colabfold_search v1.6.1 crashes using only `paired` or `unpaired`

Hi,
I tried to use the --pair-mode paired or unpaired with colabfold_search on the H1140 CASP16 target, using either only the first sequence as a monomer or both sequences as a multimer, and using local templates. I get these results:

• H1140 chain 1 with unpaired works: I get a a3m and a m8 files
• H1140 chain 1 with paired crashes directly:
  FileNotFoundError: [Errno 2] No such file or directory: '/H1140_chain1_paired/0.m8'
• H1140 complex with unpaired crashes:

Input /output/H1140_all_paired/tmp/1150175913593999343/profile_1 does not exist
Error: Alignment died
Traceback (most recent call last):
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/bin/colabfold_search", line 6, in <module>
    sys.exit(main())
             ~~~~^^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 481, in main
    mmseqs_search_monomer(
    ~~~~~~~~~~~~~~~~~~~~~^
        mmseqs=args.mmseqs,
        ^^^^^^^^^^^^^^^^^^^
    ...<19 lines>...
        unpack=args.unpack,
        ^^^^^^^^^^^^^^^^^^^
    )
    ^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 131, in mmseqs_search_monomer
    run_mmseqs(mmseqs, ["search", base.joinpath("qdb"), dbbase.joinpath(uniref_db), base.joinpath("res"), base.joinpath("tmp"), "--threads", str(threads)] + search_param)
    ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 47, in run_mmseqs
    subprocess.check_call([mmseqs] + params)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/subprocess.py", line 419, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '[PosixPath('mmseqs'), 'search', PosixPath('/output/H1140_all_paired/qdb'), PosixPath('/shared/databases2/colabfold_db_20240603/uniref30_2302_db'), PosixPath('/output/H1140_all_paired/res'), PosixPath('/output/H1140_all_paired/tmp'), '--threads', '64', '--num-iterations', '3', '--db-load-mode', '0', '-a', '-e', '0.1', '--max-seqs', '10000', '--prefilter-mode', '0', '--k-score', "'seq:96,prof:80'"]' returned non-zero exit status 1.

• H1140 complex with paired crashes:

Traceback (most recent call last):
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/bin/colabfold_search", line 6, in <module>
    sys.exit(main())
             ~~~~^^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/mmseqs/search.py", line 588, in main
    msa = msa_to_str(
        unpaired_msa, paired_msa, query_sequences, query_seqs_cardinality
    )
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/input.py", line 85, in msa_to_str
    msa += pair_msa(query_seqs_unique, query_seqs_cardinality, paired_msa, unpaired_msa)
           ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/input.py", line 65, in pair_msa
    + pad_sequences(unpaired_msa, query_seqs_unique, query_seqs_cardinality)
      ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/software/miniconda3/envs/mf-colabfold-1.6.1/lib/python3.13/site-packages/colabfold/input.py", line 38, in pad_sequences
    lines = a3m_lines[n].split("\n")
            ~~~~~~~~~^^^
IndexError: list index out of range

Start in colabfold/mmseqs/search.py at the reported mmseqs_search_monomer and msa_to_str call sites, then inspect colabfold/input.py around pair_msa and pad_sequences. Reproduce the four H1140 chain and complex cases with paired and unpaired modes, using local templates. Done means these modes no longer fail with the reported missing-file, alignment, or IndexError errors.