marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
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corOverlapper=minimap failed #730

Closed wangyugui closed 6 years ago

wangyugui commented 6 years ago

canu corOverlapper=minimap failed

canu command & log log.zip

dataset ecoli in https://github.com/PacificBiosciences/DevNet/wiki/Datasets

# canu --version
Canu snapshot v1.6 +127 changes (r8539 d88616c9bc1c62c9fe65d603e4a70e4d6e7fb901)
# /usr/hpc-bio/canu-1.6.git/Linux-amd64/bin/minimap2 --version
2.5-r622-dirty
# cat ./correction/1-overlapper/mmap.000001.out
Running job 1 based on command line options.
[M::main::1.675*1.00] loaded/built the index for 23348 target sequence(s)
[M::mm_mapopt_update::2.260*1.00] mid_occ = 50
[M::mm_idx_stat] kmer size: 19; skip: 5; is_hpc: 1; #seq: 23348
[M::mm_idx_stat::2.731*1.00] distinct minimizers: 35964521 (80.98% are singletons); average occurrences: 1.883; average spacing: 4.181
[M::worker_pipeline::11.047*23.63] mapped 23348 sequences
[M::main] Version: 2.5-r622-dirty
[M::main] CMD: /usr/hpc-bio/canu-1.6.git/Linux-amd64/bin/minimap2 -x ava-pb -t 44 ./blocks/000001.mmi ./blocks/000001.fasta
[M::main] Real time: 11.112 sec; CPU: 261.151 sec
ls: cannot access queries/000001/*.fasta: No such file or directory
mv: cannot stat ‘./results/000001.mmap.counts’: No such file or directory

# cat ./correction/ecoli.ovlStore.err
Found no overlaps to sort.
wangyugui commented 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.

skoren commented 6 years ago

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.

wangyugui commented 6 years ago

'Canu snapshot v1.6 +132 changes' works well with/without 'corOverlapper=minimap'.

Thanks a lot.