search

piercelab / tcrmodel2

Apache License 2.0
33 stars 6 forks source link

No such file or directory: 'experiments/test_clsI_6kzw/test_clsI_6kzw_pmhc_oc/model_scores.txt' #23

Closed ddiem-ri-4D closed 2 months ago

ddiem-ri-4D commented 2 months ago

Hi @bpierce12 @rui-yin @shayanask @piercelab

I'm encountering the following error after running the command:

python run_tcrmodel2.py \ --job_id=test_clsI_6kzw \ --output_dir=experiments/ \ --tcra_seq=AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSS \ --tcrb_seq=NAGVTQTPKFQVLKTGQSMTLQCSQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSIRGSRGEQFFGPGTRLTVL \ --pep_seq=RLPAKAPLL \ --mhca_seq=SHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLH \ --ori_db=/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/data/databases

Do you know what issue I might be facing, and could you help me fix it? Thank you very much.

My Diem

Traceback (most recent call last): File "run_alphafold_tcrmodel2.3.py", line 41, in from alphafold.model import data File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/data.py", line 19, in from alphafold.model import utils File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/utils.py", line 23, in import haiku as hk File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/init.py", line 19, in from haiku import data_structures File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/data_structures.py", line 18, in from haiku._src.data_structures import to_haiku_dict File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/data_structures.py", line 30, in from haiku._src import utils File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/utils.py", line 42, in def auto_repr(cls: type[Any], *args, *kwargs) -> str: TypeError: 'type' object is not subscriptable Traceback (most recent call last): File "run_alphafold_tcrmodel2.3.py", line 41, in from alphafold.model import data File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/data.py", line 19, in from alphafold.model import utils File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/utils.py", line 23, in import haiku as hk File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/init.py", line 19, in from haiku import data_structures File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/data_structures.py", line 18, in from haiku._src.data_structures import to_haiku_dict File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/data_structures.py", line 30, in from haiku._src import utils File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/utils.py", line 42, in def auto_repr(cls: type[Any], args, **kwargs) -> str: TypeError: 'type' object is not subscriptable Traceback (most recent call last): File "run_tcrmodel2.py", line 408, in app.run(main) File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "run_tcrmodel2.py", line 238, in main with open("%s/%s_pmhc_oc/model_scores.txt" % (out_dir, job_id)) as fh: FileNotFoundError: [Errno 2] No such file or directory: 'experiments/test_clsI_6kzw/test_clsI_6kzw_pmhc_oc/model_scores.txt'

bpierce12 commented 2 months ago

Hi My Diem,

Thank you for checking on that. It seems that the initial TypeError error is leading to a failed execution and the later error where model_scores.txt is not found. We tried to reproduce your error with the same inputs here with TCRmodel2, and were unable to do that, so we were wondering whether the issue stems from your environment or software versions (e.g. haiku). Could you please check and share the packages/versions that are in your conda environment? Also, does TCRmodel2 give that error for any input, or does TCRmodel2 give that error regardless of the input TCR/peptide/MHC sequences? The latter may indicate that the issue is specific to your environment versus its handling of the input.

Best, Brian

On Sat, Aug 17, 2024 at 8:41 AM Phạm Nguyễn Mỹ Diễm < @.***> wrote:

Hi @bpierce12 https://github.com/bpierce12 @rui-yin https://github.com/rui-yin @shayanask https://github.com/shayanask @piercelab https://github.com/piercelab

I'm encountering the following error after running the command:

python run_tcrmodel2.py --job_id=test_clsI_6kzw --output_dir=experiments/ --tcra_seq=AQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSS

--tcrb_seq=NAGVTQTPKFQVLKTGQSMTLQCSQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSIRGSRGEQFFGPGTRLTVL

--pep_seq=RLPAKAPLL

--mhca_seq=SHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLH

Do you know what issue I might be facing, and could you help me fix it? Thank you very much.

My Diem

Traceback (most recent call last): File "run_alphafold_tcrmodel2.3.py", line 41, in from alphafold.model import data File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/data.py", line 19, in from alphafold.model import utils File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/utils.py", line 23, in import haiku as hk File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/init.py", line 19, in from haiku import data_structures File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/data_structures.py", line 18, in from haiku._src.data_structures import to_haiku_dict File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/data_structures.py", line 30, in from haiku._src import utils File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/utils.py", line 42, in def auto_repr(cls: type[Any], *args, *kwargs) -> str: TypeError: 'type' object is not subscriptable Traceback (most recent call last): File "run_alphafold_tcrmodel2.3.py", line 41, in from alphafold.model import data File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/data.py", line 19, in from alphafold.model import utils File "/mnt/DATAR09/DATA_DIEM/DATASM02/DATATCRTOOLS/tcrmodel2/alphafold/model/utils.py", line 23, in import haiku as hk File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/init.py", line 19, in from haiku import data_structures File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/data_structures.py", line 18, in from haiku._src.data_structures import to_haiku_dict File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/data_structures.py", line 30, in from haiku._src import utils File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/haiku/_src/utils.py", line 42, in def auto_repr(cls: type[Any], args, **kwargs) -> str: TypeError: 'type' object is not subscriptable Traceback (most recent call last): File "run_tcrmodel2.py", line 408, in app.run(main) File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/home/diem/anaconda3/envs/tcrmodel/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "run_tcrmodel2.py", line 238, in main with open("%s/%s_pmhc_oc/model_scores.txt" % (out_dir, job_id)) as fh: FileNotFoundError: [Errno 2] No such file or directory: 'experiments/test_clsI_6kzw/test_clsI_6kzw_pmhc_oc/model_scores.txt'

— Reply to this email directly, view it on GitHub https://github.com/piercelab/tcrmodel2/issues/23, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSP6VKU4LT2JPGFRX2ID5TZR5AFZAVCNFSM6AAAAABMVMPYOWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ3TCNJQHE4DMOA . You are receiving this because you were mentioned.Message ID: @.***>

ddiem-ri-4D commented 2 months ago

Hi @bpierce12 Here are the results after I reran with TCR-pMHCI prediction. I'm not sure if the results below are complete; could you please help me check them?

test_clsI_6kzw.zip

bpierce12 commented 2 months ago

Those results look complete to me, as I see the PDB models and scores. Glad that it's working for you now! Let me know if you have any other issues in the future.

On Sat, Aug 24, 2024 at 12:47 AM Phạm Nguyễn Mỹ Diễm < @.***> wrote:

Hi @bpierce12 https://github.com/bpierce12 Here are the results after I reran with TCR-pMHCI prediction. I'm not sure if the results below are complete; could you please help me check them?

test_clsI_6kzw.zip https://github.com/user-attachments/files/16735261/test_clsI_6kzw.zip

— Reply to this email directly, view it on GitHub https://github.com/piercelab/tcrmodel2/issues/23#issuecomment-2308092252, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABSP6VOEX3NO42GKRLQGMU3ZTAF4LAVCNFSM6AAAAABMVMPYOWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBYGA4TEMRVGI . You are receiving this because you were mentioned.Message ID: @.***>

bpierce12 commented 2 months ago

Closing because the PDB and scores (statistics.json) files were successfully output for the user. If that error message still occurs during runtime, it does not seem consequential.