Open adhamzul opened 3 years ago
Hi, my data got the same error with you and I figured out that due to the reads in the error fastq file are too short (shorter than the default parameters), they were removed. You can adjust these parameters and run it again
Hello!
I have been trying out NanoCLUST for 16S analysis of a few of my data and it has been wonderful so far. But, a few datasets always abort during read_correction.
Even though I have 47 GB of RAM and a 24 CPU machine, I thought maybe there were too many data so I played around with
--umap_set_size
and--polishing_reads
but the same Error executing process > read_correction error comes up with an error exit status (1).I'll post the whole error along with the information I got from running .command.sh in the workdir. I don't think it is anything wrong with Canu itself as I was able to complete the pipeline on most of my datas.
The command that I used:
nextflow run main.nf -profile docker --reads 'part3/10000_lq8BC03.fastq' --db "db/16S_ribosomal_RNA" --tax "db/taxdb/" --outdir "results/part3" --umap_set_size 25000 --polishing_reads 50
NanoCLUST
.command.sh Report
I do hope that someone can shed some light on this.
I like to thank everyone who reads this in advance. Adham
Edit: I do not know how to fix the styling of the post so I am sorry. Edit 2: I was able to make the post easier to read and I added the command I used.