Hi there, community!
I am using BLASR to align PB subreads to a reference. Usually this worked pretty well, but now I added some options that were recommended for the use with PBHoney, namely -clipping soft and -noSplitSubreads.
Suddenly this job has been running for more than 24 hours already, on the same dataset that took only a few hours before.
Does anyone have a clue whether it is one of the flags that slows it down so significantly? (Otherwise it could also be a problem with the computer or whatever)
Complete command is below. $file is a .fofn with several .bax.h5 inside.
Any suggestions highly appreciated!
Thanks,
myrs
I am using BLASR to align PB subreads to a reference. Usually this worked pretty well, but now I added some options that were recommended for the use with PBHoney, namely -clipping soft and -noSplitSubreads.
Suddenly this job has been running for more than 24 hours already, on the same dataset that took only a few hours before.
Does anyone have a clue whether it is one of the flags that slows it down so significantly? (Otherwise it could also be a problem with the computer or whatever)
Complete command is below. $file is a .fofn with several .bax.h5 inside.
Any suggestions highly appreciated!
Thanks,
myrs
Code:
BLASR $file $REF\
-sa $INDEX\
-sam\
-nproc 8\
-bestn 1\
-clipping soft\
-noSplitSubreads\