firefly01 alphafold test run

(base) hqin@CS313BQin ~ % d.sh

(base) hqin@CS313BQin ~ % ssh xxx@firefly.simcenter.utc.edu

xxxx@firefly.simcenter.utc.edu's password: 

Activate the web console with: systemctl enable --now cockpit.socket

Last login: Wed Jul 27 10:24:27 2022 from 10.63.72.189

[xxxx@firefly ~]$ ssh firefly01

The authenticity of host 'firefly01 (192.168.223.3)' can't be established.

ECDSA key fingerprint is asdfasfasfasdf

Are you sure you want to continue connecting (yes/no/[fingerprint])? yes

Warning: Permanently added 'firefly01,192.168.223.3' (ECDSA) to the list of known hosts.

xxxx@firefly01's password: 

Activate the web console with: systemctl enable --now cockpit.socket

[xxxx@firefly01 ~]$ ls

 2022-06-16_unmasked.fa                   Downloads          test-scp

 anaconda3                                github             test-ts-hello.tar

'Anaconda3-2021.05-Linux-x86_64 (1).sh'   hellosts.txt       tmp

 bin                                      ibm                tmp.Rmd

 bindings.txt                             lib                tmp.txt

 cdsapp                                   old                tools

 commands.txt                             R                  trash

 csh.backup                               R-4.0.3            unison.log

 -cwd.e8271                               readme.txt        'VirtualBox VMs'

 -cwd.o8271                               scr.hqin           wget-log

 demo                                     simcenter-qinlab

 Desktop                                  T1050

[xxxx@firefly01 ~]$ bash /opt/ohpc/pub/singularity/test-scripts/alphafold-2/alphafold-singularity-run.sh

Mounting /scr -> /mnt/data_dir

Mounting /scr/alphafold-data/uniref90 -> /mnt/uniref90_database_path

Mounting /scr/alphafold-data/mgnify -> /mnt/mgnify_database_path

Mounting /scr/alphafold-data/bfd -> /mnt/bfd_database_path

Mounting /scr/alphafold-data/uniclust30/uniclust30_2018_08 -> /mnt/uniclust30_database_path

Mounting /scr/alphafold-data/pdb70 -> /mnt/pdb70_database_path

Mounting /scr/alphafold-data/pdb_mmcif -> /mnt/template_mmcif_dir

Mounting /scr/alphafold-data/pdb_mmcif -> /mnt/obsolete_pdbs_path

--data_dir=/mnt/data_dir/alphafold-data --uniref90_database_path=/mnt/uniref90_database_path/uniref90.fasta --mgnify_database_path=/mnt/mgnify_database_path/mgy_clusters_2018_12.fa --bfd_database_path=/mnt/bfd_database_path/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path=/mnt/uniclust30_database_path/uniclust30_2018_08 --pdb70_database_path=/mnt/pdb70_database_path/pdb70 --template_mmcif_dir=/mnt/template_mmcif_dir/mmcif_files --obsolete_pdbs_path=/mnt/obsolete_pdbs_path/obsolete.dat --output_dir=/mnt/output --benchmark=0 --logtostderr --fasta_paths=/opt/ohpc/pub/singularity/test-scripts/alphafold-2/T1050.fasta --max_template_date=2021-12-31

/scr:/mnt/data_dir,/scr/alphafold-data/uniref90:/mnt/uniref90_database_path,/scr/alphafold-data/mgnify:/mnt/mgnify_database_path,/scr/alphafold-data/bfd:/mnt/bfd_database_path,/scr/alphafold-data/uniclust30/uniclust30_2018_08:/mnt/uniclust30_database_path,/scr/alphafold-data/pdb70:/mnt/pdb70_database_path,/scr/alphafold-data/pdb_mmcif:/mnt/template_mmcif_dir,/scr/alphafold-data/pdb_mmcif:/mnt/obsolete_pdbs_path,/home/hqin:/mnt/output

I0801 11:48:55.799806 140491381822400 templates.py:857] Using precomputed obsolete pdbs /mnt/obsolete_pdbs_path/obsolete.dat.

I0801 11:48:56.409429 140491381822400 xla_bridge.py:244] Unable to initialize backend 'tpu_driver': NOT_FOUND: Unable to find driver in registry given worker: 

I0801 11:48:57.418743 140491381822400 xla_bridge.py:244] Unable to initialize backend 'tpu': INVALID_ARGUMENT: TpuPlatform is not available.

I0801 11:49:03.148635 140491381822400 run_alphafold.py:385] Have 5 models: ['model_1', 'model_2', 'model_3', 'model_4', 'model_5']

I0801 11:49:03.148812 140491381822400 run_alphafold.py:397] Using random seed 725758993269421837 for the data pipeline

I0801 11:49:03.149077 140491381822400 run_alphafold.py:150] Predicting T1050

Traceback (most recent call last):

  File "/app/alphafold/run_alphafold.py", line 427, in <module>

    app.run(main)

  File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run

    _run_main(main, args)

  File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main

    sys.exit(main(argv))

  File "/app/alphafold/run_alphafold.py", line 412, in main

    is_prokaryote=is_prokaryote)

  File "/app/alphafold/run_alphafold.py", line 164, in predict_structure

    msa_output_dir=msa_output_dir)

  File "/app/alphafold/alphafold/data/pipeline.py", line 148, in process

    with open(input_fasta_path) as f:

FileNotFoundError: [Errno 2] No such file or directory: '/opt/ohpc/pub/singularity/test-scripts/alphafold-2/T1050.fasta'