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Error in recent colabfold_batch with --templates option

See original GitHub issue

Hi Yoshitaka-san,

I tried your latest colabfold_batch code. With the following command, following your instruction in main page:

$ colabfold_batch --amber --templates --num-recycle 3 input_fasta/test.fasta af2_output

The input_fasta/test.fasta contains this:


$ cat input_fasta/test.fasta
>Gvb.fl_hhaw_x1.s1
HHAWEPEKKKPEGMKDQPSKQHHAW
>Gvb.fl_hhaw_x1.s10
HHAWSNYDERKQNGRYYIWKEHHAW

But I get the following error. How can I resolve it?

$ colabfold_batch --amber --templates --num-recycle 3  input_fasta/test.fasta af2_output
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, please host your own API and pass it to `--host-url`
2021-12-06 15:40:37,273 Found 8 citations for tools or databases
2021-12-06 15:40:46,439 Query 1/2: Gvb.fl_hhaw_x1.s1 (length 25)
COMPLETE: 100%|████████████████████████████████████████████████████████████████████████████████████████| 150/150 [elapsed: 00:02 remaining: 00:00]
0	no_templates_found
2021-12-06 15:40:48,450 Could not get MSA/templates for Gvb.fl_hhaw_x1.s1: expected str, bytes or os.PathLike object, not NoneType
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/colabfold/batch.py", line 603, in run
    host_url,
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/colabfold/batch.py", line 428, in get_msa_and_templates
    query_seqs_unique[index],
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/colabfold/batch.py", line 93, in mk_template
    obsolete_pdbs_path=None,
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/alphafold/data/templates.py", line 836, in __init__
    if not glob.glob(os.path.join(self._mmcif_dir, '*.cif')):
  File "/home/ubuntu/anaconda3/lib/python3.7/posixpath.py", line 80, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
2021-12-06 15:40:48,451 Query 2/2: Gvb.fl_hhaw_x1.s10 (length 25)
2021-12-06 15:40:49,415 Sleeping for 9s. Reason: RATELIMIT
2021-12-06 15:40:59,395 Sleeping for 8s. Reason: RATELIMIT
2021-12-06 15:41:08,362 Sleeping for 5s. Reason: RATELIMIT
2021-12-06 15:41:14,342 Sleeping for 5s. Reason: RATELIMIT
2021-12-06 15:41:20,315 Sleeping for 10s. Reason: RATELIMIT
COMPLETE: 100%|████████████████████████████████████████████████████████████████████████████████████████| 150/150 [elapsed: 00:43 remaining: 00:00]
0	no_templates_found
2021-12-06 15:41:32,334 Could not get MSA/templates for Gvb.fl_hhaw_x1.s10: expected str, bytes or os.PathLike object, not NoneType
Traceback (most recent call last):
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/colabfold/batch.py", line 603, in run
    host_url,
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/colabfold/batch.py", line 428, in get_msa_and_templates
    query_seqs_unique[index],
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/colabfold/batch.py", line 93, in mk_template
    obsolete_pdbs_path=None,
  File "/home/ubuntu/anaconda3/lib/python3.7/site-packages/alphafold/data/templates.py", line 836, in __init__
    if not glob.glob(os.path.join(self._mmcif_dir, '*.cif')):
  File "/home/ubuntu/anaconda3/lib/python3.7/posixpath.py", line 80, in join
    a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
2021-12-06 15:41:32,334 Done

Issue Analytics

State:
Created 2 years ago
Comments:29 (13 by maintainers)

Top GitHub Comments

3reactions

recep2244commented, Dec 11, 2021

Thanks for the suggestion. the export path worked with the template option without the hhsearch issue

export PATH=“/home/intfold/programs/alphafold2/colabfold_multimer/colabfold_batch/colabfold-conda/bin:$PATH”

colabfold_batch --amber --templates --num-recycle 12 /home/intfold/programs/alphafold2/colabfold_multimer/test/T1076/T1076.fasta /home/intfold/programs/alphafold2/colabfold_multimer/test/T1076/template/

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, please host your own API and pass it to --host-url 2021-12-11 18:57:07,715 Running colabfold 1.2.0 (115646efb015774200e8fed535affa0641529f09) 2021-12-11 18:57:07,758 Found 8 citations for tools or databases 2021-12-11 18:57:27,192 Query 1/1: T1076 (length 552) COMPLETE: 100%|██████████████████████| 150/150 [elapsed: 00:00 remaining: 00:00] 2021-12-11 18:58:10,637 Running model_3 2021-12-11 19:27:43,289 model_3 took 1755.8s (12 recycles) with pLDDT 96.3 2021-12-11 19:29:33,859 Running model_4

1reaction

A-Talaveracommented, Dec 10, 2021

Hi @YoshitakaMo

It worked!!! The trick was to install the driver that comes together with the CUDA toolkit 11.5. Now I have the same configuration as you have (NVIDIA-SMI 495.29.05 Driver Version: 495.29.05 CUDA Version: 11.5 Build cuda_11.2.r11.2/compiler.29618528_0) and everything works perfectly.

Thanks a lot again. Best regards. Ariel