Error while trying to run smartdenovo

[caonetto]

Hi, I am trying to run smartdenovo but I keep on getting this output

`ubuntu@biolinux:/mnt/Federico/TD_1/Smartdenovo_assembly$ '/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/smartdenovo.pl' /mnt/Federico/TD_1/basecalled.fasta PREFIX=wtasm

EXE_PRE=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtpre EXE_ZMO=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtzmo EXE_OBT=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtobt EXE_GBO=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtgbo EXE_CLP=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtclp EXE_LAY=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtlay EXE_CNS=/home/ubuntu/miniconda3/pkgs/smartdenovo-1.0.0-pl5.22.0_1/bin/wtcns N_THREADS=8

all:$(PREFIX).dmo.lay

$(PREFIX).fa.gz: $(EXE_PRE) -J 5000 /mnt/Federico/TD_1/basecalled.fasta | gzip -c -1 > $@

$(PREFIX).dmo.ovl:$(PREFIX).fa.gz $(EXE_ZMO) -t $(N_THREADS) -i $(PREFIX).fa.gz -fo $@ -k 16 -z 10 -Z 16 -U -1 -m 0.1 -A 1000

$(PREFIX).dmo.obt:$(PREFIX).fa.gz $(PREFIX).dmo.ovl $(EXE_CLP) -i $(PREFIX).dmo.ovl -fo $@ -d 3 -k 300 -m 0.1 -FT

$(PREFIX).dmo.lay:$(PREFIX).fa.gz $(PREFIX).dmo.obt $(PREFIX).dmo.ovl $(EXE_LAY) -i $(PREFIX).fa.gz -b $(PREFIX).dmo.obt -j $(PREFIX).dmo.ovl -fo $(PREFIX).dmo.lay -w 300 -s 200 -m 0.1 -r 0.95 -c 1 `

If I include the output > genome.mak nothing happens, Any ideas? Thanks

[ruanjue]

The scripts generated by smartdenovo,pl looks fine. Maybe you forgot to run make on it. make -f genome.mak Or there should be error message from make.

[caonetto]

Thanks Ranjue, it worked at the end. One questions, is it possible to run smartdenovo on fastq error corrected reads?

[ruanjue]

Yes, someone did it successfully. However, smartdenovo solve the problem of long noisy reads, not designed to assemble corrected long reads. If you got 'looks-better' contigs, please be careful to check the large misassewmblies, inside parameters to untangle graph may be not suit for corrected reads (I haven't tested it nor thought about it).

[caonetto]

So you would recommend doing the assembly with the raw reads and then doing a polishing (nanopolish)?

Thanks

[ruanjue]

Yes, I prefer to assemble raw reads and then polish contigs. In my view, raw reads correction doesn't consider global information of genome.