Hi I'm trying use <colabfold_search --mmseqs> generate MSA, but it not ran as I expectally, did I missed something? A lot thanks~

Expected Behavior

I thought it will generate a "msas" dictionary, and it contained all a3m files.

Current Behavior

srun colabfold_search --mmseqs /public/home/xxx/ras_scan/rasras.fasta --db1 uniref30_2302 --db2 pdb100_foldseek_230517 /public/home/xxx/MSA /public/home/xxxMSA/pdb100 /public/home/xxx/ras_scan/msas --threads 36 --use-templates 1

ColabFold Output (for bugs)

File "/public/home/xxx/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 1863, in _execute_child
with Popen(*popenargs, **kwargs) as p:
File "/public/home/xxx/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 971, in init
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')
self._execute_child(args, executable, preexec_fn, close_fds,
File "/public/home/xxx/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 1863, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')
raise child_exception_type(errno_num, err_msg, err_filename)
self._execute_child(args, executable, preexec_fn, close_fds,
File "/public/home/xxx/localcolabfold/colabfold-conda/lib/python3.10/subprocess.py", line 1863, in _execute_child
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')
raise child_exception_type(errno_num, err_msg, err_filename)
PermissionError: [Errno 13] Permission denied: PosixPath('/public/home/xxx/ras_scan/rasras.fasta')

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

I'm using HPC with intel-E5 and 180Gb RAM

#!/bin/bash
#SBATCH --job-name=RSan32
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=36
#SBATCH --mem=150G

source /public/software/profile.d/.bashrc
conda activate MMseq2
export PATH="/public/home/xxxx/localcolabfold/colabfold-conda/bin:$PATH"

The payload names no repository files or tests. Start with the colabfold_search invocation and the repeated Python PermissionError for rasras.fasta, then inspect the command's documented input and output behavior. Done should be a reproducible explanation of the failure and the expected MSA outputs, or a clearly scoped documentation correction.