Error for AlphaRed

[althea-hansel]

Hello,

my AlphaRed job id 24812 seems to have failed for reasons I cannot decipher. I have attached the error output.
back-end-error.output.txt

Since this tool only takes in the FASTA sequence, I am unsure how to avoid this error.

[roccomoretti]

This page from the old forums indicates that this is due to the ColabFold job not completing in the time limit, possibly due to the length of the input sequence.

Unfortunately, there probably isn't a workaround except for running it with a shorter sequence. If that's not helpful, you may need to look into setting up and running the protocol locally.

[althea-hansel]

Thank you so much for this answer. I ended up running the proteins separately through collabfold, then inputting the relaxed PDB from that into AlphaRed as job 24959. This seems to have failed as well. Is this also a time limit issue?

ROSETTA_CRASH.log

[AmeyaHarmalkar]

Could you attach the PDB that you generated with AlphaFold and the partners you want to dock. I believe there is some issue with the structure or the partners as that is often the cause of this error but I can debug more with the structure in hand.

[althea-hansel]

crbn_d266b_relaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb.gz

[msierk]

I get the same error. Is there some residue size limit/guideline? My input sequence had a total of 811 residues in two chains, but it apparently only got through ~13% of the job.

0.colab-fold.0.output:

/usr/local/localcolabfold/colabfold-conda/bin/rosie:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').run_script('rosie==0.0.1', 'rosie')
working directory: /home/rosie/working_dir, flags file: /home/rosie/working_dir/0.colab-fold.flags
alpha-red.colabfold sequence.fasta 

WARNING: You are welcome to use the default MSA server, however keep in mind that it's a
limited shared resource only capable of processing a few thousand MSAs per day. Please
submit jobs only from a single IP address. We reserve the right to limit access to the
server case-by-case when usage exceeds fair use. If you require more MSAs: You can 
precompute all MSAs with `colabfold_search` or host your own API and pass it to `--host-url`

2024-10-18 15:58:15,322 Running colabfold 1.5.5 (4e198f5cecc6a808daa6baf7441899e5e76f7b9e)
2024-10-18 15:58:16,387 WARNING: no GPU detected, will be using CPU
2024-10-18 15:58:17,289 Found 5 citations for tools or databases
2024-10-18 15:58:17,290 Query 1/1: sequence (length 809)

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<snipped>                                                                  

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COMPLETE: 100%|██████████| 300/300 [elapsed: 01:19 remaining: 00:00]
2024-10-18 15:58:18,755 Sleeping for 9s. Reason: PENDING
2024-10-18 15:58:28,422 Sleeping for 9s. Reason: RUNNING
2024-10-18 15:58:38,096 Sleeping for 5s. Reason: RUNNING
2024-10-18 15:58:43,766 Sleeping for 8s. Reason: RUNNING
2024-10-18 15:58:52,440 Sleeping for 8s. Reason: RUNNING
2024-10-18 15:59:01,091 Sleeping for 8s. Reason: RUNNING
2024-10-18 15:59:09,765 Sleeping for 10s. Reason: RUNNING
2024-10-18 15:59:20,415 Sleeping for 8s. Reason: RUNNING
2024-10-18 15:59:29,087 Sleeping for 5s. Reason: RUNNING

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PENDING:   0%|          | 0/300 [elapsed: 00:00 remaining: ?]
                                                             

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<snipped>                                                                  

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COMPLETE:  13%|█▎        | 39/300 [elapsed: 00:48 remaining: 04:46]
COMPLETE: 100%|██████████| 300/300 [elapsed: 00:48 remaining: 00:00]
COMPLETE: 100%|██████████| 300/300 [elapsed: 00:49 remaining: 00:00]
Killed