Closed rkimoakbioinformatics closed 3 years ago
Hi,
Reading the output it looks like the first run is successful and gives one consensus sequence located in Supplementary_File2_reads/medaka_cl_id_12/consensus.fasta
As seen from these lines in the output you pasted:
1 consensus formed.
Saving spoa references to files: Supplementary_File2_reads/consensus_reference_X.fasta
running medaka on spoa reference 12.
creating Supplementary_File2_reads/medaka_cl_id_12
medaka_consensus -i Supplementary_File2_reads/reads_to_consensus_12.fastq -d Supplementary_File2_reads/consensus_reference_12.fasta -o Supplementary_File2_reads/medaka_cl_id_12 -t 1
Saving medaka reference to file: Supplementary_File2_reads/medaka_cl_id_12/consensus.fasta
However, then there is more output following after this. I'm unsure whether you started a new run(?) as something seems truncated with this output. At any rate, for this new run, only 2 reads pass the length criteria of [700,900]
. See output below. Maybe you could try increasing/change this interval span if you are expecting a different size on your amplicons?
274 reads passed quality critera (avg phred Q val over 7.0 and length > 2*k) and will be clustered.
Sorted all reads in 0.568681001663208 seconds.
elapsed time sorting: 0.5687541961669922
Number of reads with read length in interval [700,900]: 2
I will incorporate a better error message when this happens in the next release of NGSpeciesID.
@ksahlin Thanks for the explanation. What I did was running consensus.sh
under test
folder of this repository (NGSpeciesID). I tried --s 300
instead of the original --s 100
in consensus.sh
and it ran without an error.
OS: Ubuntu 20.04 Installation: conda list shows
Installing NGSpeciesID with
pip install NGSpeciesID
did not work due to dependency (biopython version mismatch). I git cloned this repo and removed version requirements in setup.py. Also, added Python 3.8 in setup.py. Then, I didpip install -e .
in the cloned repo folder.Then,