Alignment error

[Ottovonxu]

Hi

I ran the following scripts and get the error in alignment.

python3 scripts/precompute_alignments.py data/pdb_mmcif/mmcif_files/ data/alignment/ \
    --uniref90_database_path data/uniref90/uniref90.fasta \
    --mgnify_database_path data/mgnify/mgy_clusters_2018_12.fa \
    --pdb70_database_path data/pdb70/pdb70 \
    --uniclust30_database_path data/uniclust30/uniclust30_2018_08/uniclust30_2018_08 \
    --bfd_database_path data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
    --cpus 16 \
    --jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer \
    --hhblits_binary_path lib/conda/envs/openfold_venv/bin/hhblits \
    --hhsearch_binary_path lib/conda/envs/openfold_venv/bin/hhsearch \
    --kalign_binary_path lib/conda/envs/openfold_venv/bin/kalign

Here is the error log:

ERROR:root:- 09:17:56.463 ERROR: Error in /opt/conda/conda-bld/hhsuite_1645696999782/work/src/hhalignment.cpp:3539: MergeMasterSlave:
ERROR:root:- 09:17:56.463 ERROR:        did not find 145 match states in sequence 1 of tr|A0A1D1YLJ1|A0A1D1YLJ1_9ARAE. Sequence:
ERROR:root:GYKAPELTKMKDAGKESDIYSLGVIFLEMVTRKDTNSDFLPTWDLHLSNSLKNPVFDGKISEMISHGLLRQSREQNCITGEGLLMFLQLAIACRSPSPRLRPDIKQVLGKLEEIELWKLPNQFGGDRLPNRG
ERROR:root:HHblits stderr end
WARNING:root:Failed to run alignments for 7avy_A. Skipping...
Exception in thread Thread-1:
Traceback (most recent call last):
  File "scripts/precompute_alignments.py", line 40, in run_seq_group_alignments
    fasta_path, alignment_dir
  File "/scratch1/zx22/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/openfold-1.0.0-py3.7-linux-x86_64.egg/openfold/data/data_pipeline.py", line 485, in run
    self.hhblits_bfd_uniclust_runner.query(fasta_path)
  File "/scratch1/zx22/openfold/lib/conda/envs/openfold_venv/lib/python3.7/site-packages/openfold-1.0.0-py3.7-linux-x86_64.egg/openfold/data/tools/hhblits.py", line 162, in query
    % (stdout.decode("utf-8"), stderr[:500_000].decode("utf-8"))
RuntimeError: HHblits failed
stdout:
stderr:

Could you help me with it? Thanks!

[gahdritz]

Not sure about this one. I recommend making an issue on the HHSuite GitHub page.

[gahdritz]

(didn't mean to close)