lh3/fermikit

make: nothing to be done for all

zengxi-hada opened this issue · 0 comments

Hi,

I ran the first step to get DO50374T.mak.
fermi2.pl unitig -s3g -t16 -l150 -p DO50374T DO50374T.fq > DO50374T.mak
Then run make:
make -f DO50374T.mak

But it continue to say: make: Nothing to be done for 'all'. So what is the reason of the problem? below is the content of DO50374T.mak. Thanks!

PREFIX=DO50365T

EXE_FERMI2=/home/xiz978/anaconda3/bin/fermi2
EXE_ROPEBWT2=/home/xiz978/anaconda3/bin/ropebwt2
EXE_BFC=/home/xiz978/anaconda3/bin/bfc
GENOME_SIZE=3g
K_UNITIG=51
K_CLEAN=56
K_TRIM=61
K_MERGE=76
N_THREADS=16

INPUT=cat DO50365T.fq.gz

SHELL:=/bin/bash
export SHELLOPTS:=errexit:pipefail

all:$(PREFIX).mag.gz

$(PREFIX).ec.fq.gz:
    bash -e -o pipefail -c '$(EXE_BFC) -s $(GENOME_SIZE) -t $(N_THREADS) <($(INPUT)) <($(INPUT)) 2> $@.log | gzip -1 > $@'

$(PREFIX).flt.fq.gz:$(PREFIX).ec.fq.gz
    $(EXE_BFC) -1s $(GENOME_SIZE) -k $(K_TRIM) -t $(N_THREADS) $< 2> $@.log | gzip -1 > $@

$(PREFIX).flt.fmd:$(PREFIX).flt.fq.gz
    $(EXE_ROPEBWT2) -dNCr $< > $@ 2> $@.log

$(PREFIX).pre.gz:$(PREFIX).flt.fmd
    $(EXE_FERMI2) assemble -l $(K_UNITIG) -m $(K_MERGE) -t $(N_THREADS) $< 2> $@.log | gzip -1 > $@

$(PREFIX).mag.gz:$(PREFIX).pre.gz
    $(EXE_FERMI2) simplify -CSo $(K_CLEAN) -m $(K_MERGE) -T $(K_UNITIG) $< 2> $@.log | gzip -1 > $@