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Mobile Genetic Elements Retrieving Tool

Python 99.48% Shell 0.52%
bioinformatics bioinformatics-pipeline flanking-regions genome-assemblies mgert-pipeline orf pipeline repeatmasker repeatmodeler

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kdbrumfield altingia gunzivan28 vincenzopennone sandrababirye

mgert's Issues

Installing ORF finder

Hi,

I'd like to get MGERT up and running, but I can't find any instructions for getting ORF finder up and running. I've downloaded to ORFfinder.gz file from NCBI, but what else do I need to do with it for it to work?

Thanks!
Julie

IndexError: list index out of range

Hi Andrew, I have run the pipeline but i get a trace back in the code snippet below for all my samples:
"Traceback (most recent call last):
File "../../miniconda3/envs/rMAP-1.0/config-files/MGERT.py", line 1732, in
l=args.min_length, e=args.e_value, c=args.start_codon, strnd=args.strand, g=args.genetic_code, le=args.left_end, re=args.right_end, rm_tab=args.rm_table)
File "../../miniconda3/envs/rMAP-1.0/config-files/MGERT.py", line 1398, in pipe
rmodeler(genome_file, threads)
File "../../miniconda3/envs/rMAP-1.0/config-files/MGERT.py", line 1239, in rmodeler
repmod_outfile = glob.glob("RM*/consensi.fa.classified")[0]
IndexError: list index out of range"

I am running it for .fna.gz files, both strands and would like to obtain the output files. How could i overcome this

Dockerfile please?

Hi @andrewgull

I've tried to setup the described environment from scratch, but the configuration process took too much of my spare time.
So for the second time I've tried to use conda for setup simplification, but all I've got was a bunch of conflicts, e.g:

# conda install -y --force -c bioconda \
>         repeatmasker \
>         repeatmodeler \
>         bedtools \
>         blast


WARNING: The --force flag will be removed in a future conda release.
         See 'conda install --help' for details about the --force-reinstall
         and --clobber flags.


Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: |
Found conflicts! Looking for incompatible packages.                              failed                                                                             /

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package zlib conflicts for:
repeatmodeler -> cd-hit[version='>=4.8.1'] -> zlib[version='1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8.*']
bedtools -> zlib[version='1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8.*']
blast -> zlib[version='1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8.*']
repeatmasker -> rmblast -> zlib[version='1.2.11.*|>=1.2.11,<1.3.0a0|1.2.8.*']
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0']

Package repeatmasker conflicts for:
repeatmasker
repeatmodeler -> repeatmasker

Package _libgcc_mutex conflicts for:
python=3.8 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]
blast -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex=[build=main]
bedtools -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]

Package libstdcxx-ng conflicts for:
python=3.8 -> libffi[version='>=3.2.1,<3.3a0'] -> libstdcxx-ng[version='>=7.2.0']
python=3.8 -> libstdcxx-ng[version='>=7.3.0']

Package blast conflicts for:
repeatmasker -> rmblast -> blast
blast
repeatmodeler -> rmblast -> blast

Package bzip2 conflicts for:
blast -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
repeatmasker -> rmblast -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
repeatmodeler -> rmblast[version='>=2.9.0'] -> bzip2[version='1.0.*|>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']
bedtools -> bzip2[version='>=1.0.6,<2.0a0|>=1.0.8,<2.0a0']

Package libcurl conflicts for:
blast -> curl[version='>=7.71.1,<8.0a0'] -> libcurl[version='7.64.1|7.65.2|7.65.3|7.67.0|7.68.0|7.69.1|7.71.0|7.71.1',build='h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_1']
bedtools -> curl[version='>=7.64.1,<8.0a0'] -> libcurl[version='7.64.1|7.65.2|7.65.3|7.67.0|7.68.0|7.69.1|7.71.0|7.71.1',build='h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_0|h20c2e04_1']

Package libgcc-ng conflicts for:
python=3.8 -> libgcc-ng[version='>=7.3.0']
python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0']

Package xz conflicts for:
python=3.8 -> xz[version='>=5.2.4,<6.0a0|>=5.2.5,<6.0a0']
bedtools -> xz[version='>=5.2.4,<5.3.0a0']

Anyway, could you please provide a working Docker image in order to deploy and use the tool with the best possible experience?

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