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findMitoReference.py not downloading fasta and gb files #111

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Overcraft90 opened this issue Dec 19, 2024 · 0 comments
Open

findMitoReference.py not downloading fasta and gb files #111

Overcraft90 opened this issue Dec 19, 2024 · 0 comments

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@Overcraft90
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As per the description, upon running the follownig:

docker run biocontainers/mitohifi:3.0.0_cv1 findMitoReference.py --species "Lupinus albus" --outfolder ./ --type chloroplast

this message appear

Looking for chloroplast for Lupinus albus
Looking for an appropriate organelle among Lupinus albus
output is written to ./NC_026681.1.[gb,fasta]

but no data is actually written...

I, therefore, resorted to download the FASTA and GB files directily from GeneBank and name them accordingly; however, after running mitohifi.py as follows:

docker run biocontainers/mitohifi:3.0.0_cv1 mitohifi.py -r INLUP_00165/INLUP00165.filt.fastq.gz -f NC_026681.1.fasta -g NC_026681.1.gb -t 96 -a plant -o 11

I'm prompted the with this error

2024-12-19 18:21:28 [INFO] Welcome to MitoHifi v2. Starting pipeline...
Traceback (most recent call last):
File "/opt/MitoHiFi/mitohifi.py", line 551, in
main()
File "/opt/MitoHiFi/mitohifi.py", line 89, in main
rel_mito_len = getMitoLength.get_mito_length(args.f)
File "/opt/MitoHiFi/getMitoLength.py", line 10, in get_mito_length
num_sequences = len(list(SeqIO.parse(mito_file, "fasta")))
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/init.py", line 605, in parse
return iterator_generator(handle)
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/FastaIO.py", line 183, in init
super().init(source, mode="t", fmt="Fasta")
File "/usr/local/lib/python3.6/dist-packages/Bio/SeqIO/Interfaces.py", line 48, in init
self.stream = open(source, "r" + mode)
FileNotFoundError: [Errno 2] No such file or directory: 'NC_026681.1.fasta'

which seems to be related to #104, but again it points out to the initial problem. Any help is much appreciated on how to download inputs and run MitoHiFi.

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