RoseTTAFold-All-Atom: psipred 4.01 (conda) buffer overflow with 276-residue confidential HLA sequence → missing .atab file

[A-pples]

I hope this message finds you well! I'm encountering an issue when running rf2aa.run_inference for a protein structure prediction task, and I'd greatly appreciate any guidance。
Issue Summary：When running the pipeline with a 276-residue HLA protein sequence (standard natural amino acids, valid FASTA format), psipred 4.01 (installed via conda) crashes with a buffer overflow error. This leads to a chain failure: hhsearch cannot retrieve valid secondary structure data, so the .atab template file is not generated, resulting in a final FileNotFoundError for hla/A/t000_.atab.
Below is the complete, unmodified terminal output from running the command to the occurrence of the error, which includes all logs, error traces, and system messages to facilitate the analysis of this issue.
(RFAA) [SCZ123@master RoseTTAFold-All-Atom]$ python -m rf2aa.run_inference --config-name protein_sm
/public/home/SCZ123/.conda/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/defaults_list.py:251: UserWarning: In 'protein_sm': Defaults list is missing _self_. See https://hydra.cc/docs/1.2/upgrades/1.0_to_1.1/default_composition_order for more information
warnings.warn(msg, UserWarning)
Using the cif atom ordering for TRP.
./make_msa.sh /public/home/SCZ123/RoseTTAFold-All-Atom/newkang/0201.fasta hla/A 4 64 /public/home/SCZ123/RoseTTAFold2/pdb100_2021Mar03/pdb100_2021Mar03 /public/home/SCZ123/RoseTTAFold2/pdb100_2021Mar03/pdb100_2021Mar03
Running HHblits against UniRef30 with E-value cutoff 1e-10

• 17:35:01.106 INFO: Input file = hla/A/hhblits/t000_.1e-10.a3m

• 17:35:01.106 INFO: Output file = hla/A/hhblits/t000_.1e-10.id90cov75.a3m

• 17:35:05.200 INFO: Input file = hla/A/hhblits/t000_.1e-10.a3m

• 17:35:05.200 INFO: Output file = hla/A/hhblits/t000_.1e-10.id90cov50.a3m

Running PSIPRED
*** buffer overflow detected ***: psipred terminated
======= Backtrace: =========
/lib64/libc.so.6(__fortify_fail+0x37)[0x2ba0802bb7a7]
/lib64/libc.so.6(+0x116922)[0x2ba0802b9922]
/lib64/libc.so.6(__fgets_chk+0x129)[0x2ba0802b9c49]
psipred[0x401390]
psipred[0x40158a]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ba0801c5555]
psipred[0x400a89]
======= Memory map: ========
00400000-00402000 r-xp 00000000 08:01 269845781 /public/home/SCZ123/.conda/envs/RFAA/bin/psipred
00601000-00602000 r--p 00001000 08:01 269845781 /public/home/SCZ123/.conda/envs/RFAA/bin/psipred
00602000-00603000 rw-p 00002000 08:01 269845781 /public/home/SCZ123/.conda/envs/RFAA/bin/psipred
00603000-006d3000 rw-p 00000000 00:00 0
01b73000-01b94000 rw-p 00000000 00:00 0 [heap]
2ba07fc7d000-2ba07fc9f000 r-xp 00000000 fd:00 80405 /usr/lib64/ld-2.17.so
2ba07fc9f000-2ba07fca2000 rw-p 00000000 00:00 0
2ba07fca2000-2ba07fca6000 r--p 00000000 08:01 270863073 /public/home/SCZ123/.conda/envs/RFAA/lib/libgcc_s.so.1
2ba07fca6000-2ba07fcb8000 r-xp 00004000 08:01 270863073 /public/home/SCZ123/.conda/envs/RFAA/lib/libgcc_s.so.1
2ba07fcb8000-2ba07fcbb000 r--p 00016000 08:01 270863073 /public/home/SCZ123/.conda/envs/RFAA/lib/libgcc_s.so.1
2ba07fcbb000-2ba07fcbc000 r--p 00019000 08:01 270863073 /public/home/SCZ123/.conda/envs/RFAA/lib/libgcc_s.so.1
2ba07fcbc000-2ba07fcbd000 rw-p 0001a000 08:01 270863073 /public/home/SCZ123/.conda/envs/RFAA/lib/libgcc_s.so.1
2ba07fccd000-2ba07fcd0000 rw-p 00000000 00:00 0
2ba07fe9e000-2ba07fe9f000 r--p 00021000 fd:00 80405 /usr/lib64/ld-2.17.so
2ba07fe9f000-2ba07fea0000 rw-p 00022000 fd:00 80405 /usr/lib64/ld-2.17.so
2ba07fea0000-2ba07fea1000 rw-p 00000000 00:00 0
2ba07fea1000-2ba07ffa2000 r-xp 00000000 fd:00 80415 /usr/lib64/libm-2.17.so
2ba07ffa2000-2ba0801a1000 ---p 00101000 fd:00 80415 /usr/lib64/libm-2.17.so
2ba0801a1000-2ba0801a2000 r--p 00100000 fd:00 80415 /usr/lib64/libm-2.17.so
2ba0801a2000-2ba0801a3000 rw-p 00101000 fd:00 80415 /usr/lib64/libm-2.17.so
2ba0801a3000-2ba080367000 r-xp 00000000 fd:00 80407 /usr/lib64/libc-2.17.so
2ba080367000-2ba080566000 ---p 001c4000 fd:00 80407 /usr/lib64/libc-2.17.so
2ba080566000-2ba08056a000 r--p 001c3000 fd:00 80407 /usr/lib64/libc-2.17.so
2ba08056a000-2ba08056c000 rw-p 001c7000 fd:00 80407 /usr/lib64/libc-2.17.so
2ba08056c000-2ba080571000 rw-p 00000000 00:00 0
7ffc26659000-7ffc2667b000 rw-p 00000000 00:00 0 [stack]
7ffc2678a000-7ffc2678c000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Running hhsearch

• 17:35:24.451 ERROR: In /opt/conda/conda-bld/hhsuite_1709621322429/work/src/hhalignment.cpp:223: Read:

• 17:35:24.452 ERROR: sequence ss_pred contains no residues.

Error executing job with overrides: []
Traceback (most recent call last):
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main
runner.infer()
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 153, in infer
self.parse_inference_config()
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 46, in parse_inference_config
protein_input = generate_msa_and_load_protein(
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 93, in generate_msa_and_load_protein
return load_protein(str(msa_file), str(hhr_file), str(atab_file), model_runner)
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 66, in load_protein
xyz_t, t1d, mask_t, _ = get_templates(
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/data/protein.py", line 30, in get_templates
) = parse_templates_raw(ffdb, hhr_fn=hhr_fn, atab_fn=atab_fn)
File "/public/home/SCZ123/RoseTTAFold-All-Atom/rf2aa/data/parsers.py", line 628, in parse_templates_raw
for l in open(atab_fn, "r").readlines():
FileNotFoundError: [Errno 2] No such file or directory: 'hla/A/t000_.atab'

Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.

Thank you very much for your time and assistance in troubleshooting this issue. Please let me know if you need any additional details (e.g., environment configurations, sequence characteristics) to further investigate