error2

[botellaflotante]

Hello, I want to try wengan to my yeast genome, I have Illumina adn PacBio CLR reads. My illumina reads are both 1 and 2 in one file, so I run this command

perl wengan.pl -x pacraw -a D -s illumina_reads/52530.2.367468.TTGTGTGC-TTGTGTGC.filter-RESEQ.fastq.gz -l pacbio_reads/reads.bc1015_BAK8B_OA--bc1015_BAK8B_OA.fastq.gz -p phaffia_wengan -t 20 -g 21

but some error appears

wengan-v0.2-bin-Linux/bin/abyss-pe name=phaffia_wengan.abyss2 k=96 B=20G H=4 kc=3 v=-v np=20 lib="pe1" pe1=" " contigs 2> phaffia_wengan.abyss2.err > phaffia_wengan.abyss2.log
make: *** [phaffia_wengan.mk:4: phaffia_wengan.abyss2-contigs.fa] Error 2

any suggestion? thanks

[adigenova]

Hi,
You have to split the Illumina reads into two files (forward and reverse) at the moment Wengan do not handle pairs in a single fastq file. You can split your file using the seqkit with:

seqkit split2 -p 2 sample21_pe.unmapped.fq

https://bioinf.shenwei.me/seqkit/usage/#split2

best,
Alex

[botellaflotante]

thanks, that could have worked, but now I have small reads (less than 60 apparently) so it gives that error now and maybe this won't work. Do you know where can I assemble this illumina reads + pacbio clr reads?

thanks again

[adigenova]

Hi,
You have to remove any read shorter than 60bp for running WenganD, the other Wengan modes WengaA and WenganM work with reads < 60bp. Seqkit implements a filter by read length.

Best
Alex