fermi -make command issue

[RadeshNMP]

Hello Dr.Li,

I am trying to use FERMI for a plant genome assembly using Illumina PE sequences. I ran the run_fermi.pl with the below command

/work/rn13ow/fermi-1.1/run-fermi.pl -Pt2 -e /work/rn13ow/fermi-1.1/fermi -k50 /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq > fmdef.mak &

after generating the index - fmdex.mak the make is given below

fmdef.mak file

FERMI=/work/rn13ow/fermi-1.1/fermi UNITIG_K=50 OVERLAP_K=60

all:fmdef.p5.fq.gz

Construct the FM-index for raw sequences

fmdef.raw.fmd:/work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq ($(FERMI) pe2cofq /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq) | $(FERMI) ropebwt -a bcr -v3 -btNf fmdef.raw.tmp - > $@ 2> [email protected]

Error correction

fmdef.ec.fq.gz:fmdef.raw.fmd ($(FERMI) pe2cofq /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq /work/rn13ow/BLESS_reads/PE_L005A.2.corrected.fastq) | $(FERMI) correct -pt 2 $< - 2> [email protected] | gzip -1 > $@

Construct the FM-index for corrected sequences

fmdef.ec.fmd:fmdef.ec.fq.gz $(FERMI) fltuniq $< 2> fmdef.fltuniq.log | $(FERMI) ropebwt -a bcr -v3 -btf fmdef.ec.tmp - > $@ 2> [email protected]

Generate unitigs

fmdef.ec.rank:fmdef.ec.fmd $(FERMI) seqrank -t 2 $< > $@ 2> [email protected]

fmdef.p0.mag.gz:fmdef.ec.rank fmdef.ec.fmd $(FERMI) unitig -t 2 -l $(UNITIG_K) -r $^ 2> [email protected] | gzip -1 > $@

fmdef.p1.mag.gz:fmdef.p0.mag.gz $(FERMI) clean $< 2> [email protected] | gzip -1 > $@ fmdef.p2.mag.gz:fmdef.p1.mag.gz $(FERMI) clean -CAOFo $(OVERLAP_K) $< 2> [email protected] | gzip -1 > $@

Generate scaftigs

fmdef.p3.mag.gz:fmdef.ec.rank fmdef.ec.fmd fmdef.p2.mag.gz $(FERMI) remap -t 2 -r $^ 2> [email protected] | gzip -1 > $@ fmdef.p4.fa.gz:fmdef.ec.fmd fmdef.p3.mag.gz $(FERMI) scaf -Pt 2 $^ perl -ne 'print "$$1 $$2\n" if /avg = (\S+) std = (\S+)/' fmdef.p3.mag.gz.log 2> [email protected] | gzip -1 > $@

fmdef.p5.fq.gz:fmdef.ec.rank fmdef.ec.fmd fmdef.p4.fa.gz $(FERMI) remap -c2 -t 2 -D perl -ne 'print "$$1\n" if /avg = \S+ std = \S+ cap = (\S+)/' fmdef.p3.mag.gz.log -r $^ 2> [email protected] | gzip -1 > $@

when I try to run the make command to start the assembly,I get the error message make -f fmdef.mak -j 2 &>run_fermi_4PE_L5A.log11 &

"make: *** No rule to make target /work/rn13ow/BLESS_reads/PE_L005A.1.corrrected.fastq', needed byfmdef.raw.fmd'. Stop."

I am not sure about the rule and how to specify it. I have followed the command as listed in the Readme file and have also tried the -B option, getting the same message.

I would appreciate it very much if you could let me know how to get around this issue.

Thanks and Regards, Radesh