Bogart Failed, Unknown Options Error

[bytoyo]

Hello,

I've encountered some issues while using Canu for genome assembly. Here's the command I used:

canu -p asm -d $out_dir -assemble canuIterationMax=1 stopOnLowCoverage=0 minInputCoverage=0 maxInputCoverage=10000 batMemory=200 genomeSize='3.1g' gridOptionsUTGOVL='--time=12:00:00' gridOptionsmeryl='--mem-per-cpu=4g' gridOptions='--time=24:00:00 --partition=big' ovlThreads=32 utgOvlRefBlockLength=10000000000 ovlMerThreshold=20000 minReadLength=4000 minOverlapLength=1000 batOptions="-covgaptype uncovered -D symmetricoverlaps -stop bestedges -ef 1e-5 -readlen 1-$MAX_BOGART_LEN" stopAfter=unitig -pacbio-hifi $reads "${@:3}"

However, I encountered an error that some unknown options are being used. The error message is as follows:

-- Bogart failed, tried 1 times, giving up.
--

ABORT:
ABORT: Canu 2.0
ABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.
ABORT: Try restarting.  If that doesn't work, ask for help.
ABORT:
ABORT: Disk space available:  2257422.396 GB
ABORT:
ABORT: Last 50 lines of the relevant log file (unitigging/4-unitigger/unitigger.err):
ABORT:
ABORT:                       '-nofilter coveragegap-and-HIGHERROR'
ABORT:   
ABORT:     -eg F          Do not use overlaps more than F fraction error when when finding initial best edges.
ABORT:     -eM F          Do not load overlaps more then F fraction error (useful only for -save).
ABORT:   
ABORT:     -ca L          Split a contig if there is an alternate path from an overlap of at least L bases.
ABORT:                    Default: 2100.
ABORT:     -cp P          Split a contig if there is an alternate path from an overlap at most P percent
ABORT:                    different from the length of the best overlap.  Default: 200.
ABORT:   
ABORT:     -dg D          Use overlaps upto D standard deviations from the mean when building the best
ABORT:                    overlap graph.  Default 6.0.
ABORT:     -db D          Like -dg, but for merging bubbles into primary contigs.  Default 6.0.
ABORT:     -dr D          Like -dg, but for breaking repeats.  Default 3.0.
ABORT:   
ABORT:   Secret Algorithmic Options:
ABORT:   
ABORT:     -covgapolap n      Require overlaps to overlap by at least n bases.
ABORT:     -lopsided m n      Set how lopsided reads are detected and/or treated.
ABORT:                          m = off        - don't detect at all (omit n parameter)
ABORT:                          m = noseed n   - detect, n% difference, allow edges to but don't seed overlaps with them
ABORT:                          m = nobest n   - detect, n% difference, exclude from bog graph completely
ABORT:     -minolappercent f  Set a minimum overlap length, per overlap, as f*min(readAlen, readBlen)
ABORT:   
ABORT:   Debugging and Logging
ABORT:   
ABORT:     -D <name>  enable logging/debugging for a specific component.
ABORT:     -d <name>  disable logging/debugging for a specific component.
ABORT:                  overlapScoring
ABORT:                  bestOverlaps
ABORT:                  errorProfiles
ABORT:                  optimizePositions
ABORT:                  chunkGraph
ABORT:                  buildUnitig
ABORT:                  placeUnplaced
ABORT:                  orphans
ABORT:                  splitDiscontinuous
ABORT:                  intermediateTigs
ABORT:                  setParentAndHang
ABORT:                  stderr
ABORT:   
ABORT:   Unknown option '-covgaptype'.
ABORT:   Unknown option 'uncovered'.
ABORT:   Unknown '-D' option 'symmetricoverlaps'.
ABORT:   Unknown option '-stop'.
ABORT:   Unknown option 'bestedges'.
ABORT:   Unknown option '-ef'.
ABORT:   Unknown option '1e-5'.
ABORT:   Unknown option '-readlen'.
ABORT:   Unknown option '1-1000000'.
ABORT:

I’ve checked the Canu documentation but couldn’t find these options. I’m wondering if these options have been deprecated, and if so, are there any alternative options that I can use.

The version of Canu I'm using is 2.0.

Thank you for your help!

[skoren]

Your parameters to Canu include a set of custom options for bogart, several of which are invalid, as reported. For example, your read lengths are not a number and would also be negative. Where did this set of options come from? They also don't make sense as you have a -stop bestedges which would stop the step before generating all the outputs the next steps in Canu would expect. I can run with those options once these are removed (readlen and stop)

However, I'd suggest not adding extra options unless you have a very good reason to do so. I'd also recommend upgrading to the latest as 2.0 is relatively old.

[skoren]

Idle, user provided incorrect options.