About RuntimeError of hhsearch

[Maikuraky]

Due to the network, I use non-docker version. But in the process of Inference, there was a problem with hhsearch：
RuntimeError: HHSearch failed:
stdout:
stderr:

• 00:22:03.447 INFO: /tmp/tmpkkewtvxt/query.a3m is in A2M, A3M or FASTA format
• 00:22:03.593 INFO: Searching 80799 database HHMs without prefiltering
• 00:22:03.629 INFO: Iteration 1
• 00:22:03.986 INFO: Scoring 80799 HMMs using HMM-HMM Viterbi alignment
• 00:22:04.056 INFO: Alternative alignment: 0
• 00:23:25.517 INFO: 80799 alignments done
• 00:23:25.786 INFO: Alternative alignment: 1
• 00:23:30.387 INFO: 3802 alignments done
• 00:23:30.391 INFO: Alternative alignment: 2
• 00:23:31.297 INFO: 438 alignments done
• 00:23:31.297 INFO: Alternative alignment: 3

Can someone give me some suggestions or solutions? thanks

[mestia]

I am seeing the same issue, was it solved for you? What was the problem?
Thank you!

[7itrees]

I am seeing the same issue, was it solved for you? What was the problem?
Thank you!

I have the same error，was it solved for you?

[SoniaAndrys]

Hi @Maikuraky, I encountered the same problem while running alphafold2 on supercomputer with use of singularity (non-docker version here).
Do you have any tips on how to solve the issue?

Best regards,
Sonia

[yunxiangz]

I am seeing the same issue, was it solved for you? What was the problem?

Best regards,
Frank

[AaronFeller]

I also just hit this error running in singularity. Any fix?

[wdlingit]

Hi people! I am using the docker version and I got the same error (ONLY for the first line "INFO: /tmp/tmp2wr1c410/query.a3m is in A2M, A3M or FASTA format"), either using the full database or using the reduced database. Just noticed that this might be simple. Alphafold seemed working after I removed the terminal * from the input sequence file. Hope this would work for your situation.

[wttat]

Hi people! I am using the docker version and I got the same error (ONLY for the first line "INFO: /tmp/tmp2wr1c410/query.a3m is in A2M, A3M or FASTA format"), either using the full database or using the reduced database. Just noticed that this might be simple. Alphafold seemed working after I removed the terminal * from the input sequence file. Hope this would work for your situation.

could you explain what is the terminal * from the input sequence file means, thanks

Best regards
Tong

[wdlingit]

Hi people! I am using the docker version and I got the same error (ONLY for the first line "INFO: /tmp/tmp2wr1c410/query.a3m is in A2M, A3M or FASTA format"), either using the full database or using the reduced database. Just noticed that this might be simple. Alphafold seemed working after I removed the terminal * from the input sequence file. Hope this would work for your situation.

could you explain what is the terminal * from the input sequence file means, thanks

Best regards Tong

For example:

>MCHU
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
DIDGDGQVNYEEFVQMMTAK*

The very last asterisk.

[wttat]

Hi people! I am using the docker version and I got the same error (ONLY for the first line "INFO: /tmp/tmp2wr1c410/query.a3m is in A2M, A3M or FASTA format"), either using the full database or using the reduced database. Just noticed that this might be simple. Alphafold seemed working after I removed the terminal * from the input sequence file. Hope this would work for your situation.

could you explain what is the terminal * from the input sequence file means, thanks
Best regards Tong

For example:

>MCHU MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA DIDGDGQVNYEEFVQMMTAK*

The very last asterisk.

really appreciate that.

I have found the reason why I countered this. I used AWS CodeBuild to build my alphafold2 image, but it runs on a amd64 instance, so somehow it went wrong.

solution :
wttat@51afdd7

[mohsenumn]

Make sure you have given the necessary permissions to the alphafold_data files.
You can grant permission using chmod g+r * when you're in pdb70 directory, for example.