marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies

marcelauliano/MitoHiFi Issues

No gbk.HiFiMapped.bam.filtered.assembled.[a/p]_ctg.gfa file(s). An error may have occurred when assembling reads with HiFiasm
Updated 5 months ago12
mitohifi adds second newline to input
Updated 5 months ago1
different result with mito annotation
Updated 5 months ago
samtools view: failed to add PG line to the header
Closed 6 months ago9
problem with get_ref_tRNA
Closed 5 months ago4
ModuleNotFoundError: No module named 'parse_blast'
Closed 5 months ago2
mitogenome file has more than one sequence
Closed 5 months ago1
docker pull error
Updated 5 months ago
Error: Invalid literal for int() with base 16: b''
Updated 6 months ago2
Shebang on scripts copied to Docker image
Closed 6 months ago1
Excessively long running time
Closed 6 months ago3
ValueError: max() arg is an empty sequence
Closed 6 months ago1
Problem running MitoHiFi with libssl.so.1.0.0
Closed 6 months ago2
Can I input ONT reads?
Closed 6 months ago
plant genome with raw HIFI reads
Closed 6 months ago2
Fixing long string error messages including line breaks and spaces.
Closed 6 months ago2
MitoFinder is not making annotation files when it says it did
Closed 7 months ago3
reference_tRNA = max(tRNAs, key=tRNAs.get) ValueError: max() arg is an empty sequence , even though mito finder is working properly
Closed a year ago8
ValueError: max() arg is an empty sequence
Updated 7 months ago11
No rotated contigs found
Updated 8 months ago2
Lighter weight container
Closed 8 months ago4
awk: cannot open gbk.HiFiMapped.bam.filtered.assembled.p_ctg.gfa (No such file or directory)
Closed 8 months ago4
FileNotFoundError: [Errno 2] No such file or directory: 'cdhit.out.clstr'
Closed 8 months ago8
Possible to change "minimum query length = 80% subject length" parameter?
Closed 8 months ago4
AttributeError: 'Seq' object has no attribute 'defined'
Updated 8 months ago
[makeblastdb]
Closed 8 months ago2
`makeblastdb` output/error log is suppressed
Updated 8 months ago
Example data run error: FileNotFoundError: [Errno 2] No such file or directory: 'tig00007572_1.annotation.1.individual.stats'
Updated 10 months ago5
You need to run further scripts to check if you have mito reads pulled to a large NUMT !!
Closed a year ago15
error about tRNA-Phe information(".trnas")
Closed a year ago2
multicopy genome output
Closed a year ago1
Python Version
Closed a year ago
potential contigs
Closed a year ago1
running test dataset error
Updated a year ago5
Two issues: few reads mapping to reference and no hifiasm results
Closed a year ago12
Unable to find reference_tRNA
Closed a year ago2
blast xml error
Closed a year ago8
Gene named in the reference file is not recognized by MitoFinder.
Closed a year ago5
KeyError in getGenesList
Closed a year ago1
How to assess the quality of my mitochondrial genome assembly?
Closed a year ago
Readme error
Closed a year ago1
HPC and slurm comparability - Error finding Contig tig00007550_1 does not have an annotation file
Updated a year ago4
Correct the path for singularity in the tutorial
Closed a year ago1
Preparing small example files to run it for a short time.
Updated 2 years ago4
Add error checks to check if the argument FASTA is reads or contig file.
Closed 2 years ago2
mitohifi.py: No such file or directory: 'gbk.HiFiMapped.bam.filtered.assembled.p_ctg.gfa'
Closed 2 years ago7
'parsed_blast.txt' empty due to hifiasm empty result files
Updated 2 years ago12
singularity use error, can't write
Updated 2 years ago8
where to download the Singularity image file mitohifi-v2.sif
Closed 2 years ago8
self.pid = _posixsubprocess.fork_exec( TypeError: expected str, bytes or os.PathLike object, not int
Updated 2 years ago