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A mitogenome toolkit inspired by MitoZ, while being more effective, precise and flexible.

License: GNU General Public License v3.0

Python 69.08% Grammatical Framework 17.17% Gnuplot 3.03% QMake 0.89% Roff 0.23% Rust 8.89% Genero Forms 0.71%

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mitoflex's Issues

Trouble with MEGAHIT while running test_config.py

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

Error occurred while ETE3 updating NCBI taxonomy database

Hello,
I'm having the following issue with ete3 when running the ./ncbi.py script
Do you have any ideas what the issue here might be?
Thanks in advance
Sam

(mitoflex) [leeming@l33 test1]$ ../ncbi.py
Filesystem status:
Total: 109.00 GB
Free: 98.00 GB

If the free disk space is too low (<1G), database updating can be failed!
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...
Loading node names...
2269854 names loaded.
226194 synonyms loaded.
Loading nodes...
2269854 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /home/lv71312/leeming/.etetoolkit/taxa.sqlite ...
2269000 generating entries...
Uploading to /home/lv71312/leeming/.etetoolkit/taxa.sqlite

Inserting synonyms: 60000 Errors occured when fetching data from NCBI database, falling back to the last fetched database.
Loading node names...
2269574 names loaded.
225837 synonyms loaded.
Loading nodes...
2269574 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: /home/lv71312/leeming/.etetoolkit/taxa.sqlite ...
2269000 generating entries...
Uploading to /home/lv71312/leeming/.etetoolkit/taxa.sqlite
Traceback (most recent call last):
File "../ncbi.py", line 65, in
ncbi.update_taxonomy_database()
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 129, in update_taxonomy_database
update_db(self.dbfile)
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
upload_data(dbfile)
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 802, in upload_data
db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))
sqlite3.IntegrityError: UNIQUE constraint failed: synonym.spname, synonym.taxid

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "../ncbi.py", line 80, in
ncbi = NCBITaxa(taxdump_file=os.path.abspath(dump_file))
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 106, in init
self.update_taxonomy_database(taxdump_file)
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 131, in update_taxonomy_database
update_db(self.dbfile, taxdump_file)
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
upload_data(dbfile)
File "/home/lv71312/leeming/miniconda3/envs/mitoflex/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 791, in upload_data
db.execute(cmd)
sqlite3.OperationalError: database is locked

The result from nhmmer/filter_taxanomy is empty

Dears,
I am using mitoflex to assemble coral mitochondrial genome, which belongs to the Cnidaria. However, the program can not find the mitochondrial genome from the assemblied sequences, with reports"MitoFlex : The result from nhmmer/filter_taxanomy is empty! Please check if the data is unqualified, or a wrong taxanomy class is given!
". When I ran the program, the --clade was set as Anthropoda. The same parameter of Anthropoda was used in MitoZ, and in some cases, the mitochondrial genome can be selected, however, it can not work in Mitoflex even with the same raw data used, could you give some suggestion?

Not extracting CDS regions correctly

Thanks for the interesting tool. I've been trying it out on some reads I have from insects (cicadas). All 13 protein-coding genes are identified, as one would hope for. However, the resulting *.annotated.cds.fa file does not contain the expected sequences: there is non-coding DNA added to the beginning of the CDS or appended after the CDS.

For example, with COX1 there are an additional 46 nucleotides before the start codon that should not be in the sequence. There are also ~3 missing nucleotides at the end. When I look at the final scaffold and manually locate COX1, there is a full, correct sequence there. So, something goes wrong during the process of extracting the protein-coding genes into their own file, and the genomic coordinates for the genes must also be wrong. The latter problem would likely also affect the Circos visualisation.

Is this something that could be fixed? Thanks!

Edit: I should also say that another of the options with MitoFlex doesn't appear to make sense/work as currently specified:

 --keep-temp           remove temporal files and folders after work done.
                        Default False.

If you are specifying --keep-temp, wouldn't that imply that you are telling the program to "keep temporal files and folders after work done", not "remove temporal files and folders after work done"?

Genbank support

The MitoFlex view module is said to be analogous to the MitoZ module. From what I see in the MitoZ manual it would be enough to use the command below to generate a visualization of the mitogenome, but what about MitoFlex?

"python3 MitoZ.py visualize --gb mitogenome.gb"

Specified taxanomy name not in NCBI taxanomy database.

Dears,
I installed the [MitoFlex] following your instruction with all needed modules in the conda built environment, and updated the NCBI taxanomy database using ./ncbi.py, finally the .etetoolkit directory was created at my home. I tried the ./MitoFlex.py load-modules, and the result showed that all the modules were OK:
[18:30:05 INFO ] (MitoFlex -> pre@411) : MitoFlex 0.2.9, run 1
[18:30:05 INFO ] (MitoFlex -> pre@414) : Arguments after parsed :
[18:30:05 INFO ] (MitoFlex -> pre@415) : ['__calling=load-modules']
[18:30:05 INFO ] (MitoFlex -> load_modules@382) : Loading filter module.
[18:30:05 INFO ] (MitoFlex -> load_modules@384) : Loading assemble module.
[18:30:06 INFO ] (MitoFlex -> load_modules@386) : Loading findmitoscaf module.
[18:30:35 INFO ] (MitoFlex -> load_modules@388) : Loading annotation module.
[18:30:35 INFO ] (MitoFlex -> load_modules@390) : Loading visualize module.
[18:30:35 INFO ] (MitoFlex -> load_modules@395) : All modules are loaded correctly.
[18:30:35 INFO ] (MitoFlex -> post@477) : All done! Time elapsed : 30.42s.

However, when I tried ../MitoFlex.py --config test_config.py, an error occurred showing that:
Specified taxanomy name not in NCBI taxanomy database.
Error occured, exiting.

Would you please help to see what is the problem, thanks !

Lijunyuan

Error when running SOAPdenovo-fusion

Dears,
Thanks for making a great program. I've run into an error message and I am looking for guidance on how to resolve it.

I have installed MitoFlex on my Linux Ubuntu OS and have installed all dependencies. When I run load-modules, all modules appear to be working correctly. However, when I run the test data using /path/MitoFlex.py --config /path/test_config.py, the analysis runs up until it gets to SOAPdenovo where it prints the following error message:

"Error when running command '/path/MitoFlex/assemble/SOAPdenovo-fusion -D -s /hpath/MitoFlex/test/test_generated/test_generated.temp/assemble/test_generated.scaf/soaplib.txt -p 8 -K 75 -g /path/MitoFlex/test/test_generated/test_generated.temp/assemble/test_generated.scaf/k75 -c /path/MitoFlex/test/test_generated/test_generated.temp/assemble/test_generated.result/k141.contig.fa'. Exiting.
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."

I have run the analysis with logger set to 0 but it did not clarify what the issue is. Do you have any idea what might be causing the error and how to resolve it? Please let me know if there is any other information I can provide to clarify the issue.

Many thanks.

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