Zhanglab forum

Posted: **Mon Jul 14, 2025 4:11 am**

Good afternoon,

When running DeepMSA2_noIMG.py I encounter 2 errors:

First I get the warning: WARNING! No such file .../DeepMSA2/database/UniRef30_2022_02/UniRef30_2022_02.cs219
Fall back to hhblits3. Result may be affected.

I have seen this brought up previously on the forum but never addressed. This is strange since I downloaded the UniRef30_2022_02 folder directly from this website and it contains UniRef30_2022_02_cs219.ffdata and UniRef30_2022_02_cs219.ffindex, but the actual UniRef30_2022_02.cs219 is not there

Second, I get the error:

Error in hhblits: unrecognized HMM file format in '12973060.hhm'.
Context:
'53.a3m

'
grep: /tmp/user/MSA_511076309/hhblits.a3m: No such file or directory
Traceback (most recent call last):
File ".../DeepMSA2/bin/dMSA/scripts/build_MSA.py", line 1118, in <module>
nf=build_MSA(prefix,sequence,tmpdir,db_dict,
File ".../DeepMSA2/bin/dMSA/scripts/build_MSA.py", line 917, in build_MSA
shutil.copyfile(hhblits_prefix+".a3m",prefix+".hhba3m")
File ".../DeepMSA2/anaconda3/lib/python3.9/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/user/MSA_511076309/hhblits.a3m'

If this issue has occurred before and if there are any known solutions, please let me know.

Thank you,
Dimitris

Posted: **Sat Jul 19, 2025 5:36 pm**

Thank you for your interest in our work.

The first error is caused by the missing of the file ending with .cs219.

The .cs219 file is required by hhblits3. We will regenerate it and update the file on our server within the next few days.

The second error is caused by the unexisting of the file hhblits.a3m.

Can you elaborate in more detail about how the second error occurred?

Posted: **Thu Aug 07, 2025 2:58 pm**

I haven't run into it myself yet, but this is helpful to know in case I do.Speed Stars
From the sounds of it, maybe it's a missing symlink or filename mismatch issue? Has anyone tried renaming or symbolic linking the .ffdata/.ffindex files to .cs219 to test if it resolves the fallback warning?"

Posted: **Sat Aug 09, 2025 2:18 am**

The hhblits error ended up being my fault, one of the databases didnt unzip properly so this is now fixed. However, please let me know if you und up uploading the .cs219 file and how I can download it

Posted: **Sat Aug 23, 2025 5:17 pm**

We are still working on the task and will inform you as soon as the conversion is complete.

Posted: **Mon Sep 15, 2025 10:40 pm**

dimi wrote: ↑Mon Jul 14, 2025 4:11 am Good afternoon,

When running DeepMSA2_noIMG.py I encounter 2 errors:

First I get the warning: WARNING! No such file .../DeepMSA2/database/UniRef30_2022_02/UniRef30_2022_02.cs219
Fall back to hhblits3. Result may be affected.

I have seen this brought up previously on the forum but never addressed. This is strange since I downloaded the UniRef30_2022_02 folder directly from this website and it contains UniRef30_2022_02_cs219.ffdata and UniRef30_2022_02_cs219.ffindex, but the actual UniRef30_2022_02.cs219 is not there

Second, I get the error:

Error in hhblits: unrecognized HMM file format in '12973060.hhm'.
Context:
'53.a3m

'
grep: /tmp/user/MSA_511076309/hhblits.a3m: No such file or directory
Traceback (most recent call last):
File ".../DeepMSA2/bin/dMSA/scripts/build_MSA.py", line 1118, in <module>
nf=build_MSA(prefix,sequence,tmpdir,db_dict,
File ".../DeepMSA2/bin/dMSA/scripts/build_MSA.py", line 917, in build_MSA
shutil.copyfile(hhblits_prefix+".a3m",prefix+".hhba3m")
File ".../DeepMSA2/anaconda3/lib/python3.9/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/user/MSA_511076309/hhblits.a3m'

If this issue has occurred before and if there are any known solutions, please let me know.

Thank you,
Dimitris

I'm encountering two issues when running DeepMSA2_noIMG.py:
Missing .cs219 file:
I downloaded UniRef30_2022_02 from your site, but the file UniRef30_2022_02.cs219 is missing. Only .ffdata and .ffindex are there. Is this expected?
hhblits error:
I get unrecognized HMM file format and later a FileNotFoundError for hhblits.a3m. It seems hhblits fails and doesn't generate the expected output.

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