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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.
The text was updated successfully, but these errors were encountered:
As per the description, upon running the follownig:
this message appear
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:I'm prompted the with this error
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
.The text was updated successfully, but these errors were encountered: