minimus2 dumpreads command (revised)

AMOS is a collection of tools for genome assembly

Status: Beta

Brought to you by: adelcher, aphillippy, ddsommer, decaos, and 5 others

Status: open

Owner: nobody

Labels: minimus (4)

Priority: 5

Updated: 2011-03-09

Created: 2011-03-09

Private: No

minimus2 from Amos 3.0.0 dies on step 12 with error:

Command: /Users/jay/Software/amos/bin/dumpreads swh1209.bnk -M 0 > swh1209.ref.seq exited with status: 1

steps 12 & 13 from the minimus2 script reads:

12: $(BINDIR)/dumpreads $(BANK) -M $(REFCOUNT) > $(REFSEQ)
13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ)

The help from dumpreads indicates that options should precede the bank path:

dumpreads -h

.USAGE.
dumpreads [options] -b <bank path>

changing steps 12 & 13 as shown below (reversing order of REFCOUNT and BANK) fixes this problem:

12: $(BINDIR)/dumpreads -M $(REFCOUNT) $(BANK) > $(REFSEQ)
13: $(BINDIR)/dumpreads -m $(REFCOUNT) $(BANK) > $(QRYSEQ)