error using different seed

[ilenia6]

I read that your tool was used also to assemble the rDNA locus.
I would like to assemble long reads from a single specific gene locus (human) coming from a sequencing experiment in which we should have an enrichment of that locus.
With preliminary data (althoug in this first experiment this locus didn't produced a good enrichment level) I used the following command line:

get_organelle_from_reads.py -u reads.fastq -o output/ -s seq.fasta -F anonym --genes seq.fasta

Where reads.fastq contained the reads to assemble, the seed file corresponded to the reference locus and genes corresponded to the the same sequence, i.e., a single sequence of the human gene locus we want to assemble
However, the following error occurred:

Pre-assembling failed. The estimations for anonym-hitting base-coverage and word size may be misleading.

Would you suggest some adjustments in order to use get organelle also in such cases?

Is this command line correct? Is there a minimum coverage of the locus needed? Did you already use your tool with long reads?

Thank you in advance!

[Kinggerm]

I'm sorry that the current version is not designed for long reads. It will be a while before the major update for long reads.

Here are the replies to other questions, but all of them only apply to short-read data:

• Theoretically, the minimum coverage should be >10x. There can be many reasons for pre-assembling failed. That's why I almost requested a complete log file to be attached.
• If the target locus has much higher coverage than neighboring loci, then the current command should generally be ok; otherwise, flags --max-extending-len ?? and -P 0 are highly recommended.