taxa" and "clade" resulted in errors.

I wonder if it is possible to run the pipeline with no reference *.hmm file.

Perhaps enabling "use_hmmer" in *config.py would be the way to go?

If needed, I can put together a Cnidarian (or Scleractinian) HMM file using hmmbuild or something, but I'd rather not walk this extra mile. :-)

Thanks again!

Em sex., 12 de mai. de 2023 às 04:39, Li Junyu @.***> escreveu:

By the way, may I ask what Circos version you're using? I thought the Circos version in environment.yml should work fine (v0.69.8), or maybe older machines will need an older version to work properly?

— Reply to this email directly, view it on GitHub https://github.com/Prunoideae/MitoFlex/issues/14#issuecomment-1545314585, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4TMDFN4L57BDEPUFNI4BK3XFXSMNANCNFSM6AAAAAAX33JKEU . You are receiving this because you authored the thread.Message ID: @.***>

-- Marcos S. Barbeitos

Departamento de Zoologia - Sala 360 Setor de Ciências Biológicas Universidade Federal do Paraná Caixa Postal 19020 Curitiba, PR 81531-980 Brazil

Phone: (55 41) 3361-1634

[Prunoideae]

MitoFlex tries to find Cnidarian.hmm because --clade Cnidarian is specified.

It will try to use the clade-specific HMM file specified by --clade (check out /profile/CDS_HMM/*.hmm for a list of available HMM files) to ensure accuracy in identification. Disabling taxa only removes the need for a fasta file in /profile/MT_database.