Open jianhaoc opened 3 years ago
Hi, I have run as guide (see below). python3 run_alphafold.py --fasta_paths=m.fasta --max_template_date=2015-11-10
However, I only see a folder msas/ in output dir, with both mgnify_hits.sto and uniref90_hits.sto inside folder msas/.
During running, there is log below.
I0808 12:36:13.795397 139856370325312 tpu_client.py:54] Starting the local TPU driver. I0808 12:36:13.796061 139856370325312 xla_bridge.py:214] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: local:// I0808 12:36:14.556874 139856370325312 xla_bridge.py:214] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available. I0808 12:36:19.394575 139856370325312 run_alphafold.py:293] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5'] I0808 12:36:19.394828 139856370325312 runalphafold.py:306] Using random seed 8198044181325425710 for the data pipeline I0808 12:36:19.395596 139856370325312 pipeline.py:136] loading uniref90 I0808 12:36:19.511542 139856370325312 pipeline.py:147] loading mgnify I0808 12:36:19.513229 139856370325312 pipeline.py:153] query mgnify I0808 12:36:19.513805 139856370325312 hhblits.py:128] Launching subprocess "hhblits -i m.fasta -cpu 4 -oa3m /tmp/tmpe4g0qjk/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /data01/xukui/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /data01/xukui/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08" I0808 12:36:19.571469 139856370325312 utils.py:36] Started HHblits query
I see -o /dev/null. Where should I change that option? Thank you!
Hi, I have run as guide (see below). python3 run_alphafold.py --fasta_paths=m.fasta --max_template_date=2015-11-10
However, I only see a folder msas/ in output dir, with both mgnify_hits.sto and uniref90_hits.sto inside folder msas/.
During running, there is log below.
I0808 12:36:13.795397 139856370325312 tpu_client.py:54] Starting the local TPU driver. I0808 12:36:13.796061 139856370325312 xla_bridge.py:214] Unable to initialize backend 'tpu_driver': Not found: Unable to find driver in registry given worker: local:// I0808 12:36:14.556874 139856370325312 xla_bridge.py:214] Unable to initialize backend 'tpu': Invalid argument: TpuPlatform is not available. I0808 12:36:19.394575 139856370325312 run_alphafold.py:293] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5'] I0808 12:36:19.394828 139856370325312 runalphafold.py:306] Using random seed 8198044181325425710 for the data pipeline I0808 12:36:19.395596 139856370325312 pipeline.py:136] loading uniref90 I0808 12:36:19.511542 139856370325312 pipeline.py:147] loading mgnify I0808 12:36:19.513229 139856370325312 pipeline.py:153] query mgnify I0808 12:36:19.513805 139856370325312 hhblits.py:128] Launching subprocess "hhblits -i m.fasta -cpu 4 -oa3m /tmp/tmpe4g0qjk/output.a3m -o /dev/null -n 3 -e 0.001 -maxseq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /data01/xukui/alphafold/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt -d /data01/xukui/alphafold/uniclust30/uniclust30_2018_08/uniclust30_2018_08" I0808 12:36:19.571469 139856370325312 utils.py:36] Started HHblits query
I see -o /dev/null. Where should I change that option? Thank you!