Closed wangyugui closed 6 years ago
without this option(corOverlapper=minimap), canu(v1.6 +127 ) failed too.
# cat ./correction/ecoli.corStore.err
ERROR: unknown option '-O'
ERROR: unknown option './ecoli.ovlStore'
ERROR: unknown option '-ec'
ERROR: unknown option '4'
ERROR: unknown option '-eC'
ERROR: unknown option '2000'
usage: /usr/hpc-bio/canu-1.6.git/Linux-amd64/bin/generateCorrectionLayouts -G gkpStore -O ovlStore ...
INPUTS
-G gkpStore mandatory path to gkpStore
-S file overlap score thresholds (from filterCorrectionOverlaps)
if not supplied, will be estimated from ovlStore
OUTPUTS
-C corStore output layouts to store 'corStore'
-p prefix output prefix name, for logging and summary report
READ SELECTION
-b bgnID process reads starting at bgnID
-e endID process reads up to but not including endID
EVIDENCE SELECTION
-eL length minimum length of evidence overlaps
-eM length minimum length of a corrected read
canu(v1.6 +118) + without 'corOverlapper=minimap' works well. canu(v1.6 +118) + with 'corOverlapper=minimap' failed too.
You're using the tip, which may not always be stable, we recommend the release version. In this case there was a bad commit which is now fixed causing your crash without corOverlapper=minimap
. Update the code and try again.
As for the minimap crash, I think you don't have it symlinked the binary from the Linux-amd64/bin/ folder. I updated the docs to clarify this.
'Canu snapshot v1.6 +132 changes' works well with/without 'corOverlapper=minimap'.
Thanks a lot.
canu corOverlapper=minimap failed
canu command & log log.zip
dataset ecoli in https://github.com/PacificBiosciences/DevNet/wiki/Datasets