Hello,
I used the singularity to run mitohifi in ubuntu on windows10, and my reference data is saved in /mnt/d. However, once I typed the commands as followed:
singularity exec --bind /mnt/d:/data docker://ghcr.io/marcelauliano/mitohifi:master mitohifi.py -r /home/user1/MitoHiFi/tests/ilDeiPorc1.reads.100.fa -f /mnt/d/OQ694980.1.fasta -g /mnt/d/OQ694980.1.gb -t 4 -o 5
and then I would get the feedback as followed:
INFO: Using cached SIF image
2024-05-06 21:10:56 [INFO] Welcome to MitoHifi v2. Starting pipeline...
Traceback (most recent call last):
File "/opt/MitoHiFi/src/mitohifi.py", line 566, in
main()
File "/opt/MitoHiFi/src/mitohifi.py", line 94, in main
rel_mito_len = getMitoLength.get_mito_length(args.f)
File "/opt/MitoHiFi/src/getMitoLength.py", line 18, 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: '/mnt/d/OQ694980.1.fasta'
It seems that singularity can't find the document outside /home/user1. However, if the documents are saved in /home/user1, I can get the final result. Can you help me to solve this problem? Because my data is too big, and the memory of the disks where "/home/user1" in is limited, so I have to save the data in other disks.
Hello, I used the singularity to run mitohifi in ubuntu on windows10, and my reference data is saved in /mnt/d. However, once I typed the commands as followed: singularity exec --bind /mnt/d:/data docker://ghcr.io/marcelauliano/mitohifi:master mitohifi.py -r /home/user1/MitoHiFi/tests/ilDeiPorc1.reads.100.fa -f /mnt/d/OQ694980.1.fasta -g /mnt/d/OQ694980.1.gb -t 4 -o 5
and then I would get the feedback as followed: INFO: Using cached SIF image 2024-05-06 21:10:56 [INFO] Welcome to MitoHifi v2. Starting pipeline... Traceback (most recent call last): File "/opt/MitoHiFi/src/mitohifi.py", line 566, in
main()
File "/opt/MitoHiFi/src/mitohifi.py", line 94, in main
rel_mito_len = getMitoLength.get_mito_length(args.f)
File "/opt/MitoHiFi/src/getMitoLength.py", line 18, 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: '/mnt/d/OQ694980.1.fasta'
It seems that singularity can't find the document outside /home/user1. However, if the documents are saved in /home/user1, I can get the final result. Can you help me to solve this problem? Because my data is too big, and the memory of the disks where "/home/user1" in is limited, so I have to save the data in other disks.