Description
Last day, I make some experiments in a Server to run the
./run_alphafold.sh -d /dataset/ -o result -p monomer -m model_2 -i input/T1061.fasta
and I read the log, confused, the T1061 is 949AA.
`
I0822 07:33:00.806264 140553952322112 jackhmmer.py:133] Launching subprocess "/opt/conda/bin/jackhmmer -o /dev/null -A /tmp/tmpxbrk9wt6/output.sE 0.0001 -E 0.0001 --cpu 8 -N 1 input/T1061.fasta /dataset//uniref90/uniref90.fasta"
I0822 07:33:01.157015 140553952322112 utils.py:36] Started Jackhmmer (uniref90.fasta) query
I0822 07:37:27.058227 140553952322112 utils.py:40] Finished Jackhmmer (uniref90.fasta) query in 265.901 seconds
I0822 07:37:27.072012 140553952322112 jackhmmer.py:133] Launching subprocess "/opt/conda/bin/jackhmmer -o /dev/null -A /tmp/tmpnn6am537/output.sE 0.0001 -E 0.0001 --cpu 8 -N 1 input/T1061.fasta /dataset//mgnify/mgy_clusters_2018_12.fa"
I0822 07:37:27.439405 140553952322112 utils.py:36] Started Jackhmmer (mgy_clusters_2018_12.fa) query
I0822 07:42:42.192071 140553952322112 utils.py:40] Finished Jackhmmer (mgy_clusters_2018_12.fa) query in 314.752 seconds
I0822 07:42:42.364272 140553952322112 hhsearch.py:85] Launching subprocess "/opt/conda/bin/hhsearch -i /tmp/tmpog4q4684/query.a3m -o /tmp/tmpog40/pdb70"
I0822 07:42:42.712445 140553952322112 utils.py:36] Started HHsearch query
I0822 07:44:18.199999 140553952322112 utils.py:40] Finished HHsearch query in 95.487 seconds
I0822 07:44:18.555797 140553952322112 hhblits.py:128] Launching subprocess "/opt/conda/bin/hhblits -i input/T1061.fasta -cpu 4 -oa3m /tmp/tmpz9oq 1000000 -realign_max 100000 -maxfilt 100000 -min_prefilter_hits 1000 -d /dataset//bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_optst30_2018_08"
I0822 07:44:19.050110 140553952322112 utils.py:36] Started HHblits query
I0822 09:01:02.278290 140553952322112 utils.py:40] Finished HHblits query in 4603.228 seconds
`
feature extraction spend time: 5305.185729026794
feature extraction Completed succesfully
I print the feature extraction time, find that , the 5305 is almost equals to the sum of each db search time, but according to the article, I think the feature extraction spend time should be almost equal to HHblits search, so can you explain the confusing problem?