DBG2OLC - parameter f cannot identify my PacBio reads

Question

[marcela.uliano]

Hi guys!
I'm trying to run DBG2OLC with contigs built with platanus + 13x times genome coverage in PacBio subreads (fastq). But looks like the parameter f don't understand my PacBio reads. Do I have to create any kind of info file to unpload to the f parameter?

My command is:

./DBG2OLC LD 1 Contigs /data/scratch/xxx/data/pair_end/platinus/PE.lf_contig.fa k 17 KmerCovTh 2 MinOverlap 10 AdaptiveTh 0.001 f /data/scratch/xxx/data/PacBio/subreads/BVjE7HVA_filtered_subreads-1.fastq f /data/scratch/xxx/data/PacBio/subreads/q0QwkDI0_SMRT_09-10_filtered_subreads.fastq

and the end of my log file:

Scoring method: 3
Match method: 2
Loading long read index
Loading file: ReadsInfoFrom_BVjE7HVA_filtered_subreads-1.fastq
Loading file: ReadsInfoFrom_q0QwkDI0_SMRT_09-10_filtered_subreads.fastq
0 reads loaded.

I appreciate your help! Because I can't really understand why it's not loading.. the path is right, the format too.. (I also tried to rename the reads to have a final end .fq, but it did not work too!)

Thank you so so much!!!

Answer 1

[Rohit]

Sorry for the late answer, probably you even figured out the solution. I had the same issue before, the cause was simply that you were using fastq files instead of fasta sequences of pacbio reads.