running error of create_fasta.py

[zzsunday]

hi, thank u for create such fancy tool!
recently , i have encountered a error with using create_fasta.py scirpt, below is my error report:

Traceback (most recent call last):
File "/public/home/bh2022044/00_softwares/vamb-master/src/create_fasta.py", line 28, in
for record in vamb.vambtools.byte_iterfasta(file, args.fastapath):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/bh2022044/00_softwares/micromamba/envs/avamb/lib/python3.12/site-packages/vamb/vambtools.py", line 470, in byte_iterfasta
raise TypeError(errormsg) from None
TypeError: First line does not contain bytes. Are you reading file in binary mode?

command:python ~/00_softwares/vamb-master/src/create_fasta.py ~/sunda/Single-wastewater/Meta/04_Binning/vamb/DZ09EF4/DZ09EF4.nextpolish_5000_c.fa res 100000 Bin
python version:3.12.9 #

[jakobnissen]

I'm looking into it now. Meanwhile - What version of Vamb are you running?

[zzsunday]

version 5.0.1

[zzsunday]

input.tar.gz
attached files are my input

[jakobnissen]

Ok - I'll try to reproduce the issue with your files. Having looked at the code, it all looks good, and I can run the script on my own files on my own computer.
I've made a patch in #419 which may improve the error message. Once it's merged to master (in 10 minutes, if all goes well), can you try to install Vamb from the master branch by pulling the latest master, entering the vamb directory and installing it with pip install -e .?

[jakobnissen]

I think I found the issue - the FASTA file is not a FASTA file.

[zzsunday]

you mean the fasta file is not one record per lines?

[jakobnissen]

No, I mean the file you sent me (not the compressed tarball, but the file DZ09EF4.nextpolish_5000_c.fa) is not a FASTA file at all. Try to look at its content e.g. using less. It's some kind of binary file.

[zzsunday]

i less the file, it is a fasta file

[zzsunday]

less_res.png.zip
that is my less file output

[jakobnissen]

Huh - here it how it looks on my computer, with the input.tar.gz you uploaded in this thread: https://asciinema.org/a/bNmweh2nCPWzI98SVFHcbplHj

When reading online, it could be that the tar file input.tar.gz is created with the BSD tar program on Apple computers, which is incompatible with the GNU tar program?

[nejcstopno]

I got the same error today.

Solved it by changing the code:

import sys
import argparse
import vamb
import pathlib

parser = argparse.ArgumentParser(
    description="""Command-line bin creator.
Will read the entire content of the FASTA file into memory - beware.""",                                                                      
    formatter_class=argparse.RawDescriptionHelpFormatter,
    add_help=False,
)

parser.add_argument("fastapath", help="Path to FASTA file")
parser.add_argument("clusterspath", help="Path to clusters.tsv")
parser.add_argument("minsize", help="Minimum size of bin in bp", type=int, default=0)                                                         
parser.add_argument("outdir", help="Directory to create")

if len(sys.argv) == 1:
    parser.print_help()
    sys.exit()

args = parser.parse_args()

# Read in FASTA files to get lengths in binary mode
lens: dict[str, int] = dict()
with open(args.fastapath, 'rb') as file:  # Open in binary mode
    for record in vamb.vambtools.byte_iterfasta(file):
        lens[record.identifier] = len(record)

# Read clusters
with open(args.clusterspath) as file:
    clusters = vamb.vambtools.read_clusters(file)

# Filter clusters by minimum size
clusters = {
    cluster: contigs
    for (cluster, contigs) in clusters.items()
    if sum(lens[c] for c in contigs) >= args.minsize
}

# Write bins using binary mode
with open(args.fastapath, 'rb') as file:  # Open in binary mode again
    vamb.vambtools.write_bins(pathlib.Path(args.outdir), clusters, file, maxbins=None)

[jakobnissen]

@nejcstopno Can you share an example FASTA file and clusters file that triggers the error? I still can't reproduce on my end. What version of Vamb did you run?

[szimmerman92]

Hi all. I have this error too. I have so far isolated it to the byte_iterfasta function in vambtools.py

Specifically it is the line of code if stripped.startswith(comment): that is throwing the error.

I think that the line of code stripped = probeline.lstrip() is not performing the lstrip operation like it is supposed to and as a result the variable "stripped" is of type byte instead of type character like the programmer most likely intended. I will update if I find a solution.

Best,
Sam