bishopia / my_reasonate Goto Github PK

Dear @bishopia
Greetings!

Now must software is running with standard parameters.
but the programme has been running for more than 10 days.
Now it is in the final stage [BLAT], but this step has been running for more than 5 days.
I wonder why it takes so long or if I need to change the number of threads.

“Spliting the genome into 10 sub-genomes ... [SubFiles:10] [done] [Elapsed time: 817 seconds]

Scanning the nucleotide sequences for potential MITEs ... Total calculation time elapsed: 72093 seconds.

Loading the annotation data ... [RawMITEs:929224] [done] [Time:43 seconds]

Removing redundancy in the predicted MITEs ... [RuleBasedRemoving:29] [MITE:929195] [done] [Time:44 seconds]

Clustering ... [BLAST] [done] [ClusterNum:21285] [Time:190391 seconds]

Deciding the strand information of each valid MITE ... [done] [Time:2425 seconds]

Saving the data ... [done] [ValidMITENum:282561] [Time:2184 seconds]

Screening for all the MITE copies ... [BackupMITEs:220053] [Templates:220053] [BLAT]”

Professor Fengfeng Zhou (the author of the software) suggested that the BLAT step tries to detect the flanking TIR signals of the detected MITEs. My scanning found 220053 candidate MITEs, which may cause a slow running. He also mentioned that he has never handled that large number of candidate MITEs. He is not sure whether it helps by increasing the number of threads.

Please send me your suggestion. Thank you for your kindness.
With regards
Ramky