DBG2OLC - parameter f cannot identify my PacBio reads

[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!!!

[bowhan]

The following is the part of the code dbg2olc uses to parse the option 'f':

		if (strcmp(argv[i], "f") == 0)
		{
			i++;
			LongReadFilenameVec.push_back(argv[i]);
			string name1= argv[i];
			int n = 0;
			for (n = name1.size() - 1; n >= 0; --n)
			{
				if (name1[n] == '\\'||name1[n]=='/')
				{
					break;
				}
			}
			name1 = name1.substr(n + 1, name1.size());

			name1="ReadsInfoFrom_" + name1;
			LongReadsInfoFiles.push_back(name1);
			name1 = argv[i];
			n = 0;
			for (n = name1.size() - 1; n >= 0; --n)
			{
				if (name1[n] == '\\' || name1[n] == '/')
				{
					break;
				}
			}
			name1 = name1.substr(n + 1, name1.size());

			name1 = "NonContainedReadsFrom_" + name1;
			NonContainedReadsFiles.push_back(name1);
			continue;
		}

Looks like that it gets the basename of that string and append prefixes of "ReadsInfoFrom_" and "NonContainedReadsFrom_", hence the log file said:

Loading file: ReadsInfoFrom_BVjE7HVA_filtered_subreads-1.fastq
Loading file: ReadsInfoFrom_q0QwkDI0_SMRT_09-10_filtered_subreads.fastq

Reading its manual, I believe the authors assume that you run "SparseAssembler" first with your data. It generates ReadsInfoFrom_XXX and NonContainedReadsFrom_XXX for you.

[kehey]

Are you sure you can already set your LD paramater at 1? Because if you've never had a successful run, I think it's supposed to be 0.

[Marcela Uliano]

Kehey and bowhan,

I'm sorry for the delay! You were completely right: for the first time run, it must be 0.

It run like a charm and really helped with my repetitive genome!!

Thank you, guys!